output/spades.log Version 1
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_07_allReads_meta-assembly/
SEEK ID: https://fairdomhub.org/documents/2491?version=1
Filename:
output/spades.log
Format: Plain text document
Size: 350 KB
Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101,127 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq
System information:
SPAdes version: 3.13.0
Python version: 2.7.15
OS: Linux-4.13.0-41-generic-x86_64-with-debian-stretch-sid
Output dir: /DATA/markop/CPB_metaSpades/output
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_1.fq']
right reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_2.fq']
interlaced reads: not specified
single reads: ['/DATA/markop/CPB_metaSpades/input/merged.fq']
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Assembly parameters:
k: [21, 41, 71, 101, 127]
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /DATA/markop/CPB_metaSpades/output/tmp
Threads: 32
Memory limit (in Gb): 230
======= SPAdes pipeline started. Log can be found here: /DATA/markop/CPB_metaSpades/output/spades.log
===== Read error correction started.
== Running read error correction tool: /home/administrator/SPAdes-3.13.0-Linux/bin/spades-hammer /DATA/markop/CPB_metaSpades/output/corrected/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /DATA/markop/CPB_metaSpades/output/corrected/configs/config.info
0:00:00.001 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb
0:00:00.001 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.002 4M / 4M INFO General (main.cpp : 92) Determined value is 33
0:00:00.002 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.002 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.002 4M / 4M INFO K-mer Counting (kmer_data.cpp : 280) Estimating k-mer count
0:00:00.357 516M / 516M INFO K-mer Counting (kmer_data.cpp : 285) Processing /DATA/markop/CPB_metaSpades/input/unmerged_1.fq
0:10:52.896 640M / 640M INFO K-mer Counting (kmer_data.cpp : 294) Processed 135321241 reads
0:10:52.896 640M / 640M INFO K-mer Counting (kmer_data.cpp : 285) Processing /DATA/markop/CPB_metaSpades/input/unmerged_2.fq
0:21:16.796 640M / 640M INFO K-mer Counting (kmer_data.cpp : 294) Processed 270642482 reads
0:21:16.797 640M / 640M INFO K-mer Counting (kmer_data.cpp : 285) Processing /DATA/markop/CPB_metaSpades/input/merged.fq
1:21:39.897 644M / 648M INFO K-mer Counting (kmer_data.cpp : 294) Processed 833145089 reads
1:21:39.897 644M / 648M INFO K-mer Counting (kmer_data.cpp : 299) Total 833145089 reads processed
1:21:42.995 644M / 648M INFO K-mer Counting (kmer_data.cpp : 306) Estimated 5536627456 distinct kmers
1:21:43.028 132M / 648M INFO K-mer Counting (kmer_data.cpp : 311) Filtering singleton k-mers
42 8 0
nslots: 17179869184
bits per slot: 8 range: 0000040000000000
1:21:43.028 20G / 20G INFO K-mer Counting (kmer_data.cpp : 317) Processing /DATA/markop/CPB_metaSpades/input/unmerged_1.fq
3:35:39.885 20G / 20G INFO K-mer Counting (kmer_data.cpp : 326) Processed 135321241 reads
3:35:39.885 20G / 20G INFO K-mer Counting (kmer_data.cpp : 317) Processing /DATA/markop/CPB_metaSpades/input/unmerged_2.fq
5:19:27.930 20G / 20G INFO K-mer Counting (kmer_data.cpp : 326) Processed 270642482 reads
5:19:27.930 20G / 20G INFO K-mer Counting (kmer_data.cpp : 317) Processing /DATA/markop/CPB_metaSpades/input/merged.fq
23:01:29.626 20G / 20G INFO K-mer Counting (kmer_data.cpp : 326) Processed 833145089 reads
23:01:29.626 20G / 20G INFO K-mer Counting (kmer_data.cpp : 331) Total 833145089 reads processed
23:01:29.686 20G / 20G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
23:01:29.686 20G / 20G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
23:01:29.687 20G / 20G INFO General (file_limit.hpp : 32) Open file limit set to 10000
23:01:29.687 20G / 20G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.18331 Gb
23:01:29.687 20G / 20G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072
23:01:29.811 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/CPB_metaSpades/input/unmerged_1.fq
23:02:11.417 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 6886928 reads
23:03:13.120 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 14453232 reads
23:04:22.934 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 22335640 reads
23:05:27.908 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 30039291 reads
23:06:34.280 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 37323794 reads
23:07:42.614 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 44905083 reads
23:08:50.710 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 52824642 reads
23:10:02.256 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 60678220 reads
23:11:07.680 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 68460414 reads
23:12:16.978 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 76009455 reads
23:13:04.491 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 80542103 reads
23:14:05.077 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 88311649 reads
23:20:50.814 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 135321241 reads
23:20:50.814 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/CPB_metaSpades/input/unmerged_2.fq
23:40:53.864 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 270642482 reads
23:40:53.864 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/CPB_metaSpades/input/merged.fq
24:42:25.612 38G / 38G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 540135745 reads
25:47:06.454 38G / 39G INFO K-mer Splitting (kmer_data.cpp : 112) Total 833145089 reads processed
25:47:08.077 20G / 39G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
26:40:38.728 20G / 39G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3120000706 kmers in total.
26:40:38.729 20G / 39G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
26:41:02.440 20G / 39G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
26:43:10.220 21G / 39G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
26:47:26.435 21G / 39G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1446784560 bytes occupied (3.7097 bits per kmer).
26:47:28.840 1G / 39G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order
26:49:53.105 48G / 48G INFO General (main.cpp : 148) Clustering Hamming graph.
28:02:01.240 48G / 48G INFO General (main.cpp : 155) Extracting clusters
28:47:48.122 48G / 129G INFO General (main.cpp : 167) Clustering done. Total clusters: 1532504054
28:47:50.197 24G / 129G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while.
28:48:29.227 94G / 129G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/CPB_metaSpades/input/unmerged_1.fq
29:10:47.912 94G / 129G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/CPB_metaSpades/input/unmerged_2.fq
29:29:21.484 94G / 129G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/CPB_metaSpades/input/merged.fq
32:36:57.339 94G / 129G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing.
32:37:16.092 94G / 129G INFO K-mer Counting (kmer_data.cpp : 403) There are 3120000706 kmers in total. Among them 3041950 (0.0974984%) are singletons.
32:37:16.092 94G / 129G INFO General (main.cpp : 173) Subclustering Hamming graph
35:14:41.443 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 359281 non-read kmers were generated.
35:14:41.443 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics:
35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1191444616. Among them 1184615962 (99.4269%) are good
35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 518460250. Among them 518442934 (99.9967%) are good
35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 272307007. Among them 270571702 (99.3627%) are good
35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 7.08571 kmers
35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 2.31856
35:14:41.449 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1973630598
35:14:41.450 94G / 129G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.875603,0.0291038,0.043367,0.0519263),(0.051958,0.835411,0.0284625,0.0841685),(0.0830735,0.0281767,0.836087,0.0526624),(0.0512449,0.0429051,0.028877,0.876973))
35:14:43.418 94G / 129G INFO General (main.cpp : 178) Finished clustering.
35:14:43.424 94G / 129G INFO General (main.cpp : 197) Starting solid k-mers expansion in 32 threads.
36:42:13.437 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 763959153 new k-mers.
38:07:06.720 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 41154402 new k-mers.
39:31:49.536 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 6499177 new k-mers.
40:56:26.918 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 1137087 new k-mers.
42:21:08.920 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 211594 new k-mers.
43:45:43.820 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 42244 new k-mers.
45:10:18.248 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 10903 new k-mers.
46:35:08.228 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 7 produced 1877 new k-mers.
47:59:55.424 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 8 produced 265 new k-mers.
49:24:51.296 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 9 produced 51 new k-mers.
50:49:43.040 94G / 129G INFO General (main.cpp : 218) Solid k-mers iteration 10 produced 0 new k-mers.
50:49:43.040 94G / 129G INFO General (main.cpp : 222) Solid k-mers finalized
50:49:43.048 94G / 129G INFO General (hammer_tools.cpp : 220) Starting read correction in 32 threads.
50:49:43.048 94G / 129G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /DATA/markop/CPB_metaSpades/input/unmerged_1.fq and /DATA/markop/CPB_metaSpades/input/unmerged_2.fq
50:50:03.349 97G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads.
50:50:22.216 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 0
50:50:28.083 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 0
50:51:09.378 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads.
50:51:27.236 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 1
50:51:33.572 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 1
50:52:14.496 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads.
50:52:33.396 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 2
50:52:40.541 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 2
50:53:21.505 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads.
50:53:40.139 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 3
50:53:46.364 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 3
50:54:28.838 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads.
50:54:47.792 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 4
50:54:54.052 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 4
50:55:34.207 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads.
50:55:52.871 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 5
50:55:59.817 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 5
50:56:41.705 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads.
50:57:00.074 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 6
50:57:06.367 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 6
50:57:48.069 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads.
50:58:07.128 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 7
50:58:13.269 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 7
50:58:52.791 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads.
50:59:11.550 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 8
50:59:18.660 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 8
51:00:00.687 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 3200000 reads.
51:00:19.154 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 9
51:00:25.410 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 9
51:01:07.420 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 3200000 reads.
51:01:26.156 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 10
51:01:32.287 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 10
51:02:12.014 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 3200000 reads.
51:02:30.620 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 11
51:02:37.882 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 11
51:03:19.375 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 3200000 reads.
51:03:37.594 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 12
51:03:44.021 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 12
51:04:26.269 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 3200000 reads.
51:04:44.784 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 13
51:04:51.009 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 13
51:05:31.579 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 3200000 reads.
51:05:50.322 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 14
51:05:57.847 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 14
51:06:39.753 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 3200000 reads.
51:06:58.305 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 15
51:07:04.828 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 15
51:07:48.024 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 3200000 reads.
51:08:06.884 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 16
51:08:13.196 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 16
51:08:53.342 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 3200000 reads.
51:09:11.916 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 17
51:09:18.803 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 17
51:10:00.182 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 3200000 reads.
51:10:18.464 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 18
51:10:24.589 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 18
51:11:08.720 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 3200000 reads.
51:11:27.563 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 19
51:11:34.099 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 19
51:12:15.723 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 3200000 reads.
51:12:34.460 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 20
51:12:40.545 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 20
51:13:21.725 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 3200000 reads.
51:13:40.916 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 21
51:13:47.007 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 21
51:14:31.003 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 3200000 reads.
51:14:49.882 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 22
51:14:56.461 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 22
51:15:40.041 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 3200000 reads.
51:15:57.992 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 23
51:16:04.131 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 23
51:16:47.324 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 3200000 reads.
51:17:05.765 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 24
51:17:11.736 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 24
51:17:55.060 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 3200000 reads.
51:18:14.105 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 25
51:18:21.042 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 25
51:19:03.235 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 3200000 reads.
51:19:21.500 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 26
51:19:27.621 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 26
51:20:07.278 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 27 of 3200000 reads.
51:20:25.742 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 27
51:20:31.852 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 27
51:21:16.180 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 28 of 3200000 reads.
51:21:36.957 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 28
51:21:44.340 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 28
51:22:29.358 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 29 of 3200000 reads.
51:22:47.224 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 29
51:22:53.287 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 29
51:23:35.062 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 30 of 3200000 reads.
51:23:54.250 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 30
51:24:00.530 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 30
51:24:43.207 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 31 of 3200000 reads.
51:25:01.815 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 31
51:25:08.380 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 31
51:25:51.489 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 32 of 3200000 reads.
51:26:09.736 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 32
51:26:15.919 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 32
51:26:57.692 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 33 of 3200000 reads.
51:27:16.127 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 33
51:27:22.642 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 33
51:28:05.164 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 34 of 3200000 reads.
51:28:23.463 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 34
51:28:29.875 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 34
51:29:12.884 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 35 of 3200000 reads.
51:29:31.241 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 35
51:29:37.439 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 35
51:30:20.534 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 36 of 3200000 reads.
51:30:39.210 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 36
51:30:46.066 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 36
51:31:27.669 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 37 of 3200000 reads.
51:31:46.302 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 37
51:31:52.534 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 37
51:32:35.492 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 38 of 3200000 reads.
51:32:54.932 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 38
51:33:01.115 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 38
51:33:45.186 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 39 of 3200000 reads.
51:34:03.756 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 39
51:34:10.632 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 39
51:34:52.043 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 40 of 3200000 reads.
51:35:10.396 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 40
51:35:16.421 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 40
51:36:00.297 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 41 of 3200000 reads.
51:36:18.716 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 41
51:36:25.018 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 41
51:36:32.972 98G / 129G INFO General (hammer_tools.cpp : 168) Prepared batch 42 of 921241 reads.
51:36:38.740 98G / 129G INFO General (hammer_tools.cpp : 175) Processed batch 42
51:36:40.572 98G / 129G INFO General (hammer_tools.cpp : 185) Written batch 42
51:36:43.629 94G / 129G INFO General (hammer_tools.cpp : 264) Correcting single reads: /DATA/markop/CPB_metaSpades/input/merged.fq
51:37:06.719 96G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 3200000 reads.
51:37:19.232 97G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 0
51:37:24.031 97G / 129G INFO General (hammer_tools.cpp : 136) Written batch 0
51:37:36.113 98G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 3200000 reads.
51:37:48.160 98G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 1
51:37:52.898 98G / 129G INFO General (hammer_tools.cpp : 136) Written batch 1
51:38:02.947 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 2 of 3200000 reads.
51:38:15.362 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 2
51:38:21.490 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 2
51:38:57.694 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 3 of 3200000 reads.
51:39:09.747 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 3
51:39:14.544 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 3
51:39:25.256 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 4 of 3200000 reads.
51:39:37.879 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 4
51:39:42.798 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 4
51:40:06.249 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 5 of 3200000 reads.
51:40:18.616 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 5
51:40:23.438 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 5
51:40:46.114 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 6 of 3200000 reads.
51:40:58.286 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 6
51:41:03.576 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 6
51:41:20.793 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 7 of 3200000 reads.
51:41:33.010 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 7
51:41:38.036 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 7
51:41:47.988 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 8 of 3200000 reads.
51:42:00.261 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 8
51:42:05.627 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 8
51:42:37.988 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 9 of 3200000 reads.
51:42:50.164 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 9
51:42:55.870 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 9
51:43:06.925 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 10 of 3200000 reads.
51:43:19.053 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 10
51:43:23.942 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 10
51:43:46.927 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 11 of 3200000 reads.
51:43:59.338 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 11
51:44:05.373 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 11
51:44:29.685 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 12 of 3200000 reads.
51:44:42.408 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 12
51:44:47.197 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 12
51:44:56.710 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 13 of 3200000 reads.
51:45:09.069 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 13
51:45:14.200 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 13
51:45:38.293 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 14 of 3200000 reads.
51:45:50.863 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 14
51:45:55.720 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 14
51:46:06.412 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 15 of 3200000 reads.
51:46:18.732 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 15
51:46:23.499 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 15
51:46:33.299 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 16 of 3200000 reads.
51:46:48.275 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 16
51:46:54.248 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 16
51:47:24.289 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 17 of 3200000 reads.
51:47:36.698 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 17
51:47:41.515 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 17
51:47:52.376 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 18 of 3200000 reads.
51:48:05.152 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 18
51:48:11.529 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 18
51:48:34.904 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 19 of 3200000 reads.
51:48:47.192 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 19
51:48:52.012 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 19
51:49:15.433 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 20 of 3200000 reads.
51:49:27.814 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 20
51:49:32.664 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 20
51:49:43.449 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 21 of 3200000 reads.
51:49:56.458 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 21
51:50:01.921 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 21
51:50:28.117 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 22 of 3200000 reads.
51:50:40.601 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 22
51:50:45.453 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 22
51:50:56.196 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 23 of 3200000 reads.
51:51:08.493 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 23
51:51:13.750 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 23
51:51:37.352 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 24 of 3200000 reads.
51:51:49.612 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 24
51:51:54.457 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 24
51:52:04.982 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 25 of 3200000 reads.
51:52:17.831 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 25
51:52:24.029 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 25
51:52:47.068 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 26 of 3200000 reads.
51:52:59.350 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 26
51:53:04.146 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 26
51:53:28.084 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 27 of 3200000 reads.
51:53:41.430 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 27
51:53:46.306 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 27
51:54:11.139 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 28 of 3200000 reads.
51:54:23.326 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 28
51:54:28.163 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 28
51:54:38.247 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 29 of 3200000 reads.
51:54:50.569 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 29
51:54:56.129 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 29
51:55:22.160 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 30 of 3200000 reads.
51:55:34.501 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 30
51:55:39.487 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 30
51:56:02.917 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 31 of 3200000 reads.
51:56:14.912 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 31
51:56:19.844 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 31
51:56:32.131 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 32 of 3200000 reads.
51:56:44.622 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 32
51:56:50.599 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 32
51:57:00.554 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 33 of 3200000 reads.
51:57:12.744 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 33
51:57:17.885 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 33
51:57:56.302 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 34 of 3200000 reads.
51:58:09.819 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 34
51:58:15.344 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 34
51:58:39.569 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 35 of 3200000 reads.
51:58:51.482 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 35
51:58:56.566 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 35
51:59:21.508 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 36 of 3200000 reads.
51:59:34.183 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 36
51:59:39.394 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 36
51:59:49.800 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 37 of 3200000 reads.
52:00:02.251 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 37
52:00:07.379 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 37
52:00:33.086 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 38 of 3200000 reads.
52:00:45.242 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 38
52:00:50.171 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 38
52:01:01.471 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 39 of 3200000 reads.
52:01:14.032 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 39
52:01:19.471 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 39
52:01:43.193 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 40 of 3200000 reads.
52:01:55.184 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 40
52:02:00.114 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 40
52:02:10.260 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 41 of 3200000 reads.
52:02:22.456 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 41
52:02:29.453 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 41
52:02:54.042 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 42 of 3200000 reads.
52:03:06.168 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 42
52:03:11.056 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 42
52:03:35.175 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 43 of 3200000 reads.
52:03:47.549 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 43
52:03:52.441 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 43
52:04:06.040 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 44 of 3200000 reads.
52:04:18.730 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 44
52:04:23.618 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 44
52:04:34.144 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 45 of 3200000 reads.
52:04:46.317 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 45
52:04:51.348 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 45
52:05:28.137 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 46 of 3200000 reads.
52:05:40.364 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 46
52:05:46.026 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 46
52:05:57.618 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 47 of 3200000 reads.
52:06:09.698 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 47
52:06:14.984 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 47
52:06:37.822 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 48 of 3200000 reads.
52:06:50.985 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 48
52:06:57.215 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 48
52:07:20.944 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 49 of 3200000 reads.
52:07:32.949 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 49
52:07:38.092 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 49
52:07:48.628 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 50 of 3200000 reads.
52:08:01.220 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 50
52:08:07.269 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 50
52:08:35.323 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 51 of 3200000 reads.
52:08:47.489 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 51
52:08:52.443 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 51
52:09:18.201 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 52 of 3200000 reads.
52:09:30.407 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 52
52:09:35.374 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 52
52:09:45.909 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 53 of 3200000 reads.
52:09:58.387 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 53
52:10:03.999 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 53
52:10:28.033 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 54 of 3200000 reads.
52:10:40.402 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 54
52:10:45.351 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 54
52:11:10.284 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 55 of 3200000 reads.
52:11:22.324 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 55
52:11:28.210 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 55
52:11:39.942 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 56 of 3200000 reads.
52:11:52.244 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 56
52:11:57.127 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 56
52:12:07.130 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 57 of 3200000 reads.
52:12:19.443 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 57
52:12:24.498 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 57
52:13:02.443 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 58 of 3200000 reads.
52:13:14.560 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 58
52:13:19.424 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 58
52:13:44.094 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 59 of 3200000 reads.
52:13:56.586 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 59
52:14:01.525 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 59
52:14:11.749 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 60 of 3200000 reads.
52:14:23.914 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 60
52:14:29.523 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 60
52:14:54.244 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 61 of 3200000 reads.
52:15:06.796 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 61
52:15:12.221 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 61
52:15:22.976 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 62 of 3200000 reads.
52:15:35.133 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 62
52:15:41.655 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 62
52:16:04.960 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 63 of 3200000 reads.
52:16:17.100 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 63
52:16:21.999 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 63
52:16:34.649 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 64 of 3200000 reads.
52:16:47.384 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 64
52:16:53.158 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 64
52:17:04.006 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 65 of 3200000 reads.
52:17:16.228 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 65
52:17:21.808 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 65
52:17:51.532 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 66 of 3200000 reads.
52:18:03.870 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 66
52:18:08.821 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 66
52:18:20.928 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 67 of 3200000 reads.
52:18:33.360 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 67
52:18:38.625 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 67
52:19:01.678 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 68 of 3200000 reads.
52:19:13.986 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 68
52:19:18.943 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 68
52:19:44.038 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 69 of 3200000 reads.
52:19:56.546 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 69
52:20:02.177 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 69
52:20:21.668 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 70 of 3200000 reads.
52:20:33.923 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 70
52:20:38.811 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 70
52:20:49.132 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 71 of 3200000 reads.
52:21:01.585 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 71
52:21:07.343 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 71
52:21:33.769 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 72 of 3200000 reads.
52:21:45.980 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 72
52:21:50.840 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 72
52:22:15.146 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 73 of 3200000 reads.
52:22:27.338 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 73
52:22:32.238 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 73
52:22:42.780 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 74 of 3200000 reads.
52:22:55.333 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 74
52:23:01.001 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 74
52:23:25.670 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 75 of 3200000 reads.
52:23:38.060 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 75
52:23:42.984 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 75
52:23:54.294 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 76 of 3200000 reads.
52:24:06.761 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 76
52:24:12.756 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 76
52:24:36.614 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 77 of 3200000 reads.
52:24:48.782 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 77
52:24:53.801 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 77
52:25:17.940 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 78 of 3200000 reads.
52:25:30.593 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 78
52:25:36.741 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 78
52:25:48.056 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 79 of 3200000 reads.
52:25:59.960 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 79
52:26:05.333 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 79
52:26:29.268 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 80 of 3200000 reads.
52:26:41.530 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 80
52:26:46.465 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 80
52:27:12.334 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 81 of 3200000 reads.
52:27:24.480 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 81
52:27:29.373 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 81
52:27:45.407 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 82 of 3200000 reads.
52:27:58.193 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 82
52:28:03.177 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 82
52:28:13.755 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 83 of 3200000 reads.
52:28:26.399 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 83
52:28:32.293 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 83
52:29:05.237 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 84 of 3200000 reads.
52:29:19.591 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 84
52:29:24.525 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 84
52:29:50.113 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 85 of 3200000 reads.
52:30:02.621 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 85
52:30:08.747 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 85
52:30:18.690 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 86 of 3200000 reads.
52:30:30.646 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 86
52:30:36.437 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 86
52:31:01.709 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 87 of 3200000 reads.
52:31:14.388 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 87
52:31:19.362 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 87
52:31:45.138 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 88 of 3200000 reads.
52:31:57.118 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 88
52:32:02.037 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 88
52:32:13.231 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 89 of 3200000 reads.
52:32:25.403 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 89
52:32:30.387 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 89
52:32:41.186 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 90 of 3200000 reads.
52:32:53.435 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 90
52:32:59.966 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 90
52:33:35.614 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 91 of 3200000 reads.
52:33:47.685 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 91
52:33:52.732 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 91
52:34:03.906 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 92 of 3200000 reads.
52:34:16.103 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 92
52:34:22.527 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 92
52:34:46.520 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 93 of 3200000 reads.
52:34:58.776 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 93
52:35:03.814 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 93
52:35:13.887 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 94 of 3200000 reads.
52:35:26.286 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 94
52:35:32.626 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 94
52:35:59.283 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 95 of 3200000 reads.
52:36:11.539 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 95
52:36:16.519 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 95
52:36:27.570 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 96 of 3200000 reads.
52:36:39.878 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 96
52:36:45.298 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 96
52:37:09.743 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 97 of 3200000 reads.
52:37:22.114 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 97
52:37:27.375 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 97
52:37:53.028 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 98 of 3200000 reads.
52:38:05.251 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 98
52:38:10.229 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 98
52:38:20.845 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 99 of 3200000 reads.
52:38:33.048 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 99
52:38:39.466 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 99
52:39:03.735 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 100 of 3200000 reads.
52:39:15.971 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 100
52:39:20.950 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 100
52:39:32.107 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 101 of 3200000 reads.
52:39:44.364 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 101
52:39:49.456 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 101
52:40:00.565 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 102 of 3200000 reads.
52:40:12.565 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 102
52:40:17.551 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 102
52:40:57.298 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 103 of 3200000 reads.
52:41:10.031 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 103
52:41:15.039 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 103
52:41:26.089 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 104 of 3200000 reads.
52:41:38.419 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 104
52:41:44.151 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 104
52:42:10.871 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 105 of 3200000 reads.
52:42:23.266 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 105
52:42:28.240 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 105
52:42:55.214 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 106 of 3200000 reads.
52:43:07.786 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 106
52:43:13.333 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 106
52:43:24.580 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 107 of 3200000 reads.
52:43:38.297 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 107
52:43:43.243 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 107
52:43:53.761 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 108 of 3200000 reads.
52:44:05.965 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 108
52:44:12.386 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 108
52:44:50.859 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 109 of 3200000 reads.
52:45:02.917 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 109
52:45:07.894 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 109
52:45:33.391 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 110 of 3200000 reads.
52:45:46.441 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 110
52:45:51.363 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 110
52:46:03.505 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 111 of 3200000 reads.
52:46:15.474 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 111
52:46:20.464 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 111
52:46:30.744 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 112 of 3200000 reads.
52:46:43.201 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 112
52:46:49.278 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 112
52:47:26.801 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 113 of 3200000 reads.
52:47:39.354 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 113
52:47:44.792 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 113
52:48:09.813 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 114 of 3200000 reads.
52:48:22.425 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 114
52:48:27.375 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 114
52:48:39.473 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 115 of 3200000 reads.
52:48:51.741 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 115
52:48:58.467 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 115
52:49:22.311 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 116 of 3200000 reads.
52:49:34.190 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 116
52:49:39.059 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 116
52:50:04.161 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 117 of 3200000 reads.
52:50:16.400 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 117
52:50:21.435 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 117
52:50:36.414 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 118 of 3200000 reads.
52:50:48.474 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 118
52:50:53.428 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 118
52:51:03.826 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 119 of 3200000 reads.
52:51:15.695 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 119
52:51:20.773 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 119
52:52:01.765 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 120 of 3200000 reads.
52:52:14.278 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 120
52:52:19.622 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 120
52:52:45.162 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 121 of 3200000 reads.
52:52:57.703 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 121
52:53:02.684 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 121
52:53:28.591 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 122 of 3200000 reads.
52:53:41.463 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 122
52:53:47.374 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 122
52:53:57.599 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 123 of 3200000 reads.
52:54:09.721 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 123
52:54:15.392 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 123
52:54:44.034 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 124 of 3200000 reads.
52:54:56.687 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 124
52:55:02.238 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 124
52:55:27.931 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 125 of 3200000 reads.
52:55:40.264 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 125
52:55:45.175 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 125
52:56:09.619 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 126 of 3200000 reads.
52:56:22.321 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 126
52:56:27.256 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 126
52:56:37.984 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 127 of 3200000 reads.
52:56:50.581 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 127
52:56:56.615 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 127
52:57:27.401 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 128 of 3200000 reads.
52:57:40.102 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 128
52:57:44.986 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 128
52:58:12.362 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 129 of 3200000 reads.
52:58:24.650 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 129
52:58:30.056 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 129
52:58:41.062 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 130 of 3200000 reads.
52:58:53.152 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 130
52:58:58.211 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 130
52:59:24.892 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 131 of 3200000 reads.
52:59:37.905 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 131
52:59:44.191 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 131
52:59:55.574 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 132 of 3200000 reads.
53:00:07.947 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 132
53:00:13.357 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 132
53:00:39.858 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 133 of 3200000 reads.
53:00:52.712 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 133
53:00:57.757 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 133
53:01:09.001 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 134 of 3200000 reads.
53:01:21.115 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 134
53:01:26.855 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 134
53:01:53.741 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 135 of 3200000 reads.
53:02:05.914 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 135
53:02:10.834 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 135
53:02:22.424 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 136 of 3200000 reads.
53:02:34.839 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 136
53:02:40.114 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 136
53:02:51.106 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 137 of 3200000 reads.
53:03:03.604 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 137
53:03:09.343 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 137
53:03:47.122 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 138 of 3200000 reads.
53:03:59.295 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 138
53:04:05.575 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 138
53:04:31.800 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 139 of 3200000 reads.
53:04:44.045 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 139
53:04:49.024 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 139
53:05:01.997 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 140 of 3200000 reads.
53:05:14.577 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 140
53:05:19.570 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 140
53:05:30.085 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 141 of 3200000 reads.
53:05:42.367 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 141
53:05:47.761 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 141
53:06:26.829 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 142 of 3200000 reads.
53:06:38.760 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 142
53:06:43.801 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 142
53:07:03.688 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 143 of 3200000 reads.
53:07:16.233 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 143
53:07:21.467 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 143
53:07:32.344 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 144 of 3200000 reads.
53:07:44.678 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 144
53:07:50.134 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 144
53:08:19.267 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 145 of 3200000 reads.
53:08:31.396 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 145
53:08:37.439 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 145
53:09:04.720 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 146 of 3200000 reads.
53:09:16.859 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 146
53:09:21.837 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 146
53:09:34.294 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 147 of 3200000 reads.
53:09:46.710 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 147
53:09:51.765 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 147
53:10:02.667 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 148 of 3200000 reads.
53:10:15.044 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 148
53:10:20.279 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 148
53:11:03.218 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 149 of 3200000 reads.
53:11:15.909 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 149
53:11:21.013 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 149
53:11:31.531 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 150 of 3200000 reads.
53:11:44.188 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 150
53:11:49.938 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 150
53:12:18.181 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 151 of 3200000 reads.
53:12:30.742 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 151
53:12:35.696 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 151
53:13:01.791 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 152 of 3200000 reads.
53:13:14.012 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 152
53:13:20.136 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 152
53:13:48.085 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 153 of 3200000 reads.
53:14:00.910 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 153
53:14:05.927 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 153
53:14:16.218 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 154 of 3200000 reads.
53:14:28.489 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 154
53:14:34.537 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 154
53:15:02.196 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 155 of 3200000 reads.
53:15:14.596 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 155
53:15:19.613 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 155
53:15:46.769 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 156 of 3200000 reads.
53:15:59.087 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 156
53:16:04.191 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 156
53:16:30.597 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 157 of 3200000 reads.
53:16:43.322 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 157
53:16:48.364 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 157
53:16:59.762 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 158 of 3200000 reads.
53:17:12.307 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 158
53:17:17.816 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 158
53:17:43.067 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 159 of 3200000 reads.
53:17:55.333 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 159
53:18:00.897 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 159
53:18:16.480 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 160 of 3200000 reads.
53:18:31.023 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 160
53:18:36.039 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 160
53:18:46.675 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 161 of 3200000 reads.
53:18:58.815 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 161
53:19:06.092 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 161
53:19:37.413 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 162 of 3200000 reads.
53:19:49.300 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 162
53:19:54.200 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 162
53:20:05.544 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 163 of 3200000 reads.
53:20:18.010 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 163
53:20:23.495 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 163
53:20:50.314 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 164 of 3200000 reads.
53:21:02.793 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 164
53:21:07.731 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 164
53:21:34.254 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 165 of 3200000 reads.
53:21:46.977 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 165
53:21:51.885 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 165
53:22:04.029 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 166 of 3200000 reads.
53:22:16.565 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 166
53:22:22.200 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 166
53:22:46.986 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 167 of 3200000 reads.
53:22:59.089 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 167
53:23:04.048 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 167
53:23:15.591 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 168 of 3200000 reads.
53:23:28.254 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 168
53:23:34.416 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 168
53:24:00.445 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 169 of 3200000 reads.
53:24:12.456 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 169
53:24:17.455 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 169
53:24:44.548 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 170 of 3200000 reads.
53:24:57.708 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 170
53:25:03.625 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 170
53:25:31.349 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 171 of 3200000 reads.
53:25:43.753 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 171
53:25:48.667 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 171
53:26:14.259 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 172 of 3200000 reads.
53:26:26.765 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 172
53:26:31.699 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 172
53:26:44.284 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 173 of 3200000 reads.
53:26:56.358 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 173
53:27:02.156 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 173
53:27:27.392 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 174 of 3200000 reads.
53:27:39.571 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 174
53:27:44.594 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 174
53:27:52.873 99G / 129G INFO General (hammer_tools.cpp : 127) Prepared batch 175 of 2502607 reads.
53:28:02.869 99G / 129G INFO General (hammer_tools.cpp : 132) Processed batch 175
53:28:08.260 99G / 129G INFO General (hammer_tools.cpp : 136) Written batch 175
53:28:10.415 94G / 129G INFO General (hammer_tools.cpp : 274) Correction done. Changed 68218099 bases in 28721685 reads.
53:28:10.415 94G / 129G INFO General (hammer_tools.cpp : 275) Failed to correct 799344 bases out of 189800670900.
53:28:21.017 148M / 129G INFO General (main.cpp : 255) Saving corrected dataset description to /DATA/markop/CPB_metaSpades/output/corrected/corrected.yaml
53:28:21.025 148M / 129G INFO General (main.cpp : 262) All done. Exiting.
== Compressing corrected reads (with pigz)
== Dataset description file was created: /DATA/markop/CPB_metaSpades/output/corrected/corrected.yaml
===== Read error correction finished.
===== Assembling started.
== Running assembler: K21
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K21/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K21/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K21/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=21
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0
0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction
0:00:00.002 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while)
0:00:00.002 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads
0:00:00.237 80M / 80M INFO General (binary_converter.hpp : 93) 16384 reads processed
0:00:00.388 96M / 96M INFO General (binary_converter.hpp : 93) 32768 reads processed
0:00:00.682 124M / 124M INFO General (binary_converter.hpp : 93) 65536 reads processed
0:00:01.280 180M / 180M INFO General (binary_converter.hpp : 93) 131072 reads processed
0:00:02.587 292M / 292M INFO General (binary_converter.hpp : 93) 262144 reads processed
0:00:04.975 516M / 516M INFO General (binary_converter.hpp : 93) 524288 reads processed
0:00:12.392 864M / 864M INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:00:24.556 868M / 868M INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:00:50.579 868M / 868M INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:01:42.941 880M / 880M INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:03:28.271 884M / 884M INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:06:58.300 888M / 888M INFO General (binary_converter.hpp : 93) 33554432 reads processed
0:14:04.956 884M / 888M INFO General (binary_converter.hpp : 93) 67108864 reads processed
0:27:18.614 876M / 892M INFO General (binary_converter.hpp : 117) 129219073 reads written
0:27:19.792 8M / 892M INFO General (read_converter.hpp : 87) Converting single reads
0:27:20.021 140M / 892M INFO General (binary_converter.hpp : 93) 16384 reads processed
0:27:20.100 144M / 892M INFO General (binary_converter.hpp : 93) 32768 reads processed
0:27:20.256 156M / 892M INFO General (binary_converter.hpp : 93) 65536 reads processed
0:27:20.568 184M / 892M INFO General (binary_converter.hpp : 93) 131072 reads processed
0:27:21.189 232M / 892M INFO General (binary_converter.hpp : 93) 262144 reads processed
0:27:22.437 336M / 892M INFO General (binary_converter.hpp : 93) 524288 reads processed
0:27:24.917 540M / 892M INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:27:30.982 948M / 948M INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:27:40.916 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:28:10.643 2G / 2G INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:29:22.860 3G / 3G INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:31:48.702 3G / 3G INFO General (binary_converter.hpp : 93) 33554432 reads processed
0:36:48.011 3G / 3G INFO General (binary_converter.hpp : 93) 67108864 reads processed
0:46:52.539 3G / 3G INFO General (binary_converter.hpp : 93) 134217728 reads processed
1:06:57.549 3G / 3G INFO General (binary_converter.hpp : 93) 268435456 reads processed
1:46:25.941 3G / 3G INFO General (binary_converter.hpp : 93) 536870912 reads processed
1:51:14.544 3G / 3G INFO General (binary_converter.hpp : 117) 568147731 reads written
1:51:17.278 16M / 3G INFO General (read_converter.hpp : 95) Converting merged reads
1:51:17.384 144M / 3G INFO General (binary_converter.hpp : 117) 0 reads written
1:51:17.393 16M / 3G INFO General (construction.cpp : 111) Max read length 391
1:51:17.393 16M / 3G INFO General (construction.cpp : 117) Average read length 229.3
1:51:17.393 16M / 3G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
1:51:17.399 16M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
1:51:17.406 12M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 10000
1:51:17.406 12M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39571 Gb
1:51:17.407 12M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536
1:51:41.990 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 23060198 reads
1:52:04.730 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 38860813 reads
1:52:27.188 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 54500365 reads
1:52:49.588 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 69799795 reads
1:53:11.221 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 84751366 reads
1:53:33.172 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 100157733 reads
1:53:54.852 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 115491813 reads
1:54:16.502 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 130776909 reads
1:54:39.241 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 146182226 reads
1:55:02.265 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 161718785 reads
1:55:22.854 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 176177207 reads
1:55:45.325 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 191941724 reads
1:56:07.366 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 207313175 reads
1:57:51.572 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 280389552 reads
2:04:09.993 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 542854058 reads
2:17:01.002 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1080412228 reads
2:24:17.575 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
2:24:19.087 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads
2:24:19.087 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
2:26:24.301 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2045839657 kmers in total.
2:26:24.301 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
2:26:53.532 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
2:26:53.532 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
2:26:53.532 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
2:26:53.532 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000
2:26:53.532 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb
2:26:53.532 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072
2:26:54.111 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4305316 kmers
2:26:54.655 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8922913 kmers
2:26:55.173 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14054761 kmers
2:26:55.738 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 20071655 kmers
2:26:56.425 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28522850 kmers
2:26:58.328 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68079738 kmers
2:26:58.850 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 72685210 kmers
2:26:59.419 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 77793004 kmers
2:27:00.002 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 83773103 kmers
2:27:01.247 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 92053406 kmers
2:27:03.235 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 132002095 kmers
2:27:03.839 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 136608580 kmers
2:27:04.405 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 141717446 kmers
2:27:05.004 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 147697234 kmers
2:27:05.669 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 155979364 kmers
2:27:07.595 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 195932484 kmers
2:27:08.187 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 200538003 kmers
2:27:08.762 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 205645244 kmers
2:27:13.206 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 269582468 kmers
2:27:32.225 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539559427 kmers
2:28:10.065 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1090993447 kmers
2:29:16.937 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 2045844777 kmers.
2:29:17.236 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
2:29:52.135 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1976321898 kmers in total.
2:29:52.136 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
2:30:07.090 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
2:31:23.993 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
2:34:51.529 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 916465000 bytes occupied (3.70978 bits per kmer).
2:34:53.100 2G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
2:36:40.899 2G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
2:36:40.902 2G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping
2:36:40.902 2G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K)
2:36:40.902 2G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping
2:41:16.092 2G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 229648019 22-mers were removed by early tip clipper
2:41:16.092 2G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
2:41:16.117 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
2:43:54.012 11G / 19G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 171315498 sequences extracted
2:45:10.300 11G / 19G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
2:45:53.048 11G / 19G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 2835 loops collected
2:47:09.997 47G / 61G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
2:47:09.997 47G / 61G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
2:47:09.997 47G / 61G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
2:48:13.017 48G / 61G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 948693702 bytes occupied (3.70975 bits per kmer).
2:48:18.208 55G / 61G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
3:41:11.074 55G / 61G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
3:41:27.535 55G / 61G INFO General (construction.cpp : 464) Processed 32000000 edges
3:41:38.107 55G / 61G INFO General (construction.cpp : 464) Processed 64000000 edges
3:41:48.304 55G / 61G INFO General (construction.cpp : 464) Processed 96000000 edges
3:41:58.557 55G / 61G INFO General (construction.cpp : 464) Processed 128000000 edges
3:42:09.166 55G / 61G INFO General (construction.cpp : 464) Processed 160000000 edges
3:42:19.184 55G / 61G INFO General (construction.cpp : 464) Processed 192000000 edges
3:42:29.652 55G / 61G INFO General (construction.cpp : 464) Processed 224000000 edges
3:42:39.920 55G / 61G INFO General (construction.cpp : 464) Processed 256000000 edges
3:42:50.202 55G / 61G INFO General (construction.cpp : 464) Processed 288000000 edges
3:43:00.856 55G / 61G INFO General (construction.cpp : 464) Processed 320000000 edges
3:43:07.900 55G / 61G INFO General (construction.cpp : 464) Processed 342601160 edges
3:43:14.890 44G / 61G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
3:43:14.896 44G / 61G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
3:43:14.897 44G / 61G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled
3:43:14.897 44G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
3:43:25.569 44G / 61G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times
3:43:25.569 44G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper
3:43:44.900 44G / 61G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 185693 times
3:43:44.900 44G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover
3:58:28.242 46G / 61G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 16564542 times
3:58:28.242 46G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover
3:58:42.648 46G / 61G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 363151 times
3:58:58.872 46G / 61G INFO StageManager (stage.cpp : 132) STAGE == Simplification
3:58:58.872 46G / 61G INFO General (simplification.cpp : 357) Graph simplification started
3:58:58.872 46G / 61G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
3:58:58.872 46G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
3:58:58.872 46G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
3:59:15.269 46G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 240409 times
3:59:15.269 46G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
6:32:23.841 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11534116 times
6:32:23.841 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
6:32:48.282 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
6:32:48.282 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
6:32:48.282 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
6:33:30.357 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 44381 times
6:33:30.357 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
6:33:45.544 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1592 times
6:33:45.544 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
6:34:30.581 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 722588 times
6:34:30.581 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
6:34:30.581 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
6:34:33.063 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 13014 times
6:34:33.064 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
6:37:38.374 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 107553 times
6:37:38.374 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
6:42:11.413 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4531017 times
6:42:11.413 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
6:42:11.413 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
6:42:22.682 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 15269 times
6:42:22.682 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
7:57:19.647 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 466881 times
7:57:19.647 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
7:57:31.911 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 91 times
7:57:31.912 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
7:57:31.913 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
7:57:37.084 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 171 times
7:57:37.084 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 13 times
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
7:57:37.395 48G / 61G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
7:57:37.395 48G / 61G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup
7:57:37.395 48G / 61G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification
7:57:37.395 48G / 61G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
7:57:37.395 48G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
8:25:38.648 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 6922330 times
8:25:38.648 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
8:42:09.388 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 3160427 times
8:42:09.388 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
8:43:02.339 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 839872 times
8:43:02.339 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
8:46:35.670 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 36389 times
8:46:35.670 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:47:18.484 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1616922 times
8:47:18.484 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
8:47:24.823 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 443 times
8:47:24.823 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
9:25:13.739 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 359752 times
9:25:13.739 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
9:25:24.628 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
9:25:24.628 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
9:30:37.171 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 154623 times
9:30:37.171 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
9:41:34.716 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 125519 times
9:41:34.716 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
9:41:47.231 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 69179 times
9:41:47.231 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
9:44:50.325 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 2701 times
9:44:50.325 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
9:45:00.613 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 88471 times
9:45:00.613 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
9:45:07.081 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 23 times
9:45:07.081 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:17:26.900 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 20161 times
10:17:26.900 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:17:36.956 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 2 times
10:17:36.956 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:21:47.386 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 11428 times
10:21:47.386 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:23:23.100 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 3975 times
10:23:23.100 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:23:26.943 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 1143 times
10:23:26.943 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:26:34.477 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 222 times
10:26:34.478 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:26:34.918 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3204 times
10:26:34.918 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:26:35.140 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:26:35.140 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:26:43.157 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 868 times
10:26:43.157 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:26:43.315 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:26:43.315 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:30:46.345 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 305 times
10:30:46.345 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:30:48.538 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 182 times
10:30:48.538 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:30:52.461 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 46 times
10:30:52.462 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:33:58.877 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 6 times
10:33:58.877 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:33:58.901 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 132 times
10:33:58.901 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:33:58.908 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:33:58.908 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:33:59.294 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 33 times
10:33:59.294 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:33:59.298 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:33:59.298 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:38:08.272 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 12 times
10:38:08.272 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:38:08.364 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 12 times
10:38:08.364 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:38:12.116 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 6 times
10:38:12.116 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:41:15.611 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
10:41:15.611 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:41:15.613 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6 times
10:41:15.613 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:41:15.613 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:41:15.613 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:41:15.659 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times
10:41:15.659 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:41:15.659 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:41:15.659 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:45:19.813 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1 times
10:45:19.813 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:45:19.820 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times
10:45:19.820 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:45:23.339 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
10:45:23.341 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:48:26.032 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:48:26.034 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
10:48:26.034 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:48:26.034 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:48:26.034 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:52:31.324 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
10:52:31.324 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:52:31.324 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times
10:52:31.324 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:52:34.875 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
10:52:34.875 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:55:38.550 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:55:38.550 47G / 61G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta)
10:55:45.083 47G / 61G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges
10:59:27.001 47G / 61G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges
10:59:32.923 47G / 61G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 31778 times
10:59:32.923 47G / 61G INFO General (simplification.cpp : 470) Counting average coverage
11:00:37.448 47G / 61G INFO General (simplification.cpp : 476) Average coverage = 189.154
11:00:37.448 47G / 61G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
11:00:37.450 47G / 61G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K21/assembly_graph_with_scaffolds.gfa
11:05:21.809 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/before_rr.fasta
11:10:08.032 47G / 61G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K21/assembly_graph.fastg
11:24:16.886 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/simplified_contigs.fasta
11:28:50.920 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/final_contigs.fasta
11:33:23.821 47G / 61G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
11:33:23.821 47G / 61G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K21/assembly_graph_with_scaffolds.gfa
11:38:24.040 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/before_rr.fasta
11:43:16.536 47G / 61G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K21/assembly_graph.fastg
11:57:57.132 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/simplified_contigs.fasta
12:02:28.771 47G / 61G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K21/final_contigs.fasta
12:07:06.222 47G / 61G INFO General (launch.hpp : 149) SPAdes finished
12:11:43.469 132M / 61G INFO General (main.cpp : 109) Assembling time: 12 hours 11 minutes 43 seconds
Max read length detected as 391
== Running assembler: K41
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K41/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K41/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K41/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=41
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0
0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction
0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.003 4M / 4M INFO General (construction.cpp : 111) Max read length 391
0:00:00.003 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3
0:00:00.003 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
0:00:00.003 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
0:00:00.004 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000
0:00:00.004 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb
0:00:00.004 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
0:00:14.888 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 16293987 reads
0:00:27.830 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 24540202 reads
0:00:41.425 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 32625211 reads
0:00:54.640 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 40833963 reads
0:01:08.459 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 49092129 reads
0:01:21.292 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 57098839 reads
0:01:35.852 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 65450358 reads
0:01:49.476 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 73639915 reads
0:02:00.566 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 80421720 reads
0:02:14.301 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 88742707 reads
0:02:28.068 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 96938140 reads
0:02:40.831 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 104812314 reads
0:03:33.144 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 136384116 reads
0:07:12.600 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 269591402 reads
0:14:43.093 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 543849052 reads
0:29:30.658 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1079698136 reads
0:39:59.314 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
0:48:25.158 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads
0:48:25.158 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
1:29:37.310 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2949512921 kmers in total.
1:29:37.311 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
1:30:26.763 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
1:30:26.769 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
1:30:26.769 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
1:30:26.769 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000
1:30:26.769 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb
1:30:26.769 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536
1:30:27.386 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5359330 kmers
1:30:28.050 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11046516 kmers
1:30:28.803 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17028244 kmers
1:30:29.482 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 22961657 kmers
1:30:30.150 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28750468 kmers
1:30:30.825 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34741732 kmers
1:30:31.511 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 41368877 kmers
1:30:32.173 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 47501198 kmers
1:30:32.946 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 53857576 kmers
1:30:33.872 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 60210724 kmers
1:30:34.550 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 66153150 kmers
1:30:35.232 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 72141995 kmers
1:30:35.945 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 78346001 kmers
1:30:36.635 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 84403574 kmers
1:30:37.421 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 90421604 kmers
1:30:38.281 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 97516787 kmers
1:30:39.211 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 103204193 kmers
1:30:43.716 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 139675929 kmers
1:30:58.070 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 268710320 kmers
1:31:54.481 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539143445 kmers
1:33:35.829 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1074092382 kmers
1:37:02.143 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2148740858 kmers
1:39:33.127 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 2949528281 kmers.
1:39:33.403 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
1:44:04.028 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2915367632 kmers in total.
1:44:04.028 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
1:48:00.924 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
1:50:01.625 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
1:56:17.323 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1351920592 bytes occupied (3.70978 bits per kmer).
1:56:19.727 4G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
1:59:11.278 4G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
1:59:11.283 4G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping
1:59:11.283 4G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K)
1:59:11.284 4G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping
2:06:03.213 4G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 330223819 42-mers were removed by early tip clipper
2:06:03.213 4G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
2:06:03.246 4G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
2:10:00.703 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 103911528 sequences extracted
2:11:42.093 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
2:12:49.042 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 2864 loops collected
2:13:40.207 33G / 42G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
2:13:40.207 33G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
2:13:40.207 33G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
2:15:18.630 34G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1367723606 bytes occupied (3.70969 bits per kmer).
2:15:25.224 45G / 45G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
3:06:46.954 45G / 45G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
3:07:16.918 45G / 45G INFO General (construction.cpp : 464) Processed 32000000 edges
3:07:41.295 45G / 45G INFO General (construction.cpp : 464) Processed 64000000 edges
3:08:05.632 45G / 45G INFO General (construction.cpp : 464) Processed 96000000 edges
3:08:29.949 45G / 45G INFO General (construction.cpp : 464) Processed 128000000 edges
3:08:54.247 45G / 45G INFO General (construction.cpp : 464) Processed 160000000 edges
3:09:18.533 45G / 45G INFO General (construction.cpp : 464) Processed 192000000 edges
3:09:30.925 45G / 45G INFO General (construction.cpp : 464) Processed 207817849 edges
3:09:44.712 29G / 45G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
3:09:44.718 29G / 45G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
3:09:44.719 29G / 45G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled
3:09:44.719 29G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
3:09:51.352 29G / 45G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 429 times
3:09:51.352 29G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper
3:10:10.893 29G / 45G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 415433 times
3:10:10.893 29G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover
3:20:12.151 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 10537302 times
3:20:12.151 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover
3:20:44.064 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 2511683 times
3:20:52.955 30G / 45G INFO StageManager (stage.cpp : 132) STAGE == Simplification
3:20:52.955 30G / 45G INFO General (simplification.cpp : 357) Graph simplification started
3:20:52.955 30G / 45G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
3:20:52.955 30G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
3:20:52.955 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
3:21:06.625 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 344169 times
3:21:06.625 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
4:21:50.355 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11150066 times
4:21:50.355 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
4:21:58.652 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 379 times
4:21:58.652 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
4:21:58.652 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
4:22:27.177 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 63769 times
4:22:27.177 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
4:22:29.911 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2500 times
4:22:29.911 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
4:22:52.292 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 298264 times
4:22:52.292 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
4:22:52.292 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
4:22:53.641 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 9335 times
4:22:53.641 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
4:23:57.108 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 59208 times
4:23:57.108 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
4:25:52.255 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1497180 times
4:25:52.255 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
4:25:52.255 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
4:25:57.886 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 19645 times
4:25:57.886 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
4:41:04.623 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 309436 times
4:41:04.623 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
4:41:10.221 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 96 times
4:41:10.221 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
4:41:10.222 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
4:41:13.571 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 561 times
4:41:13.571 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 39 times
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
4:41:13.706 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
4:41:13.706 31G / 45G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
4:41:13.706 31G / 45G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
4:41:13.707 31G / 45G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup
4:41:13.707 31G / 45G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification
4:41:13.707 31G / 45G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
4:41:13.707 31G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
4:51:21.864 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 2606848 times
4:51:21.864 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
4:59:45.014 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1575117 times
4:59:45.014 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
5:00:11.821 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 434812 times
5:00:11.821 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
5:01:54.180 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 107703 times
5:01:54.180 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
5:02:19.368 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 823150 times
5:02:19.368 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
5:02:22.549 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 675 times
5:02:22.549 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
5:08:28.372 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 190368 times
5:08:28.372 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
5:08:39.652 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 13 times
5:08:39.652 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
5:10:23.192 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 75481 times
5:10:23.192 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
5:16:58.623 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 195233 times
5:16:58.623 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
5:17:06.017 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 38173 times
5:17:06.017 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
5:18:21.305 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 4589 times
5:18:21.305 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
5:18:31.742 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 167694 times
5:18:31.742 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
5:18:34.591 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 195 times
5:18:34.591 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
5:22:29.783 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 29334 times
5:22:29.783 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
5:22:40.688 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 2 times
5:22:40.689 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
5:23:52.158 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 12991 times
5:23:52.158 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
5:25:39.919 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 5755 times
5:25:39.919 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
5:25:42.328 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 1644 times
5:25:42.328 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
5:26:50.942 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 785 times
5:26:50.942 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
5:26:51.625 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4833 times
5:26:51.625 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
5:26:51.990 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 6 times
5:26:51.990 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
5:26:57.635 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1492 times
5:26:57.635 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
5:26:57.903 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
5:26:57.903 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
5:28:07.534 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 619 times
5:28:07.534 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
5:28:11.001 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 269 times
5:28:11.001 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
5:28:13.471 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 43 times
5:28:13.471 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
5:29:19.484 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 33 times
5:29:19.485 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
5:29:19.523 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 215 times
5:29:19.523 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
5:29:19.538 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 1 times
5:29:19.538 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
5:29:19.979 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 57 times
5:29:19.979 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
5:29:19.985 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
5:29:19.986 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
5:30:27.842 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 31 times
5:30:27.842 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
5:30:27.932 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 18 times
5:30:27.932 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
5:30:30.193 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 5 times
5:30:30.193 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
5:31:36.751 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 3 times
5:31:36.751 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
5:31:36.754 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times
5:31:36.755 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
5:31:36.756 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
5:31:36.756 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
5:31:36.788 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times
5:31:36.788 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
5:31:36.788 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
5:31:36.788 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
5:32:43.750 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1 times
5:32:43.750 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
5:32:43.761 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times
5:32:43.761 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
5:32:45.970 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
5:32:45.970 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
5:33:52.586 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
5:33:52.588 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times
5:33:52.588 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
5:33:52.588 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
5:33:52.588 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
5:35:00.131 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
5:35:00.131 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
5:35:00.131 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times
5:35:00.131 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
5:35:02.373 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
5:35:02.373 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
5:36:08.466 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
5:36:08.466 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
5:36:08.467 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
5:36:08.467 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
5:36:08.467 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
5:36:08.468 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
5:36:08.468 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
5:36:08.468 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
5:36:08.469 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
5:36:08.469 30G / 45G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta)
5:36:11.734 30G / 45G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges
5:37:39.593 30G / 45G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges
5:37:43.037 30G / 45G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 35463 times
5:37:43.038 30G / 45G INFO General (simplification.cpp : 470) Counting average coverage
5:38:06.951 30G / 45G INFO General (simplification.cpp : 476) Average coverage = 132.33
5:38:06.951 30G / 45G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
5:38:06.957 30G / 45G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K41/assembly_graph_with_scaffolds.gfa
5:40:01.984 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/before_rr.fasta
5:41:41.771 30G / 45G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K41/assembly_graph.fastg
5:47:14.978 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/simplified_contigs.fasta
5:49:00.009 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/final_contigs.fasta
5:50:41.375 30G / 45G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
5:50:41.375 30G / 45G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K41/assembly_graph_with_scaffolds.gfa
5:52:13.938 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/before_rr.fasta
5:53:54.465 30G / 45G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K41/assembly_graph.fastg
5:59:13.326 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/simplified_contigs.fasta
6:00:55.344 30G / 45G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K41/final_contigs.fasta
6:02:38.383 30G / 45G INFO General (launch.hpp : 149) SPAdes finished
6:04:42.273 140M / 45G INFO General (main.cpp : 109) Assembling time: 6 hours 4 minutes 42 seconds
== Running assembler: K71
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K71/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K71/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K71/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=71
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0
0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached
0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction
0:00:00.008 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.011 4M / 4M INFO General (construction.cpp : 111) Max read length 391
0:00:00.011 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3
0:00:00.011 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
0:00:00.011 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
0:00:00.012 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000
0:00:00.012 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb
0:00:00.012 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 21845
0:00:12.755 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 15207297 reads
0:00:22.042 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 21278852 reads
0:00:32.468 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 27307485 reads
0:00:42.414 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 33368915 reads
0:00:53.024 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 39309976 reads
0:01:03.036 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 45387241 reads
0:01:13.673 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 51595562 reads
0:01:23.042 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 57268238 reads
0:01:33.422 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 63443181 reads
0:01:43.883 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 69517639 reads
0:01:53.477 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 75265631 reads
0:02:02.118 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 80838718 reads
0:03:30.489 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 135552843 reads
0:07:09.234 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 272905024 reads
0:14:19.384 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 537123187 reads
0:32:41.110 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1074107474 reads
0:53:26.068 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
1:02:49.854 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads
1:02:49.854 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
2:12:42.967 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3590364827 kmers in total.
2:12:42.967 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
2:18:01.505 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
2:18:01.511 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
2:18:01.511 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
2:18:01.512 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000
2:18:01.512 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb
2:18:01.512 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690
2:18:02.098 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 3614726 kmers
2:18:02.681 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7378981 kmers
2:18:03.196 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11183311 kmers
2:18:03.795 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14969735 kmers
2:18:04.412 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 19025172 kmers
2:18:05.090 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 22921320 kmers
2:18:05.697 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26974987 kmers
2:18:06.363 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 30768015 kmers
2:18:07.437 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34688653 kmers
2:18:08.981 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 38532352 kmers
2:18:10.750 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 42609769 kmers
2:18:12.513 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46893943 kmers
2:18:14.488 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 51170187 kmers
2:18:16.206 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 55296215 kmers
2:18:18.192 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 59213498 kmers
2:18:20.313 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 63291984 kmers
2:18:22.561 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 67609739 kmers
2:18:50.082 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 135146701 kmers
2:19:39.706 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 271312352 kmers
2:21:21.698 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 540486341 kmers
2:24:43.257 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1077410505 kmers
2:31:19.331 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2150852268 kmers
2:52:28.639 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 3590393499 kmers.
2:52:28.838 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
3:07:28.575 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3577643922 kmers in total.
3:07:28.576 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
3:15:14.743 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
3:18:32.613 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
3:32:37.209 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1659000600 bytes occupied (3.70971 bits per kmer).
3:32:40.248 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
3:53:11.070 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
3:53:11.077 5G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
3:53:11.142 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
3:58:34.619 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 90760601 sequences extracted
4:00:58.940 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
4:03:49.230 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 172 loops collected
4:04:44.874 32G / 41G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
4:04:44.880 32G / 41G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
4:04:44.880 32G / 41G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
4:13:53.100 34G / 41G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1664941782 bytes occupied (3.7098 bits per kmer).
4:14:01.597 47G / 47G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
4:59:18.625 47G / 47G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
5:00:03.404 47G / 47G INFO General (construction.cpp : 464) Processed 32000000 edges
5:00:43.110 47G / 47G INFO General (construction.cpp : 464) Processed 64000000 edges
5:01:23.014 47G / 47G INFO General (construction.cpp : 464) Processed 96000000 edges
5:02:03.140 47G / 47G INFO General (construction.cpp : 464) Processed 128000000 edges
5:02:43.322 47G / 47G INFO General (construction.cpp : 464) Processed 160000000 edges
5:03:10.275 47G / 47G INFO General (construction.cpp : 464) Processed 181518961 edges
5:03:29.970 27G / 47G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
5:03:29.976 27G / 47G INFO General (graph_pack.hpp : 101) Index refill
5:03:29.976 27G / 47G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
5:03:29.976 27G / 47G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
5:03:29.977 27G / 47G INFO General (file_limit.hpp : 32) Open file limit set to 10000
5:03:29.977 27G / 47G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.10779 Gb
5:03:29.977 27G / 47G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690
5:03:55.292 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 32003376 edges
5:04:17.221 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 63999718 edges
5:04:46.370 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 96020239 edges
5:06:58.769 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 128047309 edges
5:09:06.625 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 160043632 edges
5:10:33.681 45G / 47G INFO General (edge_index_builders.hpp : 77) Processed 181519121 edges
5:10:33.681 45G / 47G INFO General (edge_index_builders.hpp : 82) Used 181519121 sequences.
5:10:34.952 27G / 47G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
5:21:46.655 27G / 47G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3590364827 kmers in total.
5:21:46.656 27G / 47G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
5:32:21.481 27G / 47G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
5:35:21.204 29G / 47G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
5:44:20.456 29G / 47G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1664888054 bytes occupied (3.70968 bits per kmer).
5:45:12.659 109G / 109G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
5:47:25.927 109G / 109G INFO General (edge_index.hpp : 92) Index refilled
5:47:26.220 109G / 109G INFO General (gap_closer.cpp : 159) Preparing shift maps
5:50:31.887 113G / 113G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
5:53:07.273 114G / 114G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads
5:53:07.273 114G / 114G INFO General (gap_closer.cpp : 140) Merging paired indices
5:53:42.128 110G / 114G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
6:03:48.008 110G / 118G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 112713 gaps after checking 994271 candidates
6:05:22.433 109G / 118G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
6:05:28.293 27G / 118G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
6:05:28.295 27G / 118G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled
6:05:28.295 27G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
6:05:35.550 27G / 118G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 183 times
6:05:35.550 27G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper
6:12:26.114 28G / 118G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 15402076 times
6:12:26.114 28G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover
6:16:58.280 28G / 118G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 4147418 times
6:16:58.280 28G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover
6:18:02.890 28G / 118G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 5463077 times
6:18:10.648 28G / 118G INFO StageManager (stage.cpp : 132) STAGE == Simplification
6:18:10.648 28G / 118G INFO General (simplification.cpp : 357) Graph simplification started
6:18:10.648 28G / 118G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
6:18:10.648 28G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
6:18:10.648 28G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
6:18:42.970 28G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1264098 times
6:18:42.970 28G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:21:50.763 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7039138 times
8:21:50.763 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:21:55.237 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 185 times
8:21:55.237 112G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
8:21:55.237 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:22:09.571 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 40908 times
8:22:09.571 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:22:14.244 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1767 times
8:22:14.244 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:22:21.151 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 107521 times
8:22:21.151 112G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
8:22:21.151 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:22:21.602 112G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5565 times
8:22:21.602 112G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:23:20.743 113G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 27925 times
8:23:20.743 113G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:24:10.658 113G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 705547 times
8:24:10.658 113G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
8:24:10.658 113G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:24:15.080 113G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 23351 times
8:24:15.081 113G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:34:27.333 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 190061 times
8:34:27.333 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:34:30.849 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 35 times
8:34:30.849 115G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
8:34:30.849 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:34:32.553 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 757 times
8:34:32.553 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 48 times
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
8:34:32.811 115G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
8:34:32.811 115G / 118G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:34:32.811 115G / 118G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
8:34:32.812 115G / 118G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
8:34:32.812 115G / 118G INFO General (graph_pack.hpp : 101) Index refill
8:34:32.812 115G / 118G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
8:34:32.812 115G / 118G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
8:34:32.812 115G / 118G INFO General (file_limit.hpp : 32) Open file limit set to 10000
8:34:32.812 115G / 118G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.19157 Gb
8:34:32.812 115G / 118G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690
8:34:55.225 133G / 134G INFO General (edge_index_builders.hpp : 77) Processed 14696826 edges
8:35:52.374 133G / 134G INFO General (edge_index_builders.hpp : 77) Processed 29353942 edges
8:36:36.005 133G / 134G INFO General (edge_index_builders.hpp : 77) Processed 36139634 edges
8:36:36.005 133G / 134G INFO General (edge_index_builders.hpp : 82) Used 36139634 sequences.
8:36:37.760 115G / 134G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
8:39:31.413 115G / 134G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1661224144 kmers in total.
8:39:31.413 115G / 134G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
8:42:41.596 115G / 134G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
8:43:54.503 116G / 134G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
8:49:06.554 116G / 134G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 770339136 bytes occupied (3.70974 bits per kmer).
8:49:37.707 153G / 153G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
8:50:37.790 153G / 153G INFO General (edge_index.hpp : 92) Index refilled
8:50:37.792 153G / 153G INFO General (gap_closer.cpp : 159) Preparing shift maps
8:51:11.521 153G / 153G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
8:59:29.141 153G / 153G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads
8:59:29.141 153G / 153G INFO General (gap_closer.cpp : 140) Merging paired indices
8:59:31.876 153G / 153G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
9:01:08.096 153G / 154G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1530 gaps after checking 54313 candidates
9:01:18.932 153G / 154G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup
9:01:18.932 153G / 154G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification
9:01:18.932 153G / 154G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
9:01:18.932 153G / 154G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
9:19:18.187 153G / 154G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1140437 times
9:19:18.187 153G / 154G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
9:40:14.036 153G / 154G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1417969 times
9:40:14.036 153G / 154G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
9:42:19.557 153G / 154G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 236384 times
9:42:19.557 153G / 154G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
9:58:49.390 157G / 157G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 156575 times
9:58:49.390 157G / 157G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:04:44.734 157G / 157G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 840488 times
10:04:44.734 157G / 157G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:04:52.546 157G / 157G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 3106 times
10:04:52.546 157G / 157G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:13:15.738 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 140291 times
10:13:15.738 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:13:31.839 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 20 times
10:13:31.839 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:14:34.948 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 34950 times
10:14:34.949 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:21:08.397 158G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 221397 times
10:21:08.397 158G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:21:27.282 158G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 22468 times
10:21:27.282 158G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:22:51.643 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 7831 times
10:22:51.643 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:24:45.704 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 200654 times
10:24:45.704 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:24:50.533 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 997 times
10:24:50.533 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:26:50.232 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 23558 times
10:26:50.232 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:27:01.194 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:27:01.194 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:27:26.981 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 5916 times
10:27:26.981 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:28:16.637 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 6156 times
10:28:16.637 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:28:20.389 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 1623 times
10:28:20.389 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:29:03.508 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 1414 times
10:29:03.508 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:29:08.019 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5895 times
10:29:08.019 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:29:08.392 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 25 times
10:29:08.392 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:29:13.309 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 968 times
10:29:13.309 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:29:13.508 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:29:13.508 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:29:33.352 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 309 times
10:29:33.352 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:29:35.292 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 265 times
10:29:35.292 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:29:36.348 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 53 times
10:29:36.348 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:30:08.365 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 58 times
10:30:08.365 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:30:08.568 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 229 times
10:30:08.569 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:30:08.577 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:30:08.577 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:30:08.896 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 51 times
10:30:08.896 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:30:08.915 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:30:08.916 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:30:27.952 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 14 times
10:30:27.952 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:30:28.038 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 14 times
10:30:28.038 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:30:29.351 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 5 times
10:30:29.352 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:31:01.015 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 4 times
10:31:01.015 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:31:01.039 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times
10:31:01.039 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:31:01.040 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:31:01.040 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:31:01.058 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times
10:31:01.058 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:31:01.058 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:31:01.058 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:31:19.135 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1 times
10:31:19.137 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:31:19.150 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 3 times
10:31:19.150 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:31:20.180 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
10:31:20.180 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:31:52.468 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 1 times
10:31:52.468 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times
10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:31:52.472 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:32:10.448 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1 times
10:32:10.449 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:32:10.451 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times
10:32:10.451 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:32:11.448 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
10:32:11.448 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 1 times
10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:32:43.631 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:32:43.633 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times
10:32:43.633 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:32:43.633 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:32:43.633 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:33:02.181 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
10:33:02.181 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:33:02.194 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1 times
10:33:02.195 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:33:03.219 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
10:33:03.219 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:33:34.770 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
10:33:54.634 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
10:33:54.634 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
10:33:54.634 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times
10:33:54.634 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
10:33:55.676 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
10:33:55.676 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
10:34:27.580 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
10:34:27.580 159G / 159G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta)
10:34:29.808 159G / 159G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges
10:34:56.093 159G / 159G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges
10:35:12.695 159G / 159G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 33356 times
10:35:12.695 159G / 159G INFO General (simplification.cpp : 470) Counting average coverage
10:35:24.557 159G / 159G INFO General (simplification.cpp : 476) Average coverage = 92.2438
10:35:24.557 159G / 159G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
10:35:24.563 159G / 159G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K71/assembly_graph_with_scaffolds.gfa
10:36:18.591 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/before_rr.fasta
10:37:28.892 159G / 159G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K71/assembly_graph.fastg
10:40:48.693 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/simplified_contigs.fasta
10:41:50.636 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/final_contigs.fasta
10:42:52.747 159G / 159G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
10:42:52.747 159G / 159G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K71/assembly_graph_with_scaffolds.gfa
10:43:49.494 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/before_rr.fasta
10:44:51.895 159G / 159G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K71/assembly_graph.fastg
10:48:07.760 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/simplified_contigs.fasta
10:49:15.426 159G / 159G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K71/final_contigs.fasta
10:50:21.401 159G / 159G INFO General (launch.hpp : 149) SPAdes finished
11:23:17.949 136M / 159G INFO General (main.cpp : 109) Assembling time: 11 hours 23 minutes 17 seconds
== Running assembler: K101
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K101/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K101/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K101/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=101
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 0
0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached
0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction
0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.122 4M / 4M INFO General (construction.cpp : 111) Max read length 391
0:00:00.122 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3
0:00:00.122 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
0:00:00.122 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
0:00:00.124 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000
0:00:00.124 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb
0:00:00.124 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384
0:00:14.909 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 15118831 reads
0:00:33.335 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 20591011 reads
0:00:47.938 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 26067004 reads
0:01:07.061 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 31560368 reads
0:01:20.256 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 36863364 reads
0:01:33.879 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 42381438 reads
0:01:43.091 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 47730744 reads
0:01:55.983 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 53055567 reads
0:02:08.827 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 58228556 reads
0:02:22.534 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 63770533 reads
0:02:31.333 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 68881734 reads
0:02:40.063 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 74255829 reads
0:04:22.557 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 136970261 reads
0:07:58.851 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 271528096 reads
0:24:08.848 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 540003898 reads
1:04:00.395 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1077258199 reads
1:23:20.640 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
1:32:44.565 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads
1:32:44.566 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
3:03:47.764 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3774429990 kmers in total.
3:03:47.764 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
3:14:10.281 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
3:14:10.281 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
3:14:10.281 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
3:14:10.281 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000
3:14:10.281 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb
3:14:10.281 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
3:14:10.783 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2765081 kmers
3:14:11.236 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5565196 kmers
3:14:11.723 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8482599 kmers
3:14:12.247 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11379103 kmers
3:14:12.936 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14185777 kmers
3:14:13.777 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17110568 kmers
3:14:14.819 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 20142587 kmers
3:14:16.511 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23051793 kmers
3:14:18.705 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26091060 kmers
3:14:21.466 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 29014597 kmers
3:14:24.337 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 31832339 kmers
3:14:26.501 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34759173 kmers
3:14:28.075 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 37644994 kmers
3:14:29.547 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 40563380 kmers
3:14:31.465 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 43589298 kmers
3:14:33.065 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46713845 kmers
3:14:45.828 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68232287 kmers
3:15:21.984 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 135060613 kmers
3:16:34.325 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 270677633 kmers
3:18:55.224 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 536903490 kmers
3:23:50.081 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1075764187 kmers
3:35:32.432 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2149230595 kmers
4:26:08.832 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 3774469926 kmers.
4:26:09.054 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
5:00:29.652 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3772357944 kmers in total.
5:00:29.652 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
5:08:27.682 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
5:12:36.876 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
5:26:24.454 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1749268740 bytes occupied (3.70966 bits per kmer).
5:26:28.828 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
6:29:47.033 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
6:29:47.038 5G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
6:29:47.144 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
6:37:00.190 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 73106921 sequences extracted
6:40:16.132 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
6:44:22.043 11G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 130 loops collected
6:45:25.227 29G / 36G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
6:45:25.227 29G / 36G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
6:45:25.227 29G / 36G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
6:59:30.956 31G / 36G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1750271336 bytes occupied (3.70974 bits per kmer).
6:59:40.890 45G / 45G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
7:46:13.955 45G / 45G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
7:47:21.699 45G / 45G INFO General (construction.cpp : 464) Processed 32000000 edges
7:48:26.174 45G / 45G INFO General (construction.cpp : 464) Processed 64000000 edges
7:49:32.308 45G / 45G INFO General (construction.cpp : 464) Processed 96000000 edges
7:50:35.664 45G / 45G INFO General (construction.cpp : 464) Processed 128000000 edges
7:51:12.469 45G / 45G INFO General (construction.cpp : 464) Processed 146213612 edges
7:51:48.653 23G / 45G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
7:51:48.653 23G / 45G INFO General (graph_pack.hpp : 101) Index refill
7:51:48.653 23G / 45G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
7:51:48.653 23G / 45G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
7:51:48.654 23G / 45G INFO General (file_limit.hpp : 32) Open file limit set to 10000
7:51:48.654 23G / 45G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.14608 Gb
7:51:48.654 23G / 45G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
7:52:15.299 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 18794221 edges
7:52:39.473 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 37606340 edges
7:53:18.342 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 56422731 edges
7:55:04.980 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 75194331 edges
7:56:49.566 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 94007507 edges
7:58:35.755 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 112812535 edges
8:00:23.216 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 131610693 edges
8:01:46.008 41G / 45G INFO General (edge_index_builders.hpp : 77) Processed 146213836 edges
8:01:46.008 41G / 45G INFO General (edge_index_builders.hpp : 82) Used 146213836 sequences.
8:01:47.395 23G / 45G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
8:14:54.157 23G / 45G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3774429990 kmers in total.
8:14:54.157 23G / 45G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
8:28:29.162 23G / 45G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
8:32:41.253 25G / 45G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
8:48:33.646 25G / 45G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1750231774 bytes occupied (3.70966 bits per kmer).
8:49:36.200 110G / 110G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
8:52:25.957 110G / 110G INFO General (edge_index.hpp : 92) Index refilled
8:52:26.230 110G / 110G INFO General (gap_closer.cpp : 159) Preparing shift maps
8:55:32.122 115G / 115G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
8:57:23.876 116G / 116G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads
8:57:23.876 116G / 116G INFO General (gap_closer.cpp : 140) Merging paired indices
8:58:08.057 110G / 116G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
9:06:26.095 110G / 117G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 117317 gaps after checking 1105008 candidates
9:08:12.721 110G / 117G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
9:08:18.819 24G / 117G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
9:08:18.822 24G / 117G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled
9:08:18.822 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
9:08:27.265 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 36 times
9:08:27.265 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper
9:15:45.848 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 13592223 times
9:15:45.848 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover
9:18:50.992 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 2403702 times
9:18:50.992 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover
9:20:46.067 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 9080535 times
9:20:53.044 24G / 117G INFO StageManager (stage.cpp : 132) STAGE == Simplification
9:20:53.044 24G / 117G INFO General (simplification.cpp : 357) Graph simplification started
9:20:53.045 24G / 117G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
9:20:53.045 24G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
9:20:53.045 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
9:21:46.334 24G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1814615 times
9:21:46.334 24G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
11:34:49.685 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4586458 times
11:34:49.685 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
11:34:53.407 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 119 times
11:34:53.407 114G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
11:34:53.407 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
11:35:02.154 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 25922 times
11:35:02.154 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
11:35:10.144 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1352 times
11:35:10.144 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
11:35:14.941 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 64519 times
11:35:14.941 114G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
11:35:14.941 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
11:35:15.375 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3836 times
11:35:15.375 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
11:36:17.990 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19425 times
11:36:17.990 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
11:37:06.572 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 487195 times
11:37:06.572 114G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
11:37:06.572 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
11:37:11.584 114G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 25446 times
11:37:11.584 114G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
11:47:01.619 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 144200 times
11:47:01.619 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
11:47:05.952 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 24 times
11:47:05.952 117G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
11:47:05.952 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
11:47:07.542 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 973 times
11:47:07.542 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
11:47:08.084 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 64 times
11:47:08.084 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
11:47:08.084 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
11:47:08.084 117G / 117G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
11:47:08.084 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
11:47:08.085 117G / 117G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
11:47:08.086 117G / 117G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
11:47:08.086 117G / 117G INFO General (graph_pack.hpp : 101) Index refill
11:47:08.087 117G / 117G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
11:47:08.087 117G / 117G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
11:47:08.087 117G / 117G INFO General (file_limit.hpp : 32) Open file limit set to 10000
11:47:08.087 117G / 117G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.16866 Gb
11:47:08.087 117G / 117G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
11:47:32.764 135G / 136G INFO General (edge_index_builders.hpp : 77) Processed 6449115 edges
11:48:49.570 135G / 136G INFO General (edge_index_builders.hpp : 77) Processed 12889683 edges
11:50:41.821 135G / 136G INFO General (edge_index_builders.hpp : 77) Processed 19344547 edges
11:51:41.783 135G / 136G INFO General (edge_index_builders.hpp : 77) Processed 22944845 edges
11:51:41.783 135G / 136G INFO General (edge_index_builders.hpp : 82) Used 22944845 sequences.
11:51:43.025 117G / 136G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
11:57:59.597 117G / 136G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1834528053 kmers in total.
11:57:59.598 117G / 136G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
12:04:12.996 117G / 136G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
12:06:06.868 118G / 136G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
12:13:48.451 118G / 136G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 850691774 bytes occupied (3.70969 bits per kmer).
12:14:23.885 159G / 159G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
12:15:42.557 159G / 159G INFO General (edge_index.hpp : 92) Index refilled
12:15:42.558 159G / 159G INFO General (gap_closer.cpp : 159) Preparing shift maps
12:16:03.761 159G / 159G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
12:22:40.366 159G / 159G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads
12:22:40.366 159G / 159G INFO General (gap_closer.cpp : 140) Merging paired indices
12:22:42.967 159G / 159G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
12:24:08.848 159G / 160G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 540 gaps after checking 33654 candidates
12:24:15.527 159G / 160G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup
12:24:15.527 159G / 160G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification
12:24:15.527 159G / 160G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
12:24:15.527 159G / 160G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
12:38:27.581 159G / 160G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 497563 times
12:38:27.581 159G / 160G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
13:00:53.105 159G / 160G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1063287 times
13:00:53.105 159G / 160G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
13:02:44.375 159G / 160G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 117633 times
13:02:44.375 159G / 160G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
13:26:37.777 165G / 165G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 131921 times
13:26:37.777 165G / 165G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
13:35:16.336 165G / 165G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 634776 times
13:35:16.336 165G / 165G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
13:35:41.552 165G / 165G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 6552 times
13:35:41.552 165G / 165G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
13:43:49.848 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 86219 times
13:43:49.848 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
13:44:05.565 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 15 times
13:44:05.565 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
13:45:02.324 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 17507 times
13:45:02.324 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
13:49:36.243 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 100845 times
13:49:36.243 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
13:49:52.293 167G / 167G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 10065 times
13:49:52.293 167G / 167G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
13:51:27.108 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 6286 times
13:51:27.108 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
13:53:08.365 167G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 90567 times
13:53:08.365 167G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
13:53:16.646 167G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 1345 times
13:53:16.646 167G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
13:54:34.889 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9962 times
13:54:34.889 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
13:54:46.714 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 1 times
13:54:46.714 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
13:55:05.664 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 2774 times
13:55:05.664 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
13:55:28.416 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 2094 times
13:55:28.416 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
13:55:31.424 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 655 times
13:55:31.425 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
13:56:05.894 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 791 times
13:56:05.894 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
13:56:08.760 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2070 times
13:56:08.760 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
13:56:09.010 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 16 times
13:56:09.010 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
13:56:11.944 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 430 times
13:56:11.944 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
13:56:12.117 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
13:56:12.117 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
13:56:23.782 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 119 times
13:56:23.782 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
13:56:24.444 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 96 times
13:56:24.444 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
13:56:25.436 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 14 times
13:56:25.437 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
13:56:50.656 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 18 times
13:56:50.656 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
13:56:50.754 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 82 times
13:56:50.754 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
13:56:50.760 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
13:56:50.760 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
13:56:50.882 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 16 times
13:56:50.882 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
13:56:50.884 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
13:56:50.884 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
13:57:02.875 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 7 times
13:57:02.875 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
13:57:02.904 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 5 times
13:57:02.904 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
13:57:03.731 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 3 times
13:57:03.732 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
13:57:28.481 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 3 times
13:57:28.481 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
13:57:28.485 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times
13:57:28.485 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
13:57:28.486 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
13:57:28.486 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
13:57:28.493 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times
13:57:28.493 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
13:57:28.493 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
13:57:28.493 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
13:57:40.482 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 6 times
13:57:40.483 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
13:57:40.488 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 1 times
13:57:40.489 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
13:57:41.336 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
13:57:41.336 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
13:58:06.440 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
13:58:06.440 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
13:58:06.443 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times
13:58:06.444 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
13:58:06.444 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
13:58:06.444 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
13:58:06.456 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times
13:58:06.456 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
13:58:06.456 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
13:58:06.456 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
13:58:18.872 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
13:58:18.872 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage
13:58:18.874 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times
13:58:18.874 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper
13:58:19.714 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times
13:58:19.714 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta)
13:58:44.168 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times
13:58:44.168 168G / 168G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta)
13:58:46.315 168G / 168G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges
13:59:13.340 168G / 168G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges
13:59:25.289 168G / 168G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 17378 times
13:59:25.293 168G / 168G INFO General (simplification.cpp : 470) Counting average coverage
13:59:32.085 168G / 168G INFO General (simplification.cpp : 476) Average coverage = 65.1735
13:59:32.085 168G / 168G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
13:59:32.091 168G / 168G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K101/assembly_graph_with_scaffolds.gfa
14:00:29.384 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/before_rr.fasta
14:01:35.659 168G / 168G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K101/assembly_graph.fastg
14:05:11.186 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/simplified_contigs.fasta
14:06:19.370 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/final_contigs.fasta
14:07:25.813 168G / 168G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
14:07:25.813 168G / 168G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/CPB_metaSpades/output//K101/assembly_graph_with_scaffolds.gfa
14:08:28.770 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/before_rr.fasta
14:09:39.488 168G / 168G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/CPB_metaSpades/output//K101/assembly_graph.fastg
14:13:21.159 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/simplified_contigs.fasta
14:14:34.578 168G / 168G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/CPB_metaSpades/output//K101/final_contigs.fasta
14:15:45.185 168G / 168G INFO General (launch.hpp : 149) SPAdes finished
14:55:07.072 136M / 168G INFO General (main.cpp : 109) Assembling time: 14 hours 55 minutes 7 seconds
== Running assembler: K127
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=127
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 1
0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached
0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction
0:00:00.010 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.131 4M / 4M INFO General (construction.cpp : 111) Max read length 391
0:00:00.131 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3
0:00:00.131 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
0:00:00.131 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
0:00:00.132 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000
0:00:00.132 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb
0:00:00.132 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384
0:00:19.355 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 17140129 reads
0:00:32.356 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 23520925 reads
0:00:42.792 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 29992420 reads
0:01:05.448 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 36236148 reads
0:01:31.203 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 42736415 reads
0:01:54.644 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 49210758 reads
0:02:19.202 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 55280562 reads
0:02:43.190 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 61718196 reads
0:03:09.718 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 67983612 reads
0:03:35.152 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 74290861 reads
0:03:55.816 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 79477653 reads
0:04:21.658 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 85889932 reads
0:07:44.464 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 136387847 reads
0:16:18.721 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 272811252 reads
0:33:45.474 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 542509926 reads
1:08:45.923 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1079247014 reads
1:21:49.474 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
1:35:19.890 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads
1:35:19.890 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
2:50:27.610 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3723768626 kmers in total.
2:50:27.610 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
2:58:57.713 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
2:58:57.713 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
2:58:57.713 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
2:58:57.714 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000
2:58:57.714 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb
2:58:57.714 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
2:58:59.144 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2813582 kmers
2:59:00.693 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5658767 kmers
2:59:01.990 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8543596 kmers
2:59:03.466 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11428796 kmers
2:59:04.820 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14295951 kmers
2:59:06.007 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17246063 kmers
2:59:07.153 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 20211545 kmers
2:59:08.451 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23106226 kmers
2:59:09.734 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26080313 kmers
2:59:11.298 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28985625 kmers
2:59:12.732 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 31852746 kmers
2:59:14.062 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34766489 kmers
2:59:15.613 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 37655712 kmers
2:59:16.912 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 40603664 kmers
2:59:18.264 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 43598434 kmers
2:59:19.540 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46764703 kmers
2:59:29.607 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68246622 kmers
3:00:00.616 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 136575717 kmers
3:01:03.097 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 270415046 kmers
3:03:08.227 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539831168 kmers
3:07:14.860 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1076348452 kmers
3:15:37.760 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2147682876 kmers
3:51:26.844 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 3723808562 kmers.
3:51:27.068 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
4:20:33.020 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3727975608 kmers in total.
4:20:33.020 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
4:29:45.914 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
4:34:03.384 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
4:49:25.116 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1728709048 bytes occupied (3.7097 bits per kmer).
4:49:29.463 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
5:48:08.182 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
5:48:08.185 5G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
5:48:08.268 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
5:55:08.429 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 62724298 sequences extracted
5:58:18.912 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
6:00:15.946 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 83 loops collected
6:01:08.228 26G / 32G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
6:01:08.228 26G / 32G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
6:01:08.228 26G / 32G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
6:12:29.104 28G / 32G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1726776208 bytes occupied (3.70974 bits per kmer).
6:12:37.935 42G / 42G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
6:50:36.759 42G / 42G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
6:51:53.248 42G / 42G INFO General (construction.cpp : 464) Processed 32000000 edges
6:53:06.132 42G / 42G INFO General (construction.cpp : 464) Processed 64000000 edges
6:54:19.427 42G / 42G INFO General (construction.cpp : 464) Processed 96000000 edges
6:55:25.275 42G / 42G INFO General (construction.cpp : 464) Processed 125448625 edges
6:55:57.272 21G / 42G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
6:55:57.272 21G / 42G INFO General (graph_pack.hpp : 101) Index refill
6:55:57.272 21G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
6:55:57.272 21G / 42G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
6:55:57.272 21G / 42G INFO General (file_limit.hpp : 32) Open file limit set to 10000
6:55:57.272 21G / 42G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.17192 Gb
6:55:57.272 21G / 42G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
6:56:23.508 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 16516156 edges
6:56:45.900 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 33031257 edges
6:57:33.309 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 49554183 edges
6:59:27.249 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 66062702 edges
7:01:21.952 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 82572204 edges
7:03:17.488 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 99091671 edges
7:05:15.023 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 115606911 edges
7:06:24.648 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 125448849 edges
7:06:24.648 39G / 42G INFO General (edge_index_builders.hpp : 82) Used 125448849 sequences.
7:06:26.069 21G / 42G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
7:20:32.511 21G / 42G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3723768626 kmers in total.
7:20:32.511 21G / 42G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
7:35:17.329 21G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
7:39:14.384 23G / 42G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
7:57:25.403 23G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1726729784 bytes occupied (3.70964 bits per kmer).
7:58:20.946 106G / 106G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
8:01:02.538 106G / 106G INFO General (edge_index.hpp : 92) Index refilled
8:01:02.806 106G / 106G INFO General (gap_closer.cpp : 159) Preparing shift maps
8:04:04.701 112G / 112G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
8:05:38.441 113G / 113G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads
8:05:38.441 113G / 113G INFO General (gap_closer.cpp : 140) Merging paired indices
8:06:32.098 107G / 113G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
8:14:42.555 107G / 113G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 114077 gaps after checking 1027187 candidates
8:16:27.980 106G / 113G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
8:16:33.842 21G / 113G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
8:16:33.844 21G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
8:16:41.096 21G / 113G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 10 times
8:16:41.097 21G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper
8:21:28.031 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 8157417 times
8:21:28.031 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover
8:21:47.635 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 195523 times
8:21:47.635 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage
8:22:05.130 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 186440 times
8:22:05.130 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover
8:24:15.351 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 11847392 times
8:24:17.598 22G / 113G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification
8:24:17.598 22G / 113G INFO General (simplification.cpp : 357) Graph simplification started
8:24:17.598 22G / 113G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
8:24:17.598 22G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
8:24:17.598 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:26:53.656 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5320234 times
8:26:53.656 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
9:26:29.134 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1893493 times
9:26:29.134 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
9:26:36.061 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 54 times
9:26:36.061 64G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
9:26:36.061 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
9:26:45.974 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 34567 times
9:26:45.974 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
9:26:53.923 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1488 times
9:26:53.923 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
9:28:52.821 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1120709 times
9:28:52.821 64G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
9:28:52.821 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
9:29:02.674 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 94794 times
9:29:02.674 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
9:39:45.261 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 196075 times
9:39:45.261 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
9:40:40.598 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 479037 times
9:40:40.598 69G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
9:40:40.598 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
9:40:46.196 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 30005 times
9:40:46.196 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
9:48:51.023 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 113577 times
9:48:51.024 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
9:48:55.109 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 35 times
9:48:55.109 72G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
9:48:55.109 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
9:48:56.133 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1141 times
9:48:56.133 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
9:48:56.619 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 52 times
9:48:56.619 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
9:48:56.619 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
9:48:56.619 72G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
9:48:56.619 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
9:48:56.620 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
9:48:56.621 72G / 113G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
9:48:56.621 72G / 113G INFO General (graph_pack.hpp : 101) Index refill
9:48:56.621 72G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
9:48:56.621 72G / 113G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
9:48:56.621 72G / 113G INFO General (file_limit.hpp : 32) Open file limit set to 10000
9:48:56.621 72G / 113G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.64299 Gb
9:48:56.621 72G / 113G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
9:49:23.713 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 5911248 edges
9:49:53.322 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 11822813 edges
9:52:24.377 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 17728132 edges
9:54:48.976 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 23517314 edges
9:55:19.288 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 24653805 edges
9:55:19.289 89G / 113G INFO General (edge_index_builders.hpp : 82) Used 24653805 sequences.
9:55:20.532 72G / 113G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
10:04:27.100 72G / 113G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2180784948 kmers in total.
10:04:27.100 72G / 113G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
10:11:36.884 72G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
10:13:58.974 73G / 113G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
10:21:31.124 73G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1011243968 bytes occupied (3.70965 bits per kmer).
10:22:18.564 122G / 122G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
10:23:50.386 122G / 122G INFO General (edge_index.hpp : 92) Index refilled
10:23:50.388 122G / 122G INFO General (gap_closer.cpp : 159) Preparing shift maps
10:24:16.261 122G / 122G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
10:27:02.437 122G / 122G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads
10:27:02.438 122G / 122G INFO General (gap_closer.cpp : 140) Merging paired indices
10:27:04.758 122G / 122G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
10:28:23.402 122G / 123G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1054 gaps after checking 31581 candidates
10:28:32.467 122G / 123G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting
10:33:30.144 131G / 131G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 697722884 kmers to process
10:54:32.629 131G / 152G INFO General (graph_pack.hpp : 111) Normalizing done
10:54:32.629 131G / 152G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 900
10:54:32.629 131G / 152G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0
10:54:32.629 131G / 152G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)
10:54:33.036 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
10:54:44.052 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
10:54:44.115 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
10:54:44.163 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
10:54:44.221 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
10:54:44.255 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
10:54:44.290 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
10:54:44.516 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
10:54:44.992 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
10:54:53.230 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
10:55:02.302 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
10:55:26.070 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
10:56:07.638 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
10:57:32.336 132G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed
10:57:34.629 132G / 152G INFO General (pair_info_count.cpp : 209) Edge pairs: 256407501
10:57:34.629 132G / 152G INFO General (pair_info_count.cpp : 213) 16622995 paired reads (12.8642% of all) aligned to long edges
10:57:34.670 131G / 152G INFO General (pair_info_count.cpp : 354) Insert size = 400.101, deviation = 55.5732, left quantile = 341, right quantile = 458, read length = 391
10:57:34.670 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391
10:57:35.156 132G / 152G INFO General (pair_info_count.cpp : 371) Filtering data for library #0
10:57:35.157 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
10:57:44.845 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
10:57:44.854 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
10:57:44.856 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
10:57:44.885 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
10:57:44.890 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
10:57:44.900 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
10:57:45.024 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
10:57:45.762 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
10:57:53.857 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
10:58:03.994 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
10:58:31.277 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
10:59:25.534 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
11:01:05.838 132G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed
11:01:05.839 132G / 152G INFO General (pair_info_count.cpp : 383) Mapping library #0
11:01:05.839 132G / 152G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while)
11:01:05.839 132G / 152G INFO General (pair_info_count.cpp : 289) Left insert size quantile 341, right insert size quantile 458, filtering threshold 1, rounding threshold 0
11:01:05.860 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
11:01:19.118 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
11:01:19.418 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
11:01:19.457 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
11:01:19.479 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
11:01:19.480 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
11:01:19.496 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
11:01:19.576 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
11:01:19.979 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
11:01:30.665 134G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
11:01:42.001 134G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
11:02:17.085 136G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
11:03:16.116 139G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
11:05:15.515 142G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed
11:05:24.573 141G / 152G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation
11:05:24.579 141G / 152G INFO General (distance_estimation.cpp : 173) Processing library #0
11:05:24.579 141G / 152G INFO General (distance_estimation.cpp : 149) Weight Filter Done
11:05:24.580 141G / 152G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator
12:24:22.743 151G / 155G INFO General (distance_estimation.cpp : 34) Filtering info
12:24:22.743 151G / 155G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 559067957
12:29:18.703 158G / 163G INFO General (pair_info_filters.hpp : 263) Done filtering
12:29:18.994 150G / 163G INFO General (distance_estimation.cpp : 156) Refining clustered pair information
12:30:24.820 150G / 163G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished
12:30:24.820 150G / 163G INFO General (distance_estimation.cpp : 160) Improving paired information
13:06:11.337 160G / 182G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 159026392; contradictional = 0
14:21:04.044 166G / 219G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 105034138; contradictional = 0
14:21:04.044 166G / 219G INFO General (distance_estimation.cpp : 103) Filling scaffolding index
14:21:04.045 166G / 219G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator
15:25:01.695 167G / 219G INFO General (distance_estimation.cpp : 34) Filtering info
15:25:01.695 167G / 219G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 45641509
15:25:33.097 169G / 219G INFO General (pair_info_filters.hpp : 263) Done filtering
15:25:33.178 167G / 219G INFO General (distance_estimation.cpp : 182) Clearing raw paired index
15:27:03.233 157G / 219G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving
15:27:03.233 157G / 219G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings
15:27:03.233 157G / 219G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving
15:27:03.234 157G / 219G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started
<jemalloc>: Error in malloc(): out of memory. Requested: 512, active: 176018161664
== Error == system call for: "['/home/administrator/SPAdes-3.13.0-Linux/bin/spades-core', '/DATA/markop/CPB_metaSpades/output/K127/configs/config.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info']" finished abnormally, err code: -6
======= SPAdes pipeline finished abnormally and WITH WARNINGS!
=== Error correction and assembling warnings:
* 10:57:34.670 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391
======= Warnings saved to /DATA/markop/CPB_metaSpades/output/warnings.log
=== ERRORs:
* system call for: "['/home/administrator/SPAdes-3.13.0-Linux/bin/spades-core', '/DATA/markop/CPB_metaSpades/output/K127/configs/config.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info']" finished abnormally, err code: -6
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
======= SPAdes pipeline continued. Log can be found here: /DATA/markop/CPB_metaSpades/output/spades.log
Restored from Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101,127 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq
Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101,127 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq
System information:
SPAdes version: 3.13.0
Python version: 2.7.15
OS: Linux-4.13.0-41-generic-x86_64-with-debian-stretch-sid
Output dir: /DATA/markop/CPB_metaSpades/output
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_1.fq']
right reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_2.fq']
interlaced reads: not specified
single reads: ['/DATA/markop/CPB_metaSpades/input/merged.fq']
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Assembly parameters:
k: [21, 41, 71, 101, 127]
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /DATA/markop/CPB_metaSpades/output/tmp
Threads: 32
Memory limit (in Gb): 230
===== Skipping Read error correction (already processed).
===== Assembling started.
== Skipping assembler: K21 (already processed)
Max read length detected as 391
== Skipping assembler: K41 (already processed)
== Skipping assembler: K71 (already processed)
== Skipping assembler: K101 (already processed)
== Running assembler: K127
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.0, git revision 8ea46659e9b2aca35444a808db550ac333006f8b
0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/DATA/markop/CPB_metaSpades/output/dataset.info) with K=127
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 65) Two-step RR enabled: 1
0:00:00.000 4M / 4M INFO General (launch.hpp : 76) Will need read mapping, kmer mapper will be attached
0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction
0:00:00.010 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.411 4M / 4M INFO General (construction.cpp : 111) Max read length 391
0:00:00.411 4M / 4M INFO General (construction.cpp : 117) Average read length 229.3
0:00:00.411 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
0:00:00.413 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
0:00:00.415 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000
0:00:00.415 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb
0:00:00.415 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 16384
0:00:16.171 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 17140129 reads
0:00:33.963 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 23520925 reads
0:00:45.933 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 29992420 reads
0:01:08.688 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 36236148 reads
0:01:29.973 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 42736415 reads
0:01:52.069 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 49210758 reads
0:02:12.453 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 55280562 reads
0:02:31.583 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 61718196 reads
0:02:52.866 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 67983612 reads
0:03:14.486 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 74290861 reads
0:03:32.109 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 79477653 reads
0:03:57.737 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 85889932 reads
0:06:53.632 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 136387847 reads
0:14:48.730 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 272811252 reads
0:31:05.513 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 542509926 reads
1:10:43.150 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1079247014 reads
1:26:33.502 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
1:36:50.770 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1653171754 reads
1:36:50.770 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
2:49:49.105 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3723768626 kmers in total.
2:49:49.105 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
2:57:41.301 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
2:57:41.306 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
2:57:41.307 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
2:57:41.307 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 10000
2:57:41.307 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39453 Gb
2:57:41.307 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
2:57:41.863 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2813582 kmers
2:57:42.373 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5658767 kmers
2:57:42.995 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 8543596 kmers
2:57:43.498 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11428796 kmers
2:57:44.017 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 14295951 kmers
2:57:44.621 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17246063 kmers
2:57:45.177 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 20211545 kmers
2:57:45.820 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23106226 kmers
2:57:47.085 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26080313 kmers
2:57:48.723 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28985625 kmers
2:57:50.230 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 31852746 kmers
2:57:51.608 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 34766489 kmers
2:57:53.029 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 37655712 kmers
2:57:54.593 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 40603664 kmers
2:57:56.083 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 43598434 kmers
2:57:57.749 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 46764703 kmers
2:58:07.602 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68246622 kmers
2:58:38.739 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 136575717 kmers
2:59:41.970 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 270415046 kmers
3:01:48.382 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 539831168 kmers
3:05:54.823 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 1076348452 kmers
3:14:17.275 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 2147682876 kmers
3:47:47.724 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 3723808562 kmers.
3:47:47.946 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
4:07:13.238 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3727975608 kmers in total.
4:07:13.238 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
4:20:43.042 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
4:24:02.109 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
4:41:09.349 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1728709048 bytes occupied (3.7097 bits per kmer).
4:41:12.375 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
5:14:06.780 5G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
5:14:06.785 5G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
5:14:06.854 5G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
5:19:44.948 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 62724298 sequences extracted
5:22:16.340 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
5:23:53.027 10G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 83 loops collected
5:24:36.126 26G / 33G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
5:24:36.127 26G / 33G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
5:24:36.127 26G / 33G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
5:36:21.318 28G / 33G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1726776208 bytes occupied (3.70974 bits per kmer).
5:36:29.817 42G / 42G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
6:08:12.786 42G / 42G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
6:09:18.445 42G / 42G INFO General (construction.cpp : 464) Processed 32000000 edges
6:10:18.220 42G / 42G INFO General (construction.cpp : 464) Processed 64000000 edges
6:11:19.100 42G / 42G INFO General (construction.cpp : 464) Processed 96000000 edges
6:12:14.336 42G / 42G INFO General (construction.cpp : 464) Processed 125448625 edges
6:12:42.058 21G / 42G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
6:12:42.064 21G / 42G INFO General (graph_pack.hpp : 101) Index refill
6:12:42.064 21G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
6:12:42.064 21G / 42G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
6:12:42.065 21G / 42G INFO General (file_limit.hpp : 32) Open file limit set to 10000
6:12:42.065 21G / 42G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.17167 Gb
6:12:42.065 21G / 42G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
6:13:05.693 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 16516156 edges
6:13:26.192 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 33031257 edges
6:14:09.528 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 49554183 edges
6:16:10.754 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 66062702 edges
6:18:11.754 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 82572204 edges
6:20:13.857 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 99091671 edges
6:22:16.907 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 115606911 edges
6:23:30.768 39G / 42G INFO General (edge_index_builders.hpp : 77) Processed 125448849 edges
6:23:30.768 39G / 42G INFO General (edge_index_builders.hpp : 82) Used 125448849 sequences.
6:23:32.071 21G / 42G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
6:38:14.245 21G / 42G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3723768626 kmers in total.
6:38:14.246 21G / 42G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
6:53:46.899 21G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
6:57:08.465 23G / 42G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
7:12:49.726 23G / 42G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1726729784 bytes occupied (3.70964 bits per kmer).
7:13:44.644 106G / 106G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
7:16:05.733 106G / 106G INFO General (edge_index.hpp : 92) Index refilled
7:16:05.753 106G / 106G INFO General (gap_closer.cpp : 159) Preparing shift maps
7:18:37.277 112G / 112G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
7:19:35.016 113G / 113G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads
7:19:35.016 113G / 113G INFO General (gap_closer.cpp : 140) Merging paired indices
7:20:19.133 107G / 113G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
7:27:07.055 107G / 113G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 114077 gaps after checking 1027187 candidates
7:28:37.704 106G / 113G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
7:28:44.351 21G / 113G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
7:28:44.352 21G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
7:28:49.760 21G / 113G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 10 times
7:28:49.761 21G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper
7:32:46.105 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 8157417 times
7:32:46.105 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover
7:33:02.064 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 195523 times
7:33:02.064 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage
7:33:16.785 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 186440 times
7:33:16.785 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover
7:35:13.676 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 11847392 times
7:35:15.601 22G / 113G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification
7:35:15.601 22G / 113G INFO General (simplification.cpp : 357) Graph simplification started
7:35:15.601 22G / 113G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
7:35:15.601 22G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
7:35:15.601 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
7:37:35.758 22G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5320234 times
7:37:35.758 22G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:26:16.739 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1893493 times
8:26:16.739 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:26:23.141 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 54 times
8:26:23.141 64G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
8:26:23.141 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:26:30.575 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 34567 times
8:26:30.575 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:26:37.662 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1488 times
8:26:37.662 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:28:19.670 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1120709 times
8:28:19.670 64G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
8:28:19.670 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:28:27.651 64G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 94794 times
8:28:27.651 64G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:37:09.455 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 196075 times
8:37:09.455 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:37:58.513 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 479037 times
8:37:58.513 69G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
8:37:58.513 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:38:03.432 69G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 30005 times
8:38:03.432 69G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:44:55.239 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 113577 times
8:44:55.239 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:44:59.277 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 35 times
8:44:59.278 72G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
8:44:59.278 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:45:00.320 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1141 times
8:45:00.320 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:45:00.687 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 52 times
8:45:00.687 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:45:00.687 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
8:45:00.687 72G / 113G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
8:45:00.687 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
8:45:00.688 72G / 113G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
8:45:00.689 72G / 113G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
8:45:00.689 72G / 113G INFO General (graph_pack.hpp : 101) Index refill
8:45:00.689 72G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
8:45:00.689 72G / 113G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
8:45:00.689 72G / 113G INFO General (file_limit.hpp : 32) Open file limit set to 10000
8:45:00.689 72G / 113G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 1.64303 Gb
8:45:00.689 72G / 113G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
8:45:21.936 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 5911248 edges
8:45:43.458 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 11822813 edges
8:47:15.263 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 17728132 edges
8:48:48.948 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 23517314 edges
8:49:06.031 89G / 113G INFO General (edge_index_builders.hpp : 77) Processed 24653805 edges
8:49:06.046 89G / 113G INFO General (edge_index_builders.hpp : 82) Used 24653805 sequences.
8:49:07.367 72G / 113G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
8:55:02.976 72G / 113G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2180784948 kmers in total.
8:55:02.976 72G / 113G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
9:01:04.559 72G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
9:03:01.833 73G / 113G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
9:11:39.976 73G / 113G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1011243968 bytes occupied (3.70965 bits per kmer).
9:12:20.652 122G / 122G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
9:13:40.141 122G / 122G INFO General (edge_index.hpp : 92) Index refilled
9:13:40.150 122G / 122G INFO General (gap_closer.cpp : 159) Preparing shift maps
9:14:10.041 122G / 122G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
9:16:26.289 122G / 122G INFO General (gap_closer.cpp : 138) Used 129219073 paired reads
9:16:26.289 122G / 122G INFO General (gap_closer.cpp : 140) Merging paired indices
9:16:28.627 122G / 122G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
9:17:40.922 122G / 123G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 1054 gaps after checking 31581 candidates
9:17:47.286 122G / 123G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting
9:22:52.639 131G / 131G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 697722884 kmers to process
9:40:13.108 131G / 152G INFO General (graph_pack.hpp : 111) Normalizing done
9:40:13.108 131G / 152G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 900
9:40:13.108 131G / 152G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0
9:40:13.108 131G / 152G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)
9:40:13.672 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
9:40:23.328 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
9:40:23.384 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
9:40:23.457 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
9:40:23.520 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
9:40:23.583 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
9:40:23.646 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
9:40:23.926 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
9:40:24.413 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
9:40:30.775 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
9:40:38.455 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
9:40:58.460 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
9:41:35.421 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
9:42:43.247 132G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed
9:42:44.856 132G / 152G INFO General (pair_info_count.cpp : 209) Edge pairs: 256407501
9:42:44.856 132G / 152G INFO General (pair_info_count.cpp : 213) 16622995 paired reads (12.8642% of all) aligned to long edges
9:42:44.900 131G / 152G INFO General (pair_info_count.cpp : 354) Insert size = 400.101, deviation = 55.5732, left quantile = 341, right quantile = 458, read length = 391
9:42:44.900 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391
9:42:45.311 132G / 152G INFO General (pair_info_count.cpp : 371) Filtering data for library #0
9:42:45.312 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
9:42:53.069 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
9:42:53.076 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
9:42:53.077 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
9:42:53.084 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
9:42:53.099 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
9:42:53.100 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
9:42:53.152 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
9:42:53.755 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
9:43:00.361 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
9:43:09.260 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
9:43:29.340 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
9:44:08.221 132G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
9:45:27.674 132G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed
9:45:27.674 132G / 152G INFO General (pair_info_count.cpp : 383) Mapping library #0
9:45:27.675 132G / 152G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while)
9:45:27.675 132G / 152G INFO General (pair_info_count.cpp : 289) Left insert size quantile 341, right insert size quantile 458, filtering threshold 1, rounding threshold 0
9:45:27.701 132G / 152G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
9:45:39.337 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
9:45:39.338 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
9:45:39.339 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
9:45:39.341 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
9:45:39.341 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
9:45:39.345 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
9:45:39.365 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
9:45:39.631 133G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
9:45:48.241 134G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
9:45:57.634 134G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
9:46:27.608 136G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
9:47:16.383 139G / 152G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
9:48:52.178 142G / 152G INFO General (sequence_mapper_notifier.h: 98) Total 129219073 reads processed
9:48:58.559 141G / 152G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation
9:48:58.565 141G / 152G INFO General (distance_estimation.cpp : 173) Processing library #0
9:48:58.565 141G / 152G INFO General (distance_estimation.cpp : 149) Weight Filter Done
9:48:58.566 141G / 152G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator
10:58:34.418 151G / 155G INFO General (distance_estimation.cpp : 34) Filtering info
10:58:34.418 151G / 155G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 559067957
11:03:17.736 158G / 163G INFO General (pair_info_filters.hpp : 263) Done filtering
11:03:18.050 150G / 163G INFO General (distance_estimation.cpp : 156) Refining clustered pair information
11:04:17.393 150G / 163G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished
11:04:17.393 150G / 163G INFO General (distance_estimation.cpp : 160) Improving paired information
11:39:23.480 160G / 182G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 159026392; contradictional = 0
12:53:40.161 166G / 219G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 105034138; contradictional = 0
12:53:40.161 166G / 219G INFO General (distance_estimation.cpp : 103) Filling scaffolding index
12:53:40.161 166G / 219G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator
13:57:47.635 167G / 219G INFO General (distance_estimation.cpp : 34) Filtering info
13:57:47.635 167G / 219G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 45641509
13:58:17.828 169G / 219G INFO General (pair_info_filters.hpp : 263) Done filtering
13:58:17.909 167G / 219G INFO General (distance_estimation.cpp : 182) Clearing raw paired index
13:59:45.978 157G / 219G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving
13:59:45.978 157G / 219G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings
13:59:45.978 157G / 219G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving
13:59:45.978 157G / 219G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started
<jemalloc>: Error in malloc(): out of memory. Requested: 512, active: 176198516736
== Error == system call for: "['/home/administrator/SPAdes-3.13.0-Linux/bin/spades-core', '/DATA/markop/CPB_metaSpades/output/K127/configs/config.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info']" finished abnormally, err code: -6
======= SPAdes pipeline finished abnormally and WITH WARNINGS!
=== Error correction and assembling warnings:
* 9:42:44.900 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391
======= Warnings saved to /DATA/markop/CPB_metaSpades/output/warnings.log
=== ERRORs:
* system call for: "['/home/administrator/SPAdes-3.13.0-Linux/bin/spades-core', '/DATA/markop/CPB_metaSpades/output/K127/configs/config.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/mda_mode.info', '/DATA/markop/CPB_metaSpades/output/K127/configs/meta_mode.info']" finished abnormally, err code: -6
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
======= SPAdes pipeline continued. Log can be found here: /DATA/markop/CPB_metaSpades/output/spades.log
Restored from Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq
Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --meta -k 21,41,71,101 -m 230 -t 32 -o /DATA/markop/CPB_metaSpades/output -1 /DATA/markop/CPB_metaSpades/input/unmerged_1.fq -2 /DATA/markop/CPB_metaSpades/input/unmerged_2.fq -s /DATA/markop/CPB_metaSpades/input/merged.fq
System information:
SPAdes version: 3.13.0
Python version: 2.7.15
OS: Linux-4.13.0-41-generic-x86_64-with-debian-stretch-sid
Output dir: /DATA/markop/CPB_metaSpades/output
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_1.fq']
right reads: ['/DATA/markop/CPB_metaSpades/input/unmerged_2.fq']
interlaced reads: not specified
single reads: ['/DATA/markop/CPB_metaSpades/input/merged.fq']
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Assembly parameters:
k: [21, 41, 71, 101]
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /DATA/markop/CPB_metaSpades/output/tmp
Threads: 32
Memory limit (in Gb): 230
===== Skipping Read error correction (already processed).
===== Assembling started.
== Skipping assembler: K21 (already processed)
Max read length detected as 391
== Skipping assembler: K41 (already processed)
== Skipping assembler: K71 (already processed)
== Skipping assembler: K101 (already processed)
===== Assembling finished. Used k-mer sizes: 21, 41, 71, 101
* Corrected reads are in /DATA/markop/CPB_metaSpades/output/corrected/
* Assembled contigs are in /DATA/markop/CPB_metaSpades/output/contigs.fasta
* Assembly graph is in /DATA/markop/CPB_metaSpades/output/assembly_graph.fastg
* Assembly graph in GFA format is in /DATA/markop/CPB_metaSpades/output/assembly_graph_with_scaffolds.gfa
======= SPAdes pipeline finished WITH WARNINGS!
=== Error correction and assembling warnings:
* 10:57:34.670 131G / 152G WARN General (pair_info_count.cpp : 358) Estimated mean insert size 400.101 is very small compared to read length 391
======= Warnings saved to /DATA/markop/CPB_metaSpades/output/warnings.log
SPAdes log can be found here: /DATA/markop/CPB_metaSpades/output/spades.log
Thank you for using SPAdes!
Export PNG
Creators and Submitter
Activity
Views: 965 Downloads: 33
Created: 12th Nov 2021 at 23:07
Last updated: 12th Nov 2021 at 23:07
AttributionsNone
Version History
Version 1 (earliest) Created 12th Nov 2021 at 23:07 by Marko Petek
No revision comments
Related items
Advanced People list for this Document with search and filtering
https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
Advanced Programmes list for this Document with search and filtering
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
Advanced Projects list for this Document with search and filtering
This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.
Programme: NIBSys
Public web page: http://projects.nib.si/rnainval/
Start date: 1st Nov 2014
End date: 31st Oct 2017
Advanced Investigations list for this Document with search and filtering
Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_01_ns-dsRNA_trans, _S_02_metagenome_resp
Assays: _A_01-DNAisol, _A_01_RNA-Seq_dsEGFP-NGS, _A_02-DNASeq, _A_02_CLC-RNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _I_03_Omics-files, _S_01_ns-dsRNA_trans-files, _S_02_metagenome_resp-files
Advanced Studies list for this Document with search and filtering
Short Name: 02_metagenome_resp Title: CPB gut microbiome response to dsRNA feeding Description: Response of CPB gut microbiome to dsRNA feeding on the level of microbe abundance Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_03_Omics
Assays: _A_01-DNAisol, _A_02-DNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _S_02_metagenome_resp-files
Advanced Assays list for this Document with search and filtering
Short Name: 07_allReads_meta-assembly Assay Class: DRY Assay Type: assembly Title: De novo assembly of metagenome using metaSPAdes Description: De novo assembly of microbes present in the metagenome using metaSPAdes using all reads without selection but with rigorous filtering and read correction pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
