output/spades.log Version 1
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1/_A_05_assembly1-rnaSPAdes/
SEEK ID: https://fairdomhub.org/documents/3842?version=1
Filename:
output/spades.log
Format: Plain text document
Size: 207 KB
Command line: /home/administrator/SPAdes-3.13.0-Linux/bin/spades.py --rna -t 32 -o /DATA/markop/Pcitri_rnaspades/output --ss-rf --disable-gzip-output --pe1-fr --pe2-fr --pe3-fr --pe4-fr --pe1-1 /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq.gz --pe1-2 /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq.gz --pe1-s /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_orphans.R1.fastq.gz --pe2-1 /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq.gz --pe2-2 /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq.gz --pe2-s /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_orphans.R1.fastq.gz --pe3-1 /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq.gz --pe3-2 /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq.gz --pe3-s /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_orphans.R1.fastq.gz --pe4-1 /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq.gz --pe4-2 /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq.gz --pe4-s /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_orphans.R1.fastq.gz
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/Pcitri_rnaspades/output
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
RNA-seq mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq.gz']
right reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq.gz']
interlaced reads: not specified
single reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_orphans.R1.fastq.gz']
merged reads: not specified
Library number: 2, library type: paired-end
orientation: fr
left reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq.gz']
right reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq.gz']
interlaced reads: not specified
single reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_orphans.R1.fastq.gz']
merged reads: not specified
Library number: 3, library type: paired-end
orientation: fr
left reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq.gz']
right reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq.gz']
interlaced reads: not specified
single reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_orphans.R1.fastq.gz']
merged reads: not specified
Library number: 4, library type: paired-end
orientation: fr
left reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq.gz']
right reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq.gz']
interlaced reads: not specified
single reads: ['/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_orphans.R1.fastq.gz']
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will NOT be compressed
Assembly parameters:
k: auto
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/Pcitri_rnaspades/output/tmp
Threads: 32
Memory limit (in Gb): 250
======= SPAdes pipeline started. Log can be found here: /DATA/markop/Pcitri_rnaspades/output/spades.log
/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_orphans.R1.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_orphans.R1.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_orphans.R1.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq.gz: max reads length: 150
/FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_orphans.R1.fastq.gz: max reads length: 150
Reads length: 150
K values to be used: [49, 73]
===== Read error correction started.
== Running read error correction tool: /home/administrator/SPAdes-3.13.0-Linux/bin/spades-hammer /DATA/markop/Pcitri_rnaspades/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/Pcitri_rnaspades/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 250 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 Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:00:00.002 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
0:00:00.003 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024
0:00:00.003 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60413 Gb
0:00:00.003 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072
0:00:00.102 17G / 17G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq.gz
0:01:12.243 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 7425927 reads
0:02:15.660 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 14860680 reads
0:03:18.385 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 22196469 reads
0:04:19.585 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 29491328 reads
0:04:45.634 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 32561049 reads
0:04:45.634 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq.gz
0:05:48.674 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 40173588 reads
0:06:51.015 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 47889089 reads
0:07:53.836 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 55488735 reads
0:08:56.334 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 63088871 reads
0:09:13.617 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 65122098 reads
0:09:13.617 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_orphans.R1.fastq.gz
0:10:08.997 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 72797064 reads
0:10:08.997 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq.gz
0:11:11.134 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 80136589 reads
0:14:21.172 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq.gz
0:18:31.112 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_orphans.R1.fastq.gz
0:19:09.241 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 138149995 reads
0:19:09.242 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq.gz
0:24:09.111 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq.gz
0:29:01.625 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_orphans.R1.fastq.gz
0:29:44.110 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq.gz
0:34:25.960 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq.gz
0:37:41.712 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 272739462 reads
0:39:04.186 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_orphans.R1.fastq.gz
0:40:02.414 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 112) Total 290817542 reads processed
0:40:03.893 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:40:39.603 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 891404860 kmers in total.
0:40:39.603 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:40:58.064 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:41:34.642 584M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
0:42:54.117 584M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 413354612 bytes occupied (3.70969 bits per kmer).
0:42:54.119 580M / 18G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order
0:43:33.059 13G / 18G INFO General (main.cpp : 148) Clustering Hamming graph.
1:04:09.530 13G / 18G INFO General (main.cpp : 155) Extracting clusters
1:12:52.618 13G / 34G INFO General (main.cpp : 167) Clustering done. Total clusters: 361604816
1:12:53.105 7G / 34G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while.
1:13:03.820 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq.gz
1:19:06.955 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq.gz
1:24:46.237 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_orphans.R1.fastq.gz
1:25:48.679 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq.gz
1:31:15.431 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq.gz
1:36:25.984 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_orphans.R1.fastq.gz
1:37:10.005 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq.gz
1:43:40.179 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq.gz
1:49:50.551 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_orphans.R1.fastq.gz
1:50:39.561 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq.gz
1:56:48.695 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq.gz
2:02:42.475 27G / 34G INFO K-mer Counting (kmer_data.cpp : 382) Processing /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_orphans.R1.fastq.gz
2:03:49.646 27G / 34G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing.
2:03:53.431 27G / 34G INFO K-mer Counting (kmer_data.cpp : 403) There are 891404860 kmers in total. Among them 473906484 (53.164%) are singletons.
2:03:53.431 27G / 34G INFO General (main.cpp : 173) Subclustering Hamming graph
2:20:33.732 27G / 34G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 28385 non-read kmers were generated.
2:20:33.732 27G / 34G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics:
2:20:33.732 27G / 34G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 282386932. Among them 240396012 (85.13%) are good
2:20:33.732 27G / 34G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 6846541. Among them 6839051 (99.8906%) are good
2:20:33.732 27G / 34G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 92188507. Among them 82916269 (89.9421%) are good
2:20:33.732 27G / 34G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 6.60686 kmers
2:20:33.732 27G / 34G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.25016
2:20:33.732 27G / 34G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 330151332
2:20:33.732 27G / 34G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.929792,0.0229334,0.0270815,0.0201928),(0.0267959,0.931273,0.0130129,0.0289187),(0.0280339,0.012783,0.931837,0.0273463),(0.0198567,0.0268752,0.0228048,0.930463))
2:20:34.183 27G / 34G INFO General (main.cpp : 178) Finished clustering.
2:20:34.183 27G / 34G INFO General (main.cpp : 197) Starting solid k-mers expansion in 32 threads.
2:52:07.184 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 72117644 new k-mers.
3:23:24.352 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 7016259 new k-mers.
3:54:58.187 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 572329 new k-mers.
4:26:09.527 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 127284 new k-mers.
4:57:26.035 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 38836 new k-mers.
5:28:32.935 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 13249 new k-mers.
5:59:48.107 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 5474 new k-mers.
6:30:58.647 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 7 produced 2134 new k-mers.
7:02:01.487 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 8 produced 988 new k-mers.
7:33:10.723 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 9 produced 154 new k-mers.
8:04:12.935 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 10 produced 69 new k-mers.
8:35:19.011 27G / 34G INFO General (main.cpp : 218) Solid k-mers iteration 11 produced 0 new k-mers.
8:35:19.011 27G / 34G INFO General (main.cpp : 222) Solid k-mers finalized
8:35:19.011 27G / 34G INFO General (hammer_tools.cpp : 220) Starting read correction in 32 threads.
8:35:19.011 27G / 34G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq.gz and /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq.gz
8:35:44.722 30G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads.
8:36:15.680 30G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 0
8:36:21.854 30G / 34G INFO General (hammer_tools.cpp : 185) Written batch 0
8:36:46.408 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads.
8:37:15.697 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 1
8:37:21.717 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 1
8:37:45.089 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads.
8:38:13.267 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 2
8:38:19.880 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 2
8:38:41.898 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads.
8:39:11.015 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 3
8:39:16.975 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 3
8:39:39.809 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads.
8:40:07.110 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 4
8:40:13.273 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 4
8:40:36.060 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads.
8:41:04.427 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 5
8:41:10.969 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 5
8:41:33.375 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads.
8:42:04.714 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 6
8:42:11.668 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 6
8:42:34.105 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads.
8:43:02.510 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 7
8:43:08.960 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 7
8:43:31.917 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads.
8:44:00.186 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 8
8:44:06.867 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 8
8:44:29.099 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 3200000 reads.
8:44:56.878 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 9
8:45:03.308 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 9
8:45:07.198 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 561049 reads.
8:45:13.310 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 10
8:45:14.466 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 10
8:45:18.464 27G / 34G INFO General (hammer_tools.cpp : 264) Correcting single reads: /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_orphans.R1.fastq.gz
8:45:28.563 28G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 3200000 reads.
8:45:39.091 28G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 0
8:45:41.851 28G / 34G INFO General (hammer_tools.cpp : 136) Written batch 0
8:45:51.813 29G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 3200000 reads.
8:46:02.764 29G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 1
8:46:05.375 29G / 34G INFO General (hammer_tools.cpp : 136) Written batch 1
8:46:09.205 29G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 2 of 1274966 reads.
8:46:13.441 29G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 2
8:46:15.593 29G / 34G INFO General (hammer_tools.cpp : 136) Written batch 2
8:46:17.322 27G / 34G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq.gz and /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq.gz
8:46:41.279 30G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads.
8:47:11.152 30G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 0
8:47:17.896 30G / 34G INFO General (hammer_tools.cpp : 185) Written batch 0
8:47:41.455 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads.
8:48:10.386 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 1
8:48:16.170 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 1
8:48:39.723 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads.
8:49:06.822 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 2
8:49:13.430 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 2
8:49:35.511 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads.
8:50:02.327 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 3
8:50:08.837 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 3
8:50:31.563 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads.
8:50:59.056 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 4
8:51:05.201 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 4
8:51:28.187 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads.
8:51:56.208 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 5
8:52:03.224 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 5
8:52:25.803 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads.
8:52:54.536 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 6
8:53:00.690 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 6
8:53:23.270 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads.
8:53:49.634 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 7
8:53:55.803 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 7
8:54:18.658 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads.
8:54:46.530 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 8
8:54:53.419 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 8
8:55:02.049 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 1196257 reads.
8:55:12.443 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 9
8:55:14.881 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 9
8:55:18.850 27G / 34G INFO General (hammer_tools.cpp : 264) Correcting single reads: /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_orphans.R1.fastq.gz
8:55:28.986 28G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 3200000 reads.
8:55:39.290 28G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 0
8:55:42.412 28G / 34G INFO General (hammer_tools.cpp : 136) Written batch 0
8:55:49.267 29G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 2160417 reads.
8:55:56.107 29G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 1
8:55:58.429 29G / 34G INFO General (hammer_tools.cpp : 136) Written batch 1
8:55:59.964 27G / 34G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq.gz and /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq.gz
8:56:24.222 30G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads.
8:56:51.504 30G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 0
8:56:57.617 30G / 34G INFO General (hammer_tools.cpp : 185) Written batch 0
8:57:21.651 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads.
8:57:48.881 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 1
8:57:55.828 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 1
8:58:18.757 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads.
8:58:46.904 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 2
8:58:53.406 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 2
8:59:16.474 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads.
8:59:43.686 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 3
8:59:50.516 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 3
9:00:13.142 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads.
9:00:40.304 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 4
9:00:46.463 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 4
9:01:09.482 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads.
9:01:37.374 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 5
9:01:44.500 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 5
9:02:06.830 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads.
9:02:35.505 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 6
9:02:42.218 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 6
9:03:05.225 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads.
9:03:33.976 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 7
9:03:40.836 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 7
9:04:03.525 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads.
9:04:32.415 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 8
9:04:38.883 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 8
9:05:01.668 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 3200000 reads.
9:05:28.942 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 9
9:05:35.343 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 9
9:05:58.317 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 3200000 reads.
9:06:25.726 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 10
9:06:32.840 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 10
9:06:35.805 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 423516 reads.
9:06:39.659 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 11
9:06:40.465 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 11
9:06:43.497 27G / 34G INFO General (hammer_tools.cpp : 264) Correcting single reads: /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_orphans.R1.fastq.gz
9:06:53.707 28G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 3200000 reads.
9:07:04.032 28G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 0
9:07:06.885 28G / 34G INFO General (hammer_tools.cpp : 136) Written batch 0
9:07:15.944 29G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 2762971 reads.
9:07:24.547 29G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 1
9:07:27.025 29G / 34G INFO General (hammer_tools.cpp : 136) Written batch 1
9:07:28.581 27G / 34G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq.gz and /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq.gz
9:07:53.077 30G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads.
9:08:20.483 30G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 0
9:08:26.591 30G / 34G INFO General (hammer_tools.cpp : 185) Written batch 0
9:08:50.710 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads.
9:09:17.987 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 1
9:09:24.779 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 1
9:09:47.830 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads.
9:10:16.085 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 2
9:10:22.919 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 2
9:10:45.635 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads.
9:11:13.316 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 3
9:11:19.923 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 3
9:11:42.795 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads.
9:12:10.164 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 4
9:12:16.842 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 4
9:12:39.557 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads.
9:13:08.273 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 5
9:13:15.167 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 5
9:13:37.910 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads.
9:14:06.128 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 6
9:14:12.326 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 6
9:14:35.655 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads.
9:15:04.934 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 7
9:15:11.924 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 7
9:15:34.549 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads.
9:16:02.435 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 8
9:16:08.816 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 8
9:16:31.867 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 3200000 reads.
9:17:00.527 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 9
9:17:07.540 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 9
9:17:18.876 31G / 34G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 1641183 reads.
9:17:33.149 31G / 34G INFO General (hammer_tools.cpp : 175) Processed batch 10
9:17:36.414 31G / 34G INFO General (hammer_tools.cpp : 185) Written batch 10
9:17:40.008 27G / 34G INFO General (hammer_tools.cpp : 264) Correcting single reads: /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_orphans.R1.fastq.gz
9:17:50.015 28G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 0 of 3200000 reads.
9:18:00.043 28G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 0
9:18:02.989 28G / 34G INFO General (hammer_tools.cpp : 136) Written batch 0
9:18:13.085 29G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 1 of 3200000 reads.
9:18:23.482 29G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 1
9:18:26.317 29G / 34G INFO General (hammer_tools.cpp : 136) Written batch 1
9:18:31.741 29G / 34G INFO General (hammer_tools.cpp : 127) Prepared batch 2 of 1775178 reads.
9:18:37.348 29G / 34G INFO General (hammer_tools.cpp : 132) Processed batch 2
9:18:38.886 29G / 34G INFO General (hammer_tools.cpp : 136) Written batch 2
9:18:40.802 27G / 34G INFO General (hammer_tools.cpp : 274) Correction done. Changed 13830981 bases in 12424142 reads.
9:18:40.802 27G / 34G INFO General (hammer_tools.cpp : 275) Failed to correct 940 bases out of 40597341152.
9:18:43.576 128M / 34G INFO General (main.cpp : 255) Saving corrected dataset description to /DATA/markop/Pcitri_rnaspades/output/corrected/corrected.yaml
9:18:43.577 128M / 34G INFO General (main.cpp : 262) All done. Exiting.
== Dataset description file was created: /DATA/markop/Pcitri_rnaspades/output/corrected/corrected.yaml
===== Read error correction finished.
===== Assembling started.
== Running assembler: K49
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades/output/K49/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades/output/K49/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades/output/K49/configs/rna_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 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/Pcitri_rnaspades/output/dataset.info) with K=49
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 : 77) Converting reads to binary format for library #0 (takes a while)
0:00:00.001 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads
0:00:00.195 80M / 80M INFO General (binary_converter.hpp : 93) 16384 reads processed
0:00:00.332 96M / 96M INFO General (binary_converter.hpp : 93) 32768 reads processed
0:00:00.605 128M / 128M INFO General (binary_converter.hpp : 93) 65536 reads processed
0:00:01.149 184M / 184M INFO General (binary_converter.hpp : 93) 131072 reads processed
0:00:02.241 304M / 304M INFO General (binary_converter.hpp : 93) 262144 reads processed
0:00:04.426 540M / 540M INFO General (binary_converter.hpp : 93) 524288 reads processed
0:00:11.678 912M / 912M INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:00:23.015 916M / 916M INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:00:46.205 920M / 920M INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:01:40.689 944M / 944M INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:03:27.141 952M / 952M INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:06:53.513 964M / 968M INFO General (binary_converter.hpp : 117) 32477062 reads written
0:06:54.716 8M / 968M INFO General (read_converter.hpp : 87) Converting single reads
0:06:54.904 140M / 968M INFO General (binary_converter.hpp : 93) 16384 reads processed
0:06:54.975 144M / 968M INFO General (binary_converter.hpp : 93) 32768 reads processed
0:06:55.098 156M / 968M INFO General (binary_converter.hpp : 93) 65536 reads processed
0:06:55.329 184M / 968M INFO General (binary_converter.hpp : 93) 131072 reads processed
0:06:55.854 232M / 968M INFO General (binary_converter.hpp : 93) 262144 reads processed
0:06:56.863 332M / 968M INFO General (binary_converter.hpp : 93) 524288 reads processed
0:06:58.804 536M / 968M INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:07:02.689 940M / 968M INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:07:10.448 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:07:33.324 1G / 1G INFO General (binary_converter.hpp : 117) 7738345 reads written
0:07:35.217 4M / 1G INFO General (read_converter.hpp : 95) Converting merged reads
0:07:35.323 132M / 1G INFO General (binary_converter.hpp : 117) 0 reads written
0:07:35.332 4M / 1G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #1 (takes a while)
0:07:35.332 4M / 1G INFO General (read_converter.hpp : 78) Converting paired reads
0:07:35.542 84M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:07:35.692 96M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:07:35.980 128M / 1G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:07:36.578 188M / 1G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:07:37.883 304M / 1G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:07:40.292 540M / 1G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:07:48.365 908M / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:08:00.751 912M / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:08:25.970 920M / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:09:18.333 944M / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:11:04.981 952M / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:13:45.510 428M / 1G INFO General (binary_converter.hpp : 117) 29915487 reads written
0:13:45.777 8M / 1G INFO General (read_converter.hpp : 87) Converting single reads
0:13:45.925 140M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:13:45.984 144M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:13:46.128 160M / 1G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:13:46.356 184M / 1G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:13:46.804 236M / 1G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:13:47.691 336M / 1G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:13:49.490 536M / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:13:53.041 936M / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:14:00.222 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:14:12.194 620M / 1G INFO General (binary_converter.hpp : 117) 5420373 reads written
0:14:12.873 8M / 1G INFO General (read_converter.hpp : 95) Converting merged reads
0:14:12.981 136M / 1G INFO General (binary_converter.hpp : 117) 0 reads written
0:14:12.990 8M / 1G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #2 (takes a while)
0:14:12.990 8M / 1G INFO General (read_converter.hpp : 78) Converting paired reads
0:14:13.175 84M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:14:13.313 100M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:14:13.592 128M / 1G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:14:14.134 188M / 1G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:14:15.221 304M / 1G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:14:17.391 540M / 1G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:14:25.638 912M / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:14:36.908 916M / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:14:59.707 920M / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:15:49.185 928M / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:17:26.638 956M / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:20:46.160 972M / 1G INFO General (binary_converter.hpp : 93) 33554432 reads processed
0:21:10.548 476M / 1G INFO General (binary_converter.hpp : 117) 35525456 reads written
0:21:10.842 8M / 1G INFO General (read_converter.hpp : 87) Converting single reads
0:21:10.992 140M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:21:11.052 148M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:21:11.170 160M / 1G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:21:11.407 184M / 1G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:21:11.861 236M / 1G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:21:12.753 336M / 1G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:21:14.553 540M / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:21:18.134 940M / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:21:25.281 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:21:39.725 864M / 1G INFO General (binary_converter.hpp : 117) 6041970 reads written
0:21:40.735 8M / 1G INFO General (read_converter.hpp : 95) Converting merged reads
0:21:40.840 136M / 1G INFO General (binary_converter.hpp : 117) 0 reads written
0:21:40.849 8M / 1G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #3 (takes a while)
0:21:40.849 8M / 1G INFO General (read_converter.hpp : 78) Converting paired reads
0:21:41.034 84M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:21:41.173 100M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:21:41.449 128M / 1G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:21:41.996 188M / 1G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:21:43.092 308M / 1G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:21:45.272 544M / 1G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:21:52.479 912M / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:22:03.784 916M / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:22:26.689 920M / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:23:16.013 944M / 1G INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:24:52.910 956M / 1G INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:28:11.407 976M / 1G INFO General (binary_converter.hpp : 93) 33554432 reads processed
0:28:12.721 96M / 1G INFO General (binary_converter.hpp : 117) 33557381 reads written
0:28:12.739 8M / 1G INFO General (read_converter.hpp : 87) Converting single reads
0:28:12.886 140M / 1G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:28:12.944 148M / 1G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:28:13.060 160M / 1G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:28:13.286 184M / 1G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:28:13.732 236M / 1G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:28:14.637 336M / 1G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:28:16.427 536M / 1G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:28:20.006 940M / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:28:27.244 1G / 1G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:28:51.373 1G / 1G INFO General (binary_converter.hpp : 117) 8238524 reads written
0:28:53.913 8M / 1G INFO General (read_converter.hpp : 95) Converting merged reads
0:28:54.018 136M / 1G INFO General (binary_converter.hpp : 117) 0 reads written
0:28:54.027 8M / 1G INFO General (construction.cpp : 111) Max read length 150
0:28:54.027 8M / 1G INFO General (construction.cpp : 117) Average read length 139.787
0:28:54.027 8M / 1G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
0:28:54.027 8M / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
0:28:54.027 8M / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1088
0:28:54.027 8M / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60409 Gb
0:28:54.027 8M / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
0:29:06.765 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 23765085 reads
0:29:19.628 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 42406194 reads
0:29:32.603 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 61238798 reads
0:29:45.447 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 80044925 reads
0:29:58.585 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 98636514 reads
0:30:11.512 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 117293203 reads
0:30:24.844 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 135943423 reads
0:30:38.482 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 158439740 reads
0:30:51.875 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 177263919 reads
0:31:05.042 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 196231603 reads
0:31:18.659 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 215157250 reads
0:31:31.802 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 233889138 reads
0:31:45.366 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 252669744 reads
0:31:58.628 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 271438951 reads
0:34:58.521 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 540018530 reads
0:35:27.542 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
0:35:28.928 136M / 18G INFO General (kmer_splitters.hpp : 308) Used 580779968 reads
0:35:28.928 136M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:35:42.527 136M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 371021783 kmers in total.
0:35:42.528 136M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:35:48.030 132M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
0:35:48.035 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:35:48.036 132M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
0:35:48.036 132M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 1088
0:35:48.036 132M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60282 Gb
0:35:48.036 132M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536
0:35:48.729 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5772115 kmers
0:35:49.581 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 17032273 kmers
0:35:50.296 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 26028324 kmers
0:35:51.028 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 33275806 kmers
0:35:51.865 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 41575747 kmers
0:35:52.614 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 51044348 kmers
0:35:53.522 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 59860282 kmers
0:35:54.332 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68105181 kmers
0:35:55.187 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 77323348 kmers
0:35:55.997 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 86831935 kmers
0:35:56.904 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 95644877 kmers
0:35:57.656 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 104387724 kmers
0:35:58.500 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 113623676 kmers
0:35:59.337 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 122537344 kmers
0:36:00.126 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 130791182 kmers
0:36:00.934 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 139383956 kmers
0:36:01.798 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 148459681 kmers
0:36:02.638 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 157562007 kmers
0:36:13.400 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 271837716 kmers
0:36:23.146 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 371023121 kmers.
0:36:23.414 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:36:31.334 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 369258045 kmers in total.
0:36:31.334 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:36:36.937 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:36:52.047 328M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
0:37:56.560 328M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 171233768 bytes occupied (3.70979 bits per kmer).
0:37:56.875 684M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
0:38:14.590 684M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
0:38:14.594 680M / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping
0:38:14.594 680M / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K)
0:38:14.594 680M / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping
0:38:53.907 680M / 18G INFO Early tip clipping (early_simplification.hpp : 184) 76444443 50-mers were removed by early tip clipper
0:38:53.907 680M / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
0:38:53.908 680M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
0:39:16.362 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 8629010 sequences extracted
0:39:26.401 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
0:39:33.474 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 759 loops collected
0:39:38.077 3G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
0:39:38.078 3G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:39:38.078 3G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:39:48.806 3G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 172103876 bytes occupied (3.71092 bits per kmer).
0:39:49.674 4G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
0:48:53.271 4G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
0:49:08.494 4G / 18G INFO General (construction.cpp : 464) Processed 17259228 edges
0:49:10.256 2G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding
0:49:26.627 2G / 18G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 31
0:49:26.632 2G / 18G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 89.4698
0:49:26.632 2G / 18G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 1233
0:49:26.894 2G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 89.4698
0:49:26.894 2G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0
0:49:26.894 2G / 18G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
0:49:26.900 2G / 18G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
0:49:26.901 2G / 18G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled
0:49:26.901 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
0:49:27.413 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times
0:49:27.414 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges
0:49:27.414 2G / 18G INFO General (simplification.cpp : 76) Removing short polyAT
0:49:39.260 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 860 times
0:49:39.261 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges
0:49:39.857 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times
0:49:39.857 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
0:49:41.773 2G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 97992 times
0:49:41.773 2G / 18G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections
0:50:07.711 2G / 18G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 47/1267/53
0:50:07.711 2G / 18G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 4/45/317
0:50:07.731 2G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification
0:50:07.731 2G / 18G INFO General (simplification.cpp : 357) Graph simplification started
0:50:07.731 2G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
0:50:07.731 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
0:50:07.731 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:50:09.266 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 62495 times
0:50:09.266 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:50:12.144 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 206755 times
0:50:12.144 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:55:28.339 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1324208 times
0:55:28.339 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:55:29.324 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1228 times
0:55:29.324 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:55:30.630 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 2230 times
0:55:30.630 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:55:30.821 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 188 times
0:55:30.821 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:55:30.823 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times
0:55:30.823 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:55:30.824 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:56:24.324 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 926302 times
0:56:24.324 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
0:56:24.324 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:56:25.574 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 25592 times
0:56:25.574 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:56:26.188 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 9135 times
0:56:26.189 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:57:53.476 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 173271 times
0:57:53.476 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:57:53.654 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20 times
0:57:53.654 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:57:53.769 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:57:53.769 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:57:53.770 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times
0:57:53.770 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:57:53.770 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:57:53.770 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:57:53.770 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:57:53.770 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:57:53.770 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:57:53.770 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:57:56.055 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 44566 times
0:57:56.055 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
0:57:56.055 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:57:56.570 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7026 times
0:57:56.570 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:57:56.827 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 141 times
0:57:56.828 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:02.390 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 12884 times
0:58:02.390 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:02.410 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:02.410 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:02.425 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:02.425 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:02.425 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:02.425 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:03.267 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13881 times
0:58:03.267 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
0:58:03.267 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:03.581 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1829 times
0:58:03.582 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:03.791 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 15 times
0:58:03.792 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:05.774 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4002 times
0:58:05.774 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:05.781 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:05.781 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:05.785 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:05.785 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:05.785 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:05.785 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:06.299 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6701 times
0:58:06.299 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
0:58:06.299 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:06.594 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 694 times
0:58:06.594 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:06.791 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times
0:58:06.791 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:08.002 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1647 times
0:58:08.002 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:08.005 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:08.005 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:08.007 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:08.007 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:08.007 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:08.007 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:08.396 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4133 times
0:58:08.396 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
0:58:08.396 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:08.607 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 320 times
0:58:08.607 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:08.787 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:08.788 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:09.893 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 904 times
0:58:09.893 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:09.895 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:09.895 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:09.896 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:09.896 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:09.896 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:09.896 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:10.228 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2874 times
0:58:10.228 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7
0:58:10.228 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:10.443 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 201 times
0:58:10.443 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:10.647 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:10.648 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:11.487 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 580 times
0:58:11.487 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:11.488 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:11.488 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:11.489 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:11.489 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:11.489 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:11.489 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:11.772 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2154 times
0:58:11.772 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8
0:58:11.772 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:11.977 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 135 times
0:58:11.978 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:12.169 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:12.169 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:13.032 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 387 times
0:58:13.032 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:13.033 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:13.033 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:13.034 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:13.034 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:13.034 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:13.034 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:13.297 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1707 times
0:58:13.297 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9
0:58:13.297 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:13.499 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 80 times
0:58:13.500 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:13.692 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:13.693 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:14.480 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 247 times
0:58:14.480 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:14.481 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:14.481 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:14.481 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:14.481 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:14.481 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:14.481 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:14.743 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1413 times
0:58:14.743 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10
0:58:14.743 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:14.928 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 51 times
0:58:14.928 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:15.107 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:15.108 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:15.687 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 183 times
0:58:15.687 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:15.688 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:15.688 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:15.688 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:15.688 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:15.688 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:15.688 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:15.948 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1186 times
0:58:15.948 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11
0:58:15.948 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:16.158 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 48 times
0:58:16.158 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:16.356 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:16.357 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:16.961 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 134 times
0:58:16.961 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:16.962 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:16.962 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:16.962 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:16.962 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:16.962 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:16.962 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:17.164 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
0:58:17.164 2G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12
0:58:17.165 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:17.165 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:17.165 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:17.165 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:58:17.166 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:17.166 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:17.166 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:17.166 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
0:58:17.167 2G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup
0:58:17.167 2G / 18G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification
0:58:17.167 2G / 18G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled
0:58:17.167 2G / 18G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled
0:58:17.168 2G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
0:58:17.168 2G / 18G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
0:58:17.168 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
0:58:17.425 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1067 times
0:58:17.426 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
0:58:18.815 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 42342 times
0:58:18.815 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
0:58:29.348 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 2469 times
0:58:29.348 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:29.620 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 39 times
0:58:29.620 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
0:58:30.348 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 24932 times
0:58:30.348 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:30.905 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 609 times
0:58:30.905 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
0:58:31.412 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
0:58:31.412 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
0:58:31.633 2G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 61 times
0:58:31.634 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
0:58:31.934 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 59 times
0:58:31.935 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
0:58:32.144 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 183 times
0:58:32.144 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
0:58:41.830 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 73 times
0:58:41.830 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:42.107 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:42.125 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
0:58:42.308 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 74 times
0:58:42.308 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:42.877 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times
0:58:42.877 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
0:58:43.369 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
0:58:43.369 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
0:58:43.572 2G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 3 times
0:58:43.573 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
0:58:43.579 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
0:58:43.579 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
0:58:43.773 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 1 times
0:58:43.773 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
0:58:53.336 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
0:58:53.338 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:53.339 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:58:53.340 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
0:58:53.340 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
0:58:53.341 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:58:53.342 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:58:53.342 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
0:58:53.343 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
0:58:53.344 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
0:58:53.344 2G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times
0:58:53.345 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
0:58:53.345 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
0:58:53.346 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
0:58:53.598 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
0:58:53.599 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
0:59:03.271 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
0:59:03.272 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:59:03.273 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:59:03.274 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
0:59:03.274 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
0:59:03.275 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:59:03.276 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:59:03.276 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
0:59:03.277 2G / 18G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
0:59:03.278 2G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
0:59:03.278 2G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times
0:59:03.279 2G / 18G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges
0:59:05.534 2G / 18G INFO General (simplification.cpp : 470) Counting average coverage
0:59:06.768 2G / 18G INFO General (simplification.cpp : 476) Average coverage = 156.142
0:59:06.768 2G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
0:59:06.774 2G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/Pcitri_rnaspades/output//K49/assembly_graph_with_scaffolds.gfa
0:59:13.097 2G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K49/before_rr.fasta
0:59:19.453 2G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/Pcitri_rnaspades/output//K49/assembly_graph.fastg
0:59:35.509 2G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K49/simplified_contigs.fasta
0:59:41.771 2G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K49/final_contigs.fasta
0:59:47.830 2G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
0:59:47.830 2G / 18G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/Pcitri_rnaspades/output//K49/assembly_graph_with_scaffolds.gfa
0:59:54.129 2G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K49/before_rr.fasta
1:00:01.111 2G / 18G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/Pcitri_rnaspades/output//K49/assembly_graph.fastg
1:00:20.005 2G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K49/simplified_contigs.fasta
1:00:26.952 2G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K49/final_contigs.fasta
1:00:34.052 2G / 18G INFO General (launch.hpp : 149) SPAdes finished
1:00:39.140 128M / 18G INFO General (main.cpp : 109) Assembling time: 1 hours 0 minutes 39 seconds
Max read length detected as 150
== Running assembler: K73
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades/output/K73/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades/output/K73/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades/output/K73/configs/rna_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 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/Pcitri_rnaspades/output/dataset.info) with K=73
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
0:00:00.003 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.005 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.008 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.009 8M / 8M INFO General (construction.cpp : 111) Max read length 150
0:00:00.009 8M / 8M INFO General (construction.cpp : 117) Average read length 139.787
0:00:00.009 8M / 8M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
0:00:00.009 8M / 8M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
0:00:00.010 8M / 8M INFO General (file_limit.hpp : 32) Open file limit set to 1088
0:00:00.010 8M / 8M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60409 Gb
0:00:00.010 8M / 8M INFO General (kmer_splitters.hpp : 97) Using cell size of 21845
0:00:11.678 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 22790545 reads
0:00:21.348 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 39484528 reads
0:00:32.218 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 56341063 reads
0:00:42.918 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 73299496 reads
0:00:53.505 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 90007619 reads
0:01:04.674 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 106659975 reads
0:01:15.443 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 123401982 reads
0:01:26.484 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 140094108 reads
0:01:37.914 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 161310502 reads
0:01:49.627 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 178441619 reads
0:02:00.803 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 195719641 reads
0:02:11.568 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 213050582 reads
0:02:22.840 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 230103347 reads
0:02:55.195 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 285345548 reads
0:05:40.386 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 546537363 reads
0:06:02.968 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
0:06:37.478 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 580779968 reads
0:06:37.478 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:07:25.084 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 389470070 kmers in total.
0:07:25.084 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:07:50.853 132M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
0:07:50.853 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:07:50.853 132M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
0:07:50.853 132M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 1088
0:07:50.853 132M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.60282 Gb
0:07:50.853 132M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690
0:07:51.433 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 3780469 kmers
0:07:52.029 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 7824906 kmers
0:07:52.498 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11812036 kmers
0:07:53.003 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 15943897 kmers
0:07:53.578 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 19991581 kmers
0:07:54.057 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23979959 kmers
0:07:54.509 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 28116182 kmers
0:07:55.115 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 32166461 kmers
0:07:55.604 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 36156878 kmers
0:07:56.120 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 40291239 kmers
0:07:56.678 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 44334467 kmers
0:07:57.209 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 48322589 kmers
0:07:57.734 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 52466558 kmers
0:07:58.296 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 56518617 kmers
0:07:58.813 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 60507504 kmers
0:07:59.290 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 64630113 kmers
0:07:59.865 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68677669 kmers
0:08:09.841 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 137661818 kmers
0:08:28.851 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 271548858 kmers
0:08:46.135 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 389473142 kmers.
0:08:46.349 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:09:08.518 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 389582114 kmers in total.
0:09:08.518 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:09:17.100 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:09:35.738 324M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
0:11:06.298 324M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 180658088 bytes occupied (3.70978 bits per kmer).
0:11:06.631 696M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
0:11:25.762 696M / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
0:11:25.780 696M / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
0:11:25.807 696M / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
0:11:56.009 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 26023561 sequences extracted
0:12:11.417 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
0:12:18.944 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 27 loops collected
0:12:34.575 8G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
0:12:34.575 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:12:34.575 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:12:46.414 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 180629720 bytes occupied (3.71027 bits per kmer).
0:12:47.321 10G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
0:20:01.145 10G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
0:20:17.101 10G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges
0:20:25.873 10G / 18G INFO General (construction.cpp : 464) Processed 52047036 edges
0:20:28.039 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding
0:21:19.831 8G / 18G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 20
0:21:19.834 8G / 18G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 50.5545
0:21:19.834 8G / 18G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 903
0:21:20.036 8G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 50.5545
0:21:20.036 8G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0
0:21:20.036 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
0:21:20.036 8G / 18G INFO General (graph_pack.hpp : 101) Index refill
0:21:20.036 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:21:20.036 8G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
0:21:20.036 8G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 1088
0:21:20.036 8G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.51904 Gb
0:21:20.036 8G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690
0:21:35.792 25G / 26G INFO General (edge_index_builders.hpp : 77) Processed 52047036 edges
0:21:35.793 25G / 26G INFO General (edge_index_builders.hpp : 82) Used 52047036 sequences.
0:21:36.721 8G / 26G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:21:43.835 8G / 26G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 389470070 kmers in total.
0:21:43.835 8G / 26G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:21:52.157 8G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:22:09.882 8G / 26G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
0:23:40.222 8G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 180615990 bytes occupied (3.70998 bits per kmer).
0:23:45.423 17G / 26G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
0:24:01.420 17G / 26G INFO General (edge_index.hpp : 92) Index refilled
0:24:01.422 17G / 26G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:24:48.214 19G / 26G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:27:03.742 19G / 26G INFO General (gap_closer.cpp : 138) Used 32477062 paired reads
0:27:03.742 19G / 26G INFO General (gap_closer.cpp : 140) Merging paired indices
0:27:14.192 17G / 26G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:29:00.782 17G / 26G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 5811 gaps after checking 52669 candidates
0:29:05.604 17G / 26G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:29:54.687 19G / 26G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:32:10.042 19G / 26G INFO General (gap_closer.cpp : 138) Used 29915487 paired reads
0:32:10.042 19G / 26G INFO General (gap_closer.cpp : 140) Merging paired indices
0:32:20.377 17G / 26G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:34:08.094 17G / 26G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 4812 gaps after checking 42534 candidates
0:34:12.323 17G / 26G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:34:58.108 19G / 26G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:37:33.359 19G / 26G INFO General (gap_closer.cpp : 138) Used 35525456 paired reads
0:37:33.359 19G / 26G INFO General (gap_closer.cpp : 140) Merging paired indices
0:37:42.247 17G / 26G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:39:26.247 17G / 26G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 5119 gaps after checking 41404 candidates
0:39:30.730 17G / 26G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:40:15.987 19G / 26G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:42:37.303 19G / 26G INFO General (gap_closer.cpp : 138) Used 33557381 paired reads
0:42:37.303 19G / 26G INFO General (gap_closer.cpp : 140) Merging paired indices
0:42:46.490 17G / 26G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:44:31.688 17G / 26G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 4802 gaps after checking 48825 candidates
0:44:35.838 17G / 26G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
0:44:36.726 8G / 26G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
0:44:36.727 8G / 26G INFO General (graph_simplification.hpp : 662) Flanking coverage based disconnection disabled
0:44:36.727 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
0:44:38.641 8G / 26G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times
0:44:38.641 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges
0:44:38.641 8G / 26G INFO General (simplification.cpp : 76) Removing short polyAT
0:45:22.217 8G / 26G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 860 times
0:45:22.217 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges
0:45:24.784 8G / 26G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times
0:45:24.784 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
0:47:19.261 8G / 26G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 7473384 times
0:47:19.262 8G / 26G INFO General (graph_simplification.hpp : 701) Removing loops and rc loops with erroneous connections
0:48:13.521 8G / 26G INFO ECLoopRemover (erroneous_connection_remov: 440) Loops: accurately removed/deadend removed/other: 10/291/11
0:48:13.521 8G / 26G INFO ECLoopRemover (erroneous_connection_remov: 441) RC loops: accurately removed/deadend removed/other: 0/29/111
0:48:14.903 8G / 26G INFO StageManager (stage.cpp : 132) STAGE == Simplification
0:48:14.903 8G / 26G INFO General (simplification.cpp : 357) Graph simplification started
0:48:14.903 8G / 26G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
0:48:14.903 8G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
0:48:14.903 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:49:16.398 8G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3705146 times
0:49:16.398 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:49:37.008 8G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1136112 times
0:49:37.008 8G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:57:45.412 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 571348 times
0:57:45.412 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:57:46.808 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1985 times
0:57:46.808 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:57:47.516 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 170 times
0:57:47.516 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:57:47.595 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 92 times
0:57:47.595 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:57:47.596 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
0:57:47.596 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:57:47.596 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
0:57:47.596 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
0:57:47.596 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
0:57:47.596 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
0:58:11.606 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 344312 times
0:58:11.606 13G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
0:58:11.606 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:16.486 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 113252 times
0:58:16.487 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:58:17.251 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 6556 times
0:58:17.251 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:25.722 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 92062 times
1:00:25.722 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:25.853 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 23 times
1:00:25.853 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:25.959 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:25.959 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:25.961 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times
1:00:25.961 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:25.961 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:00:25.961 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:25.961 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:25.961 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:25.961 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:00:25.961 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:00:28.081 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 26740 times
1:00:28.081 14G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
1:00:28.081 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:29.528 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 26579 times
1:00:29.528 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:30.104 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 57 times
1:00:30.107 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:39.208 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6419 times
1:00:39.208 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:39.236 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:00:39.236 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:39.254 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:39.254 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:39.254 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:00:39.254 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:00:40.557 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8918 times
1:00:40.557 14G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
1:00:40.557 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:41.307 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8383 times
1:00:41.307 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:41.741 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 5 times
1:00:41.741 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:44.967 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1742 times
1:00:44.967 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:44.975 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:00:44.975 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:44.980 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:44.980 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:44.980 14G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:00:44.980 14G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:00:45.556 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4785 times
1:00:45.556 13G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
1:00:45.556 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:46.090 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3203 times
1:00:46.090 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:46.478 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:46.478 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:48.877 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 781 times
1:00:48.877 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:48.881 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:00:48.881 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:48.884 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:48.884 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:48.884 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:00:48.884 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:00:49.749 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3067 times
1:00:49.749 13G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
1:00:49.749 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:50.208 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1393 times
1:00:50.208 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:50.570 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:50.571 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:52.256 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 419 times
1:00:52.256 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:52.259 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:00:52.259 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:52.260 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:52.260 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:52.260 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:00:52.260 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:00:52.713 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2253 times
1:00:52.713 13G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7
1:00:52.713 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:53.117 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 636 times
1:00:53.117 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:53.455 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:53.456 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:55.019 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 254 times
1:00:55.019 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:55.021 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:00:55.021 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:55.022 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:55.022 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:55.022 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:00:55.022 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:00:55.739 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1677 times
1:00:55.739 13G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8
1:00:55.739 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:56.185 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 337 times
1:00:56.185 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:56.578 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:56.579 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:58.247 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 148 times
1:00:58.247 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:58.248 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:00:58.248 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:58.249 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:58.249 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:00:58.249 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:00:58.249 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:00:58.741 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1302 times
1:00:58.741 13G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9
1:00:58.741 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:00:59.119 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 200 times
1:00:59.119 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:00:59.481 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:00:59.481 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:01:00.459 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 95 times
1:01:00.459 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:01:00.460 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:01:00.460 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:01:00.460 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:01:00.460 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:01:00.460 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:01:00.460 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:01:00.863 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1089 times
1:01:00.863 13G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10
1:01:00.863 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:01:01.245 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 132 times
1:01:01.246 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:01:01.592 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:01:01.592 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:01:02.835 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 82 times
1:01:02.835 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:01:02.835 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:01:02.835 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:01:02.836 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:01:02.836 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:01:02.836 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:01:02.836 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:01:03.385 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 927 times
1:01:03.385 13G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11
1:01:03.385 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:01:03.819 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 87 times
1:01:03.820 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:01:04.202 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:01:04.203 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:01:05.715 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 66 times
1:01:05.715 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:01:05.716 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:01:05.716 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:01:05.716 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:01:05.716 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:01:05.716 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:01:05.716 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:01:06.161 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
1:01:06.161 13G / 26G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12
1:01:06.161 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:01:06.161 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:01:06.161 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:01:06.161 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:01:06.161 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:01:06.161 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:01:06.161 13G / 26G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:01:06.161 13G / 26G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
1:01:06.164 13G / 26G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
1:01:06.164 13G / 26G INFO General (graph_pack.hpp : 101) Index refill
1:01:06.164 13G / 26G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
1:01:06.164 13G / 26G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
1:01:06.165 13G / 26G INFO General (file_limit.hpp : 32) Open file limit set to 1088
1:01:06.165 13G / 26G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.4587 Gb
1:01:06.165 13G / 26G INFO General (kmer_splitters.hpp : 97) Using cell size of 43690
1:01:12.329 31G / 31G INFO General (edge_index_builders.hpp : 77) Processed 3693016 edges
1:01:12.329 31G / 31G INFO General (edge_index_builders.hpp : 82) Used 3693016 sequences.
1:01:12.944 13G / 31G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
1:01:17.165 13G / 31G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 188469688 kmers in total.
1:01:17.166 13G / 31G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
1:01:21.171 13G / 31G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
1:01:29.126 14G / 31G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
1:02:09.428 14G / 31G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 87401752 bytes occupied (3.70995 bits per kmer).
1:02:13.233 18G / 31G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
1:02:19.094 18G / 31G INFO General (edge_index.hpp : 92) Index refilled
1:02:19.096 18G / 31G INFO General (gap_closer.cpp : 159) Preparing shift maps
1:02:26.971 18G / 31G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
1:03:24.874 18G / 31G INFO General (gap_closer.cpp : 138) Used 32477062 paired reads
1:03:24.875 18G / 31G INFO General (gap_closer.cpp : 140) Merging paired indices
1:03:27.305 18G / 31G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
1:03:35.244 18G / 31G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 820 gaps after checking 34455 candidates
1:03:37.324 18G / 31G INFO General (gap_closer.cpp : 159) Preparing shift maps
1:03:45.680 18G / 31G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
1:04:38.761 18G / 31G INFO General (gap_closer.cpp : 138) Used 29915487 paired reads
1:04:38.761 18G / 31G INFO General (gap_closer.cpp : 140) Merging paired indices
1:04:40.816 18G / 31G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
1:04:48.319 18G / 31G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 432 gaps after checking 31610 candidates
1:04:49.680 18G / 31G INFO General (gap_closer.cpp : 159) Preparing shift maps
1:04:56.022 18G / 31G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
1:05:56.527 18G / 31G INFO General (gap_closer.cpp : 138) Used 35525456 paired reads
1:05:56.527 18G / 31G INFO General (gap_closer.cpp : 140) Merging paired indices
1:05:58.565 18G / 31G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
1:06:06.283 18G / 31G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 540 gaps after checking 36218 candidates
1:06:07.956 18G / 31G INFO General (gap_closer.cpp : 159) Preparing shift maps
1:06:15.868 18G / 31G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
1:07:12.672 18G / 31G INFO General (gap_closer.cpp : 138) Used 33557381 paired reads
1:07:12.672 18G / 31G INFO General (gap_closer.cpp : 140) Merging paired indices
1:07:14.950 18G / 31G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
1:07:23.379 18G / 31G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 443 gaps after checking 37602 candidates
1:07:24.684 18G / 31G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup
1:07:24.684 18G / 31G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification
1:07:24.684 18G / 31G INFO General (graph_simplification.hpp : 453) Disconnection of relatively low covered edges disabled
1:07:24.684 18G / 31G INFO General (graph_simplification.hpp : 489) Complex tip clipping disabled
1:07:24.684 18G / 31G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
1:07:24.684 18G / 31G INFO General (graph_simplification.hpp : 634) Creating parallel br instance
1:07:24.684 18G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:07:25.450 18G / 31G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 567 times
1:07:25.450 18G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:08:49.541 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 214530 times
1:08:49.541 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
1:09:12.276 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 1903 times
1:09:12.276 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:09:13.096 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 183 times
1:09:13.096 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
1:10:03.355 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 46007 times
1:10:03.355 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:10:08.269 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1034 times
1:10:08.269 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
1:10:08.782 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
1:10:08.782 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
1:10:09.124 17G / 31G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 141 times
1:10:09.124 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:10:09.504 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 23 times
1:10:09.504 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:10:10.019 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 119 times
1:10:10.019 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
1:10:24.506 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 62 times
1:10:24.506 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:10:25.202 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times
1:10:25.203 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
1:10:25.671 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 82 times
1:10:25.671 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:10:26.309 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times
1:10:26.309 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
1:10:26.821 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
1:10:26.821 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
1:10:27.188 17G / 31G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 1 times
1:10:27.188 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:10:27.189 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
1:10:27.190 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:10:27.500 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
1:10:27.501 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
1:10:41.185 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
1:10:41.186 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:10:41.186 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:10:41.187 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
1:10:41.187 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
1:10:41.187 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:10:41.187 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:10:41.187 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
1:10:41.188 17G / 31G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
1:10:41.188 17G / 31G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
1:10:41.188 17G / 31G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times
1:10:41.188 17G / 31G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges
1:10:44.434 17G / 31G INFO General (simplification.cpp : 470) Counting average coverage
1:10:46.036 17G / 31G INFO General (simplification.cpp : 476) Average coverage = 110.896
1:10:46.036 17G / 31G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction
1:10:46.036 17G / 31G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 100137210 kmers to process
1:12:25.044 17G / 31G INFO General (graph_pack.hpp : 111) Normalizing done
1:29:19.714 50G / 50G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions
1:31:24.756 18G / 50G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed
1:31:27.144 17G / 50G INFO General (mismatch_correction.cpp : 27) Corrected 3309 nucleotides
1:31:27.160 17G / 50G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
1:31:27.160 17G / 50G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/Pcitri_rnaspades/output//K73/assembly_graph_with_scaffolds.gfa
1:31:36.725 17G / 50G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K73/before_rr.fasta
1:31:44.110 17G / 50G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/Pcitri_rnaspades/output//K73/assembly_graph.fastg
1:32:04.672 17G / 50G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K73/simplified_contigs.fasta
1:32:13.242 17G / 50G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K73/intermediate_contigs.fasta
1:32:22.742 17G / 50G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting
1:33:03.169 19G / 50G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 100401408 kmers to process
1:34:36.423 19G / 50G INFO General (graph_pack.hpp : 111) Normalizing done
1:34:38.665 19G / 50G INFO General (pair_info_count.cpp : 320) Min edge length for estimation: 245
1:34:38.665 19G / 50G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #0
1:34:38.665 19G / 50G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)
1:34:39.002 19G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:34:47.655 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:34:47.737 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:34:47.794 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:34:47.847 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:34:47.913 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:34:47.966 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:34:48.307 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:34:49.021 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:34:57.745 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:35:09.922 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:35:30.937 19G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 32477062 reads processed
1:35:32.533 19G / 50G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit)
1:35:32.533 19G / 50G INFO General (pair_info_count.cpp : 213) 15067025 paired reads (46.3928% of all) aligned to long edges
1:35:32.572 19G / 50G INFO General (pair_info_count.cpp : 354) Insert size = 234.073, deviation = 84.343, left quantile = 151, right quantile = 349, read length = 150
1:35:32.572 19G / 50G INFO General (pair_info_count.cpp : 383) Mapping library #0
1:35:32.572 19G / 50G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while)
1:35:32.572 19G / 50G INFO General (pair_info_count.cpp : 289) Left insert size quantile 151, right insert size quantile 349, filtering threshold 0, rounding threshold 0
1:35:32.581 19G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:35:49.374 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:35:49.397 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:35:49.473 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:35:49.515 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:35:49.530 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:35:49.538 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:35:49.560 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:35:49.748 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:36:06.377 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:36:23.973 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:37:00.645 19G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 32477062 reads processed
1:37:00.928 19G / 50G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #0
1:37:00.929 19G / 50G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well
1:37:00.929 19G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:37:04.928 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:37:04.966 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:37:05.014 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:37:05.044 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:37:05.077 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:37:05.105 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:37:05.295 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:37:05.754 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:37:09.706 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:37:15.043 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:37:28.685 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
1:37:53.806 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
1:37:56.502 19G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 72692469 reads processed
1:37:56.809 19G / 50G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 0
1:37:56.809 19G / 50G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #1
1:37:56.809 19G / 50G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)
1:37:57.162 20G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:38:06.015 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:38:06.099 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:38:06.148 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:38:06.210 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:38:06.272 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:38:06.332 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:38:06.496 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:38:07.011 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:38:15.625 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:38:25.895 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:38:43.187 20G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 29915487 reads processed
1:38:44.901 20G / 50G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit)
1:38:44.901 20G / 50G INFO General (pair_info_count.cpp : 213) 13678615 paired reads (45.7242% of all) aligned to long edges
1:38:44.937 19G / 50G INFO General (pair_info_count.cpp : 354) Insert size = 244.659, deviation = 87.9879, left quantile = 155, right quantile = 366, read length = 150
1:38:44.937 19G / 50G INFO General (pair_info_count.cpp : 383) Mapping library #1
1:38:44.937 19G / 50G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while)
1:38:44.937 19G / 50G INFO General (pair_info_count.cpp : 289) Left insert size quantile 155, right insert size quantile 366, filtering threshold 0, rounding threshold 0
1:38:44.950 19G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:39:01.311 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:39:01.318 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:39:01.357 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:39:01.364 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:39:01.380 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:39:01.413 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:39:01.491 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:39:01.563 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:39:17.802 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:39:34.822 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:40:03.918 19G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 29915487 reads processed
1:40:04.185 19G / 50G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #1
1:40:04.185 19G / 50G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well
1:40:04.185 19G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:40:08.412 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:40:08.458 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:40:08.496 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:40:08.528 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:40:08.573 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:40:08.612 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:40:08.819 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:40:09.333 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:40:13.596 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:40:19.064 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:40:33.177 19G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
1:40:55.612 19G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 65251347 reads processed
1:40:55.769 19G / 50G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 0
1:40:55.769 19G / 50G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #2
1:40:55.769 19G / 50G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)
1:40:56.160 20G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:41:04.787 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:41:04.864 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:41:04.909 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:41:04.976 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:41:05.010 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:41:05.043 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:41:05.284 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:41:05.848 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:41:13.952 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:41:23.508 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:41:48.036 20G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 35525456 reads processed
1:41:49.709 20G / 50G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit)
1:41:49.709 20G / 50G INFO General (pair_info_count.cpp : 213) 16103601 paired reads (45.3298% of all) aligned to long edges
1:41:49.757 19G / 50G INFO General (pair_info_count.cpp : 354) Insert size = 244.36, deviation = 86.3308, left quantile = 156, right quantile = 362, read length = 150
1:41:49.757 19G / 50G INFO General (pair_info_count.cpp : 383) Mapping library #2
1:41:49.757 19G / 50G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while)
1:41:49.757 19G / 50G INFO General (pair_info_count.cpp : 289) Left insert size quantile 156, right insert size quantile 362, filtering threshold 0, rounding threshold 0
1:41:49.766 19G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:42:03.145 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:42:03.232 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:42:03.233 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:42:03.244 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:42:03.246 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:42:03.247 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:42:03.318 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:42:03.418 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:42:16.882 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:42:30.769 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:43:06.847 20G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 35525456 reads processed
1:43:07.107 20G / 50G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #2
1:43:07.107 20G / 50G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well
1:43:07.107 20G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:43:11.188 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:43:11.234 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:43:11.271 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:43:11.307 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:43:11.340 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:43:11.374 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:43:11.577 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:43:12.032 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:43:16.108 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:43:21.488 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:43:35.187 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
1:44:00.168 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
1:44:05.903 20G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 77092882 reads processed
1:44:06.051 20G / 50G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 0
1:44:06.051 20G / 50G INFO General (pair_info_count.cpp : 331) Estimating insert size for library #3
1:44:06.051 20G / 50G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)
1:44:06.434 20G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:44:14.869 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:44:14.937 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:44:15.000 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:44:15.067 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:44:15.107 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:44:15.143 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:44:15.398 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:44:15.931 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:44:24.054 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:44:33.563 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:44:55.571 20G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 33557381 reads processed
1:44:57.181 20G / 50G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit)
1:44:57.181 20G / 50G INFO General (pair_info_count.cpp : 213) 16061662 paired reads (47.8633% of all) aligned to long edges
1:44:57.220 20G / 50G INFO General (pair_info_count.cpp : 354) Insert size = 234.484, deviation = 85.8385, left quantile = 151, right quantile = 353, read length = 150
1:44:57.220 20G / 50G INFO General (pair_info_count.cpp : 383) Mapping library #3
1:44:57.220 20G / 50G INFO General (pair_info_count.cpp : 385) Mapping paired reads (takes a while)
1:44:57.220 20G / 50G INFO General (pair_info_count.cpp : 289) Left insert size quantile 151, right insert size quantile 353, filtering threshold 0, rounding threshold 0
1:44:57.229 20G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:45:09.883 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:45:09.893 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:45:09.927 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:45:09.945 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:45:09.957 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:45:09.964 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:45:09.989 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:45:10.336 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:45:22.835 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:45:36.785 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:46:07.063 20G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 33557381 reads processed
1:46:07.283 20G / 50G INFO General (pair_info_count.cpp : 392) Mapping single reads of library #3
1:46:07.283 20G / 50G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well
1:46:07.283 20G / 50G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
1:46:11.161 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
1:46:11.208 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
1:46:11.245 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
1:46:11.276 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
1:46:11.307 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
1:46:11.354 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
1:46:11.537 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
1:46:11.967 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
1:46:15.779 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
1:46:21.164 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
1:46:34.322 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
1:46:58.916 20G / 50G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
1:47:04.484 20G / 50G INFO General (sequence_mapper_notifier.h: 98) Total 75353286 reads processed
1:47:04.628 20G / 50G INFO General (pair_info_count.cpp : 394) Total paths obtained from single reads: 0
1:47:04.628 20G / 50G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation
1:47:04.628 20G / 50G INFO General (distance_estimation.cpp : 173) Processing library #0
1:47:04.628 20G / 50G INFO General (distance_estimation.cpp : 149) Weight Filter Done
1:47:04.634 20G / 50G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator
1:47:08.630 20G / 50G INFO General (distance_estimation.cpp : 34) Filtering info
1:47:08.630 20G / 50G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 3738844
1:47:12.615 20G / 50G INFO General (pair_info_filters.hpp : 263) Done filtering
1:47:12.621 20G / 50G INFO General (distance_estimation.cpp : 156) Refining clustered pair information
1:47:13.071 20G / 50G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished
1:47:13.071 20G / 50G INFO General (distance_estimation.cpp : 160) Improving paired information
1:47:22.238 20G / 50G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 22261; contradictional = 110
1:47:31.808 20G / 50G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 981; contradictional = 0
1:47:31.808 20G / 50G INFO General (distance_estimation.cpp : 173) Processing library #1
1:47:31.808 20G / 50G INFO General (distance_estimation.cpp : 149) Weight Filter Done
1:47:31.808 20G / 50G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator
1:47:36.005 20G / 50G INFO General (distance_estimation.cpp : 34) Filtering info
1:47:36.005 20G / 50G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 3823943
1:47:39.939 20G / 50G INFO General (pair_info_filters.hpp : 263) Done filtering
1:47:39.945 20G / 50G INFO General (distance_estimation.cpp : 156) Refining clustered pair information
1:47:40.388 20G / 50G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished
1:47:40.388 20G / 50G INFO General (distance_estimation.cpp : 160) Improving paired information
1:47:46.194 20G / 50G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 25364; contradictional = 100
1:47:52.094 20G / 50G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1191; contradictional = 0
1:47:52.094 20G / 50G INFO General (distance_estimation.cpp : 173) Processing library #2
1:47:52.094 20G / 50G INFO General (distance_estimation.cpp : 149) Weight Filter Done
1:47:52.094 20G / 50G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator
1:47:55.894 20G / 50G INFO General (distance_estimation.cpp : 34) Filtering info
1:47:55.894 20G / 50G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 3817751
1:47:59.985 20G / 50G INFO General (pair_info_filters.hpp : 263) Done filtering
1:47:59.992 20G / 50G INFO General (distance_estimation.cpp : 156) Refining clustered pair information
1:48:00.441 20G / 50G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished
1:48:00.441 20G / 50G INFO General (distance_estimation.cpp : 160) Improving paired information
1:48:06.595 20G / 50G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 26246; contradictional = 110
1:48:13.239 20G / 50G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1310; contradictional = 0
1:48:13.239 20G / 50G INFO General (distance_estimation.cpp : 173) Processing library #3
1:48:13.239 20G / 50G INFO General (distance_estimation.cpp : 149) Weight Filter Done
1:48:13.239 20G / 50G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator
1:48:16.955 20G / 50G INFO General (distance_estimation.cpp : 34) Filtering info
1:48:16.955 20G / 50G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 3756623
1:48:21.026 20G / 50G INFO General (pair_info_filters.hpp : 263) Done filtering
1:48:21.032 20G / 50G INFO General (distance_estimation.cpp : 156) Refining clustered pair information
1:48:21.462 20G / 50G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished
1:48:21.463 20G / 50G INFO General (distance_estimation.cpp : 160) Improving paired information
1:48:28.365 20G / 50G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 24078; contradictional = 100
1:48:34.344 20G / 50G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 1348; contradictional = 0
1:48:34.344 20G / 50G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving
1:48:34.345 20G / 50G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving
1:48:34.345 20G / 50G INFO General (launcher.cpp : 477) ExSPAnder repeat resolving tool started
1:48:45.673 25G / 50G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000
1:49:02.832 26G / 50G INFO General (extenders_logic.cpp : 472) Using 4 paired-end libraries
1:49:02.832 26G / 50G INFO General (extenders_logic.cpp : 473) Using 4 paired-end scaffolding libraries
1:49:02.832 26G / 50G INFO General (extenders_logic.cpp : 474) Using 0 single read libraries
1:49:02.832 26G / 50G INFO General (launcher.cpp : 420) Total number of extenders is 20
1:49:02.832 26G / 50G INFO General (path_extender.hpp : 885) Processed 0 paths from 1311972 (0%)
1:49:03.090 26G / 50G INFO General (path_extender.hpp : 883) Processed 128 paths from 1311972 (0%)
1:49:03.566 26G / 50G INFO General (path_extender.hpp : 883) Processed 256 paths from 1311972 (0%)
1:49:04.051 26G / 50G INFO General (path_extender.hpp : 883) Processed 512 paths from 1311972 (0%)
1:49:05.214 26G / 50G INFO General (path_extender.hpp : 883) Processed 1024 paths from 1311972 (0%)
1:49:07.173 26G / 50G INFO General (path_extender.hpp : 883) Processed 2048 paths from 1311972 (0%)
1:49:10.979 26G / 50G INFO General (path_extender.hpp : 883) Processed 4096 paths from 1311972 (0%)
1:49:17.768 26G / 50G INFO General (path_extender.hpp : 883) Processed 8192 paths from 1311972 (0%)
1:49:30.159 27G / 50G INFO General (path_extender.hpp : 883) Processed 16384 paths from 1311972 (1%)
1:49:50.024 27G / 50G INFO General (path_extender.hpp : 883) Processed 32768 paths from 1311972 (2%)
1:50:18.353 27G / 50G INFO General (path_extender.hpp : 883) Processed 65536 paths from 1311972 (4%)
1:50:58.941 27G / 50G INFO General (path_extender.hpp : 883) Processed 131072 paths from 1311972 (9%)
1:50:58.988 27G / 50G INFO General (path_extender.hpp : 885) Processed 131198 paths from 1311972 (10%)
1:52:05.682 28G / 50G INFO General (path_extender.hpp : 883) Processed 262144 paths from 1311972 (19%)
1:52:05.749 28G / 50G INFO General (path_extender.hpp : 885) Processed 262396 paths from 1311972 (20%)
1:52:51.452 29G / 50G INFO General (path_extender.hpp : 885) Processed 393594 paths from 1311972 (30%)
1:53:32.150 30G / 50G INFO General (path_extender.hpp : 883) Processed 524288 paths from 1311972 (39%)
1:53:32.301 30G / 50G INFO General (path_extender.hpp : 885) Processed 524792 paths from 1311972 (40%)
1:54:08.773 31G / 50G INFO General (path_extender.hpp : 885) Processed 655990 paths from 1311972 (50%)
1:55:05.534 32G / 50G INFO General (path_extender.hpp : 885) Processed 787188 paths from 1311972 (60%)
1:55:51.712 33G / 50G INFO General (path_extender.hpp : 885) Processed 918386 paths from 1311972 (70%)
1:56:23.794 34G / 50G INFO General (path_extender.hpp : 883) Processed 1048576 paths from 1311972 (79%)
1:56:24.035 34G / 50G INFO General (path_extender.hpp : 885) Processed 1049584 paths from 1311972 (80%)
1:56:54.930 35G / 50G INFO General (path_extender.hpp : 885) Processed 1180782 paths from 1311972 (90%)
1:57:24.675 36G / 50G INFO General (launcher.cpp : 234) Finalizing paths
1:57:24.675 36G / 50G INFO General (launcher.cpp : 236) Deduplicating paths
1:57:31.064 36G / 50G INFO General (launcher.cpp : 240) Paths deduplicated
1:57:31.064 36G / 50G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps
1:57:31.064 36G / 50G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps
1:57:31.064 36G / 50G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps
1:57:34.609 36G / 50G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths
1:57:35.085 36G / 50G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths
1:57:36.792 36G / 50G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed
1:57:41.944 36G / 50G INFO General (launcher.cpp : 257) Paths finalized
1:57:41.944 36G / 50G INFO General (launcher.cpp : 427) Closing gaps in paths
1:57:48.255 36G / 50G INFO General (launcher.cpp : 455) Gap closing completed
1:57:50.968 36G / 50G INFO General (launcher.cpp : 286) Traversing tandem repeats
1:58:04.982 36G / 50G INFO General (launcher.cpp : 296) Traversed 88 loops
1:58:04.982 36G / 50G INFO General (launcher.cpp : 234) Finalizing paths
1:58:04.982 36G / 50G INFO General (launcher.cpp : 236) Deduplicating paths
1:58:06.700 36G / 50G INFO General (launcher.cpp : 240) Paths deduplicated
1:58:06.700 36G / 50G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps
1:58:06.700 36G / 50G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps
1:58:06.700 36G / 50G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps
1:58:09.948 36G / 50G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths
1:58:10.106 36G / 50G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths
1:58:11.854 36G / 50G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed
1:58:16.997 36G / 50G INFO General (launcher.cpp : 257) Paths finalized
1:58:22.225 41G / 50G INFO General (launcher.cpp : 462) Finalizing main paths
1:58:22.225 41G / 50G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 122
1:58:22.225 41G / 50G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 122
1:58:22.225 41G / 50G INFO General (launcher.cpp : 281) Length cutoff: 122
1:58:23.432 41G / 50G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 167
1:58:23.432 41G / 50G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 167
1:58:23.432 41G / 50G INFO General (launcher.cpp : 281) Length cutoff: 167
1:58:23.694 41G / 50G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 152
1:58:23.694 41G / 50G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 152
1:58:23.694 41G / 50G INFO General (launcher.cpp : 281) Length cutoff: 152
1:58:24.253 41G / 50G INFO General (launcher.cpp : 467) Finalizing paths - hard
1:58:26.671 41G / 50G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 152
1:58:26.671 41G / 50G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 152
1:58:26.671 41G / 50G INFO General (launcher.cpp : 281) Length cutoff: 152
1:58:27.816 41G / 50G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 227
1:58:27.817 41G / 50G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 227
1:58:27.817 41G / 50G INFO General (launcher.cpp : 281) Length cutoff: 227
1:58:27.991 41G / 50G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 227
1:58:27.991 41G / 50G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 227
1:58:27.991 41G / 50G INFO General (launcher.cpp : 281) Length cutoff: 227
1:58:33.160 41G / 50G INFO General (launcher.cpp : 467) Finalizing paths - soft
1:58:36.106 41G / 50G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 84
1:58:36.106 41G / 50G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 84
1:58:36.106 41G / 50G INFO General (launcher.cpp : 281) Length cutoff: 84
1:58:36.833 41G / 50G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 152
1:58:36.833 41G / 50G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 152
1:58:36.833 41G / 50G INFO General (launcher.cpp : 281) Length cutoff: 152
1:58:36.980 41G / 50G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 107
1:58:36.980 41G / 50G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 107
1:58:36.981 41G / 50G INFO General (launcher.cpp : 281) Length cutoff: 107
1:58:46.265 36G / 50G INFO General (launcher.cpp : 529) ExSPAnder repeat resolving tool finished
1:58:59.771 22G / 50G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
1:58:59.771 22G / 50G INFO General (contig_output_stage.cpp : 40) Writing GFA to /DATA/markop/Pcitri_rnaspades/output//K73/assembly_graph_with_scaffolds.gfa
1:59:07.560 22G / 50G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades/output//K73/before_rr.fasta
1:59:18.391 22G / 50G INFO General (contig_output_stage.cpp : 51) Outputting FastG graph to /DATA/markop/Pcitri_rnaspades/output//K73/assembly_graph.fastg
1:59:42.551 22G / 50G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /DATA/markop/Pcitri_rnaspades/output//K73/transcripts.paths
1:59:50.844 22G / 50G INFO General (launch.hpp : 149) SPAdes finished
2:01:18.169 148M / 50G INFO General (main.cpp : 109) Assembling time: 2 hours 1 minutes 18 seconds
===== Assembling finished. Used k-mer sizes: 49, 73
* Corrected reads are in /DATA/markop/Pcitri_rnaspades/output/corrected/
* Assembled transcripts are in /DATA/markop/Pcitri_rnaspades/output/transcripts.fasta
* Paths in the assembly graph corresponding to the transcripts are in /DATA/markop/Pcitri_rnaspades/output/transcripts.paths
* Hard filtered transcripts are in /DATA/markop/Pcitri_rnaspades/output/hard_filtered_transcripts.fasta
* Soft filtered transcripts are in /DATA/markop/Pcitri_rnaspades/output/soft_filtered_transcripts.fasta
======= SPAdes pipeline finished.
SPAdes log can be found here: /DATA/markop/Pcitri_rnaspades/output/spades.log
Thank you for using SPAdes!
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Created: 16th May 2022 at 11:48
Last updated: 6th Nov 2024 at 15:27
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Version 1 (earliest) Created 16th May 2022 at 11:48 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
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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
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SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.
Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036
Programme: NIBSys
Public web page: http://susphire.info/susphireproject/
Start date: 1st Apr 2018
End date: 30th Sep 2021
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Short Name: T31_mealybug Title: Mealybug genome and transcriptome analyses Description: Searching for enzymes involved in the mealybug pheromone biosynthesis pathways. These pheromones are known to be released by virgin females. Phenodata: ./phenodata_20190523.txt Featuredata: Principal investigator: Heribert Warzecha, Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_P3_expressionEcoli, _S_P4_AdPathGenes, _S_P4_Pcitri_IsoSeq, _S_P4_Pcitri_genome, _S_P4_Pcitri_genome_extSamples, _S_P4_Pcitri_tr1, _S_P4_Pcitri_tr1tr2combo, _S_P4_Pcitri_tr2, _S_P4_cand_all, _S_P4_cand_genomic
Assays: _A_01-CoEXpNetViz_tr2-coexpr, _A_01_NGI-IsoSeq, _A_01_RNAseq-CLC, _A_01_assembly2-rnaSPAdes, _A_01_mapToGenomeAll-STAR, _A_01_renameFASTA-Bioinfo, _A_02-CoEXpNetViz_gen-coexpr, _A_02_CDHIT-Bioinfo, _A_02_assembly2-IPS, _A_02_cDNAcupcake-dry, _A_02_limma-R, _A_02_mapToGenomeAll_limma-R, _A_03-IPS, _A_03_CDHIT2-Bioinfo, _A_03_limma_min50counts-R, _A_03_mapAs2ToGenome-STAR, _A_04_limma_min10counts-R, _A_04_mapIllumina-STAR, _A_04_mapReadsToAs2-STAR, _A_05_As2_tr_limmaDE-R, _A_05_DE_limma-R, _A_05_assembly1-rnaSPAdes, _A_06_assembly1-IPS, _A_07_mapAs1ToGenome-STAR, _A_08_mapReadsToAs1-STAR, _A_09_As1_tr_limmaDE-R, _A_C98F-EcoliExpr, _A_IDIsearch-Bioinfo, _A_IPS-bioinfo, _A_MAST-bioinfo, _A_MEME-bioinfo, _A_MSA-bioinfo, _A_MeUppS-EcoliExpr, _A_Node14610-EcoliExpr, _A_Node14610DmTP-EcoliExpr, _A_OtherMealybugCandidates-Alignment, _A_Pc1599-EcoliExpr, _A_Pc23180-EcoliExpr, _A_Pc2704-EcoliExpr, _A_Pc32607-EcoliExpr, _A_Pc7366II-EcoliExpr, _A_PcCis24-EcoliExpr, _A_Strep_CLDS-bioinfo, _A_TPS_phy-bioinfo, _A_Terzyme-bioinfo, _A_Trans1153-EcoliExpr, _A_Trans2-EcoliExpr, _A_Trans39-EcoliExpr, _A_Trans57-EcoliExpr, _A_Trans64-EcoliExpr, _A_Trans94-EcoliExpr, _A_candidatemining-bioinfo, _A_g14825_recon-bioinfo, _A_smallIDSsubunit-motifs, _I_T31_mealybug-files, _S_P3_expressionEcoli-files, _S_P4_AdPathGenes-files, _S_P4_Pcitri_IsoSeq-files, _S_P4_Pcitri_genome-files, _S_P4_Pcitri_genome_extSamples-files, _S_P4_Pcitri_tr1-files, _S_P4_Pcitri_tr1tr2combo-files, _S_P4_Pcitri_tr2-files, _S_P4_cand_all-files, _S_P4_cand_genomic-files
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Investigation: _I_T3.1_mealybug project: _p_SUSPHIRE Short Name: P4_Pcitri_tr Title: P. citri transcriptome study Description: We are interested in certain mealybugs both because they are important pests and very difficult to control but because their sex pheromones are irregular terpenoids, which are (a) very cool molecules and (b) extremely difficult and expensive to make using chemistry.In our project, we will be doing comparative transcriptomics of virgin and mated females to attempt to ...
Submitter: Marko Petek
Investigation: _I_T31_mealybug
Assays: _A_05_assembly1-rnaSPAdes, _A_06_assembly1-IPS, _A_07_mapAs1ToGenome-STAR, _A_08_mapReadsToAs1-STAR, _A_09_As1_tr_limmaDE-R, _S_P4_Pcitri_tr1-files
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Short Name: 05_assembly1-rnaSPAdes Assay Class: DRY Assay Type: rnaSPAdes Title: P citri de-novo transcriptome assembly Description: P citri VF RNA-seq samples were assembled using rnaSPAdes assembler Phenodata: ../../phenodata_20181003.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_Pcitri_tr1
