reports/spades.log Version 1
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr2/_A_01_assembly2-rnaSPAdes/
SEEK ID: https://fairdomhub.org/documents/3885?version=1
Filename:
reports/spades.log
Format: Plain text document
Size: 174 KB
Command line: /home/administrator/Software/SPAdes-3.13.1-Linux/bin/rnaspades.py --only-assembler -k 29,49 -m 245 -t 32 -o /DATA/markop/Pcitri_rnaspades_alldata/output --ss-rf --pe1-fr --pe2-fr --pe3-fr --pe1-12 /DATA/markop/Pcitri_rnaspades_alldata/input/SUSPHIRE_unmerged.fastq --pe1-s /DATA/markop/Pcitri_rnaspades_alldata/input/SUSPHIRE_SE.fastq --pe2-12 /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh50_unmerged.fastq --pe2-s /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh50_SE.fastq --pe3-12 /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh75_unmerged.fastq --pe3-s /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh75_SE.fastq
System information:
SPAdes version: 3.13.1
Python version: 2.7.12
OS: Linux-4.13.0-41-generic-x86_64-with-LinuxMint-18.2-sonya
Output dir: /DATA/markop/Pcitri_rnaspades_alldata/output
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF
Dataset parameters:
RNA-seq mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: not specified
right reads: not specified
interlaced reads: ['/DATA/markop/Pcitri_rnaspades_alldata/input/SUSPHIRE_unmerged.fastq']
single reads: ['/DATA/markop/Pcitri_rnaspades_alldata/input/SUSPHIRE_SE.fastq']
merged reads: not specified
Library number: 2, library type: paired-end
orientation: fr
left reads: not specified
right reads: not specified
interlaced reads: ['/DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh50_unmerged.fastq']
single reads: ['/DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh50_SE.fastq']
merged reads: not specified
Library number: 3, library type: paired-end
orientation: fr
left reads: not specified
right reads: not specified
interlaced reads: ['/DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh75_unmerged.fastq']
single reads: ['/DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh75_SE.fastq']
merged reads: not specified
Assembly parameters:
k: [29, 49]
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_alldata/output/tmp
Threads: 32
Memory limit (in Gb): 245
======= SPAdes pipeline started. Log can be found here: /DATA/markop/Pcitri_rnaspades_alldata/output/spades.log
== Splitting /DATA/markop/Pcitri_rnaspades_alldata/input/SUSPHIRE_unmerged.fastq into left and right reads (in /DATA/markop/Pcitri_rnaspades_alldata/output/split_input directory)
== Splitting /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh50_unmerged.fastq into left and right reads (in /DATA/markop/Pcitri_rnaspades_alldata/output/split_input directory)
== Splitting /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh75_unmerged.fastq into left and right reads (in /DATA/markop/Pcitri_rnaspades_alldata/output/split_input directory)
===== Assembling started.
== Running assembler: K29
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades_alldata/output/K29/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades_alldata/output/K29/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades_alldata/output/K29/configs/rna_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 245 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.1, git revision 9a9d54db2ff9abaac718155bf74c12ec9464e8ca
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_alldata/output/dataset.info) with K=29
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 : 52) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 66) 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
0:00:00.169 80M / 80M INFO General (binary_converter.hpp : 93) 16384 reads processed
0:00:00.261 96M / 96M INFO General (binary_converter.hpp : 93) 32768 reads processed
0:00:00.455 124M / 124M INFO General (binary_converter.hpp : 93) 65536 reads processed
0:00:00.816 176M / 176M INFO General (binary_converter.hpp : 93) 131072 reads processed
0:00:01.598 288M / 288M INFO General (binary_converter.hpp : 93) 262144 reads processed
0:00:03.338 508M / 508M INFO General (binary_converter.hpp : 93) 524288 reads processed
0:00:09.739 852M / 852M INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:00:20.163 860M / 860M INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:00:42.468 868M / 868M INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:01:30.087 876M / 876M INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:03:01.327 896M / 896M INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:06:00.086 908M / 912M INFO General (binary_converter.hpp : 93) 33554432 reads processed
0:08:25.902 804M / 912M INFO General (binary_converter.hpp : 117) 47754126 reads written
0:08:26.588 8M / 912M INFO General (read_converter.hpp : 87) Converting single reads
0:08:26.770 140M / 912M INFO General (binary_converter.hpp : 93) 16384 reads processed
0:08:26.829 152M / 912M INFO General (binary_converter.hpp : 93) 32768 reads processed
0:08:26.949 172M / 912M INFO General (binary_converter.hpp : 93) 65536 reads processed
0:08:27.183 208M / 912M INFO General (binary_converter.hpp : 93) 131072 reads processed
0:08:27.657 288M / 912M INFO General (binary_converter.hpp : 93) 262144 reads processed
0:08:28.615 440M / 912M INFO General (binary_converter.hpp : 93) 524288 reads processed
0:08:31.384 752M / 912M INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:08:35.987 1G / 1G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:08:45.333 2G / 2G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:09:09.732 2G / 2G INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:09:55.248 2G / 2G INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:11:32.696 2G / 2G INFO General (binary_converter.hpp : 93) 33554432 reads processed
0:14:49.176 2G / 2G INFO General (binary_converter.hpp : 93) 67108864 reads processed
0:21:31.285 2G / 2G INFO General (binary_converter.hpp : 93) 134217728 reads processed
0:35:43.317 2G / 2G INFO General (binary_converter.hpp : 93) 268435456 reads processed
0:37:29.736 1G / 2G INFO General (binary_converter.hpp : 117) 283878849 reads written
0:37:32.456 8M / 2G INFO General (read_converter.hpp : 95) Converting merged reads
0:37:32.565 136M / 2G INFO General (binary_converter.hpp : 117) 0 reads written
0:37:32.922 8M / 2G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #1 (takes a while)
0:37:32.922 8M / 2G INFO General (read_converter.hpp : 78) Converting paired reads
0:37:33.058 76M / 2G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:37:33.109 84M / 2G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:37:33.210 100M / 2G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:37:33.432 132M / 2G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:37:33.864 196M / 2G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:37:34.778 328M / 2G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:37:37.608 532M / 2G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:37:43.609 532M / 2G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:37:54.387 532M / 2G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:38:15.440 532M / 2G INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:38:56.849 532M / 2G INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:40:29.770 532M / 2G INFO General (binary_converter.hpp : 93) 33554432 reads processed
0:43:33.348 532M / 2G INFO General (binary_converter.hpp : 93) 67108864 reads processed
0:49:44.275 532M / 2G INFO General (binary_converter.hpp : 93) 134217728 reads processed
0:50:17.668 324M / 2G INFO General (binary_converter.hpp : 117) 139945158 reads written
0:50:18.014 8M / 2G INFO General (read_converter.hpp : 87) Converting single reads
0:50:18.185 136M / 2G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:50:18.221 144M / 2G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:50:18.294 152M / 2G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:50:18.438 172M / 2G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:50:18.726 216M / 2G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:50:19.301 296M / 2G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:50:20.539 460M / 2G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:50:22.685 772M / 2G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:50:25.894 1G / 2G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:50:35.732 1G / 2G INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:50:52.330 484M / 2G INFO General (binary_converter.hpp : 117) 13472854 reads written
0:50:52.934 8M / 2G INFO General (read_converter.hpp : 95) Converting merged reads
0:50:53.042 136M / 2G INFO General (binary_converter.hpp : 117) 0 reads written
0:50:53.051 8M / 2G INFO General (read_converter.hpp : 77) Converting reads to binary format for library #2 (takes a while)
0:50:53.051 8M / 2G INFO General (read_converter.hpp : 78) Converting paired reads
0:50:53.323 80M / 2G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:50:53.537 88M / 2G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:50:53.677 108M / 2G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:50:53.990 148M / 2G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:50:54.663 228M / 2G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:50:55.940 384M / 2G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:50:59.831 628M / 2G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:51:05.823 628M / 2G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:51:21.708 632M / 2G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:51:51.724 632M / 2G INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:52:49.146 632M / 2G INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:54:31.781 372M / 2G INFO General (binary_converter.hpp : 117) 31883074 reads written
0:54:32.133 8M / 2G INFO General (read_converter.hpp : 87) Converting single reads
0:54:32.308 140M / 2G INFO General (binary_converter.hpp : 93) 16384 reads processed
0:54:32.351 148M / 2G INFO General (binary_converter.hpp : 93) 32768 reads processed
0:54:32.453 164M / 2G INFO General (binary_converter.hpp : 93) 65536 reads processed
0:54:32.664 192M / 2G INFO General (binary_converter.hpp : 93) 131072 reads processed
0:54:33.091 252M / 2G INFO General (binary_converter.hpp : 93) 262144 reads processed
0:54:34.019 372M / 2G INFO General (binary_converter.hpp : 93) 524288 reads processed
0:54:35.754 612M / 2G INFO General (binary_converter.hpp : 93) 1048576 reads processed
0:54:39.366 1G / 2G INFO General (binary_converter.hpp : 93) 2097152 reads processed
0:54:47.848 1G / 2G INFO General (binary_converter.hpp : 93) 4194304 reads processed
0:55:08.940 2G / 2G INFO General (binary_converter.hpp : 93) 8388608 reads processed
0:55:51.204 2G / 2G INFO General (binary_converter.hpp : 93) 16777216 reads processed
0:57:15.837 2G / 2G INFO General (binary_converter.hpp : 93) 33554432 reads processed
1:00:00.446 2G / 2G INFO General (binary_converter.hpp : 93) 67108864 reads processed
1:04:51.293 2G / 2G INFO General (binary_converter.hpp : 93) 134217728 reads processed
1:07:31.417 1020M / 2G INFO General (binary_converter.hpp : 117) 170271519 reads written
1:07:33.034 8M / 2G INFO General (read_converter.hpp : 95) Converting merged reads
1:07:33.139 136M / 2G INFO General (binary_converter.hpp : 117) 0 reads written
1:07:33.149 8M / 2G INFO General (construction.cpp : 111) Max read length 391
1:07:33.149 8M / 2G INFO General (construction.cpp : 117) Average read length 125.802
1:07:33.149 8M / 2G INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
1:07:33.155 8M / 2G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
1:07:33.157 8M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 65535
1:07:33.157 8M / 2G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.552 Gb
1:07:33.157 8M / 2G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536
1:07:48.761 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 13677801 reads
1:08:01.000 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 27350868 reads
1:08:14.068 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 40599178 reads
1:08:33.226 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 59085538 reads
1:08:42.703 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 69753146 reads
1:09:03.409 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 85166752 reads
1:09:15.210 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 98494920 reads
1:09:27.051 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 109586681 reads
1:09:45.911 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 126683120 reads
1:09:56.019 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 139231864 reads
1:10:09.119 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 153481808 reads
1:10:27.313 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 167572961 reads
1:10:37.316 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 180360412 reads
1:12:14.217 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 277397458 reads
1:16:34.898 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 543213574 reads
1:21:25.180 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1076393532 reads
1:26:37.267 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
1:26:38.675 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1813575876 reads
1:26:38.675 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
1:26:57.690 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 621018647 kmers in total.
1:26:57.690 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
1:27:02.203 132M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
1:27:02.204 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
1:27:02.204 132M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
1:27:02.204 132M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 65535
1:27:02.204 132M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.55074 Gb
1:27:02.204 132M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072
1:27:02.771 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 4424075 kmers
1:27:03.886 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 23766902 kmers
1:27:04.916 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 43172239 kmers
1:27:06.039 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 62575801 kmers
1:27:07.219 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 81975593 kmers
1:27:08.388 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 101384128 kmers
1:27:09.502 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 120798080 kmers
1:27:10.695 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 140209836 kmers
1:27:11.908 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 159617784 kmers
1:27:13.210 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 179025274 kmers
1:27:14.333 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 198429138 kmers
1:27:15.471 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 217833862 kmers
1:27:16.597 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 237235089 kmers
1:27:17.753 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 256646003 kmers
1:27:18.982 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 276053216 kmers
1:27:20.179 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 295465746 kmers
1:27:21.346 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 314876077 kmers
1:27:22.488 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 334286385 kmers
1:27:23.658 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 353684689 kmers
1:27:36.003 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 547761733 kmers
1:27:40.340 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 621019671 kmers.
1:27:40.567 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
1:27:49.049 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 616694987 kmers in total.
1:27:49.049 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
1:27:53.725 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
1:28:16.386 456M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
1:28:45.554 456M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 285993972 bytes occupied (3.71002 bits per kmer).
1:28:46.060 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
1:29:15.229 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
1:29:15.234 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping
1:29:15.235 1G / 18G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K)
1:29:15.236 1G / 18G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping
1:30:21.250 1G / 18G INFO Early tip clipping (early_simplification.hpp : 184) 109602424 30-mers were removed by early tip clipper
1:30:21.250 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
1:30:21.251 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
1:31:01.075 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 27782428 sequences extracted
1:31:19.125 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
1:31:31.582 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 3013 loops collected
1:31:46.103 8G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
1:31:46.103 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
1:31:46.103 8G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
1:32:04.271 9G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 287994198 bytes occupied (3.70996 bits per kmer).
1:32:05.672 11G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
1:50:11.182 11G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
1:50:28.307 11G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges
1:50:40.303 11G / 18G INFO General (construction.cpp : 464) Processed 55569613 edges
1:50:42.938 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding
1:51:49.891 8G / 18G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 56
1:51:49.901 8G / 18G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 171.45
1:51:49.901 8G / 18G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 1618
1:52:03.469 8G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 171.45
1:52:03.469 8G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0
1:52:03.469 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
1:52:03.476 8G / 18G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
1:52:03.477 8G / 18G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled
1:52:03.477 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
1:52:05.622 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times
1:52:05.623 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges
1:52:05.623 8G / 18G INFO General (simplification.cpp : 76) Removing short polyAT
1:52:51.598 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 565642 times
1:52:51.598 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges
1:52:53.360 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times
1:52:53.361 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
1:53:02.825 8G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 812130 times
1:53:02.825 8G / 18G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections
1:54:45.256 8G / 18G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 10/4772/226
1:54:45.256 8G / 18G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 2/379/1086
1:54:45.344 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification
1:54:45.344 8G / 18G INFO General (simplification.cpp : 357) Graph simplification started
1:54:45.344 8G / 18G INFO General (graph_simplification.hpp : 641) Creating parallel br instance
1:54:45.344 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:54:45.344 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
1:54:45.344 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:54:49.706 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 146523 times
1:54:49.706 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:54:58.834 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 609539 times
1:54:58.834 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:06:02.620 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2587352 times
2:06:02.620 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:06:07.557 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4263 times
2:06:07.557 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:06:11.875 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 8004 times
2:06:11.875 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:06:12.744 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 895 times
2:06:12.744 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:06:12.756 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times
2:06:12.756 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:06:12.758 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times
2:06:12.758 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:06:12.759 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:06:12.759 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:06:12.759 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:06:12.759 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:06:12.759 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:06:12.759 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:06:12.759 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:06:12.759 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:06:25.476 9G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:10:35.006 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4217716 times
2:10:35.006 9G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
2:10:35.006 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:10:38.103 9G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 45078 times
2:10:38.103 9G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:10:40.725 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 32380 times
2:10:40.725 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:12:50.068 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 281090 times
2:12:50.069 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:12:50.838 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 98 times
2:12:50.838 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:12:51.328 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:12:51.329 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:12:51.332 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10 times
2:12:51.332 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:12:51.332 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:12:51.332 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:12:51.332 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:12:51.332 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:12:51.332 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:12:51.332 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:12:53.658 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:13:05.458 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 215129 times
2:13:05.458 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
2:13:05.458 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:13:06.945 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6997 times
2:13:06.945 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:13:07.876 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 351 times
2:13:07.876 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:13:30.383 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 33330 times
2:13:30.384 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:13:30.521 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times
2:13:30.521 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:13:30.620 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:13:32.056 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:13:35.254 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 69165 times
2:13:35.254 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
2:13:35.254 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:13:36.289 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2111 times
2:13:36.289 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:13:37.079 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 41 times
2:13:37.079 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:13:47.804 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11391 times
2:13:47.805 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:13:47.866 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times
2:13:47.866 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:13:47.905 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:13:49.151 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:13:50.528 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 34449 times
2:13:50.528 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
2:13:50.528 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:13:51.483 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1009 times
2:13:51.483 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:13:52.246 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 9 times
2:13:52.247 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:13:59.172 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5683 times
2:13:59.172 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:13:59.201 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:13:59.201 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:13:59.220 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:13:59.220 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:13:59.220 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:13:59.220 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:14:00.362 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:14:01.158 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 20518 times
2:14:01.158 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
2:14:01.158 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:01.957 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 554 times
2:14:01.957 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:02.659 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 3 times
2:14:02.660 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:07.909 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3264 times
2:14:07.909 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:07.925 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:14:07.925 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:07.935 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:14:07.935 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:07.935 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:14:07.935 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:14:09.005 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:14:09.494 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13636 times
2:14:09.494 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7
2:14:09.494 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:10.285 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 371 times
2:14:10.286 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:11.027 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 3 times
2:14:11.028 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:15.545 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2096 times
2:14:15.546 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:15.556 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:14:15.556 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:15.562 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:14:15.562 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:15.562 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:14:15.562 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:14:16.499 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:14:16.837 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9822 times
2:14:16.837 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8
2:14:16.837 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:17.599 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 238 times
2:14:17.599 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:18.305 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times
2:14:18.305 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:21.975 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1422 times
2:14:21.975 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:21.982 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:14:21.982 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:21.986 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:14:21.986 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:21.986 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:14:21.986 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:14:22.948 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:14:23.202 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7392 times
2:14:23.202 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9
2:14:23.202 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:23.974 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 186 times
2:14:23.975 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:24.697 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 3 times
2:14:24.697 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:27.988 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1068 times
2:14:27.988 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:27.993 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:14:27.993 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:27.995 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:14:27.995 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:27.995 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:14:27.995 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:14:28.895 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:14:29.094 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5723 times
2:14:29.094 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10
2:14:29.094 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:29.845 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 152 times
2:14:29.846 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:30.596 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times
2:14:30.597 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:33.800 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 760 times
2:14:33.800 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:33.804 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:14:33.804 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:33.806 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:14:33.806 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:33.806 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:14:33.806 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:14:34.600 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:14:34.750 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4612 times
2:14:34.750 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11
2:14:34.750 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:35.469 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 122 times
2:14:35.470 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:36.253 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times
2:14:36.254 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:39.345 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 654 times
2:14:39.345 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:39.348 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:14:39.348 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:39.349 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:14:39.349 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:39.349 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:14:39.349 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:14:40.057 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:14:40.059 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 30 times
2:14:40.060 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12
2:14:40.060 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:40.061 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:14:40.061 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:40.061 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:14:40.061 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4 times
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:14:40.085 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
2:14:40.085 8G / 18G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 13
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
2:14:40.085 8G / 18G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
2:14:40.085 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
2:14:40.086 8G / 18G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup
2:14:40.086 8G / 18G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification
2:14:40.086 8G / 18G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled
2:14:40.086 8G / 18G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled
2:14:40.086 8G / 18G INFO General (graph_simplification.hpp : 641) Creating parallel br instance
2:14:40.086 8G / 18G INFO General (graph_simplification.hpp : 641) Creating parallel br instance
2:14:40.086 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover
2:14:42.043 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 39449 times
2:14:42.043 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
2:14:46.700 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 102416 times
2:14:46.700 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
2:15:30.839 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 2863 times
2:15:30.839 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:15:31.871 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 290 times
2:15:31.871 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
2:15:34.200 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 72560 times
2:15:34.200 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:15:36.759 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2838 times
2:15:36.759 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
2:15:38.557 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
2:15:38.557 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
2:15:39.450 8G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 10343 times
2:15:39.450 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover
2:15:40.462 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 3253 times
2:15:40.462 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
2:15:41.394 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 351 times
2:15:41.394 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
2:16:24.555 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 85 times
2:16:24.555 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:16:25.841 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6 times
2:16:25.841 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
2:16:26.596 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 403 times
2:16:26.596 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:16:28.272 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 108 times
2:16:28.272 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
2:16:29.893 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
2:16:29.893 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
2:16:30.785 8G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 84 times
2:16:30.785 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover
2:16:30.789 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 19 times
2:16:30.789 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
2:16:31.749 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 28 times
2:16:31.749 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
2:17:14.681 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 1 times
2:17:14.681 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:17:14.690 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:17:14.691 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
2:17:14.695 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 2 times
2:17:14.702 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:17:14.708 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times
2:17:14.708 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
2:17:14.710 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
2:17:14.710 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
2:17:14.710 8G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times
2:17:14.710 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover
2:17:14.710 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times
2:17:14.710 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
2:17:15.874 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
2:17:15.874 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
2:17:58.964 8G / 18G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times
2:17:58.964 8G / 18G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges
2:18:11.682 8G / 18G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges
2:18:38.104 6G / 18G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 3493947 times
2:18:38.104 6G / 18G INFO General (simplification.cpp : 470) Counting average coverage
2:18:39.296 6G / 18G INFO General (simplification.cpp : 476) Average coverage = 555.924
2:18:39.296 6G / 18G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
2:18:39.297 6G / 18G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades_alldata/output//K29/simplified_contigs.fasta
2:18:44.430 6G / 18G INFO General (launch.hpp : 151) SPAdes finished
2:18:55.101 128M / 18G INFO General (main.cpp : 109) Assembling time: 2 hours 18 minutes 55 seconds
Max read length detected as 391
== Running assembler: K49
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades_alldata/output/K49/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades_alldata/output/K49/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /DATA/markop/Pcitri_rnaspades_alldata/output/K49/configs/rna_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 245 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 87) Starting SPAdes, built from refs/heads/spades_3.13.1, git revision 9a9d54db2ff9abaac718155bf74c12ec9464e8ca
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_alldata/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 : 52) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0
0:00:00.000 4M / 4M INFO General (launch.hpp : 77) 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
0:00:00.004 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.006 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected
0:00:00.008 4M / 4M INFO General (construction.cpp : 111) Max read length 391
0:00:00.008 4M / 4M INFO General (construction.cpp : 117) Average read length 125.802
0:00:00.008 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting
0:00:00.008 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 1024 files using 32 threads. This might take a while.
0:00:00.009 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 65535
0:00:00.009 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.55204 Gb
0:00:00.009 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 32768
0:00:07.895 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 7971480 reads
0:00:14.772 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 14482628 reads
0:00:21.200 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 21734290 reads
0:00:25.134 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 26357877 reads
0:00:32.219 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 34054493 reads
0:00:33.472 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 35310264 reads
0:00:42.525 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 44793396 reads
0:00:51.433 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 53999060 reads
0:00:57.563 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 60705444 reads
0:01:03.074 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 66687887 reads
0:01:08.184 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 72449787 reads
0:01:13.726 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 78545032 reads
0:02:10.531 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 141999115 reads
0:04:08.197 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 271352186 reads
0:08:16.748 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 542135061 reads
0:10:48.454 17G / 18G INFO General (kmer_splitters.hpp : 289) Processed 1269391433 reads
0:14:50.794 17G / 18G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K
0:15:18.573 132M / 18G INFO General (kmer_splitters.hpp : 308) Used 1813575876 reads
0:15:18.573 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:15:42.979 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 617444092 kmers in total.
0:15:42.979 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:15:51.983 128M / 18G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction
0:15:51.983 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:15:51.983 128M / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
0:15:51.983 128M / 18G INFO General (file_limit.hpp : 32) Open file limit set to 65535
0:15:51.983 128M / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.55078 Gb
0:15:51.983 128M / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536
0:15:52.660 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 5250261 kmers
0:15:53.232 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 11023339 kmers
0:15:53.794 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 16798354 kmers
0:15:54.464 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 24529663 kmers
0:15:55.024 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 30313467 kmers
0:15:55.577 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 36086979 kmers
0:15:56.248 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 43821814 kmers
0:15:56.912 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 49602479 kmers
0:15:57.509 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 55378789 kmers
0:15:58.204 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 63118015 kmers
0:15:58.800 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 68897240 kmers
0:15:59.413 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 74667674 kmers
0:16:00.117 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 82418338 kmers
0:16:00.686 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 88197958 kmers
0:16:01.310 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 93968465 kmers
0:16:01.976 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 101722867 kmers
0:16:02.593 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 107507169 kmers
0:16:06.668 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 140317401 kmers
0:16:20.919 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 275378121 kmers
0:16:48.335 17G / 18G INFO General (kmer_splitters.hpp : 380) Processed 537768180 kmers
0:16:57.415 17G / 18G INFO General (kmer_splitters.hpp : 385) Used 617447164 kmers.
0:16:57.659 132M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:17:10.880 132M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 619557437 kmers in total.
0:17:10.881 132M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:17:20.061 132M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:17:45.180 456M / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
0:19:45.799 456M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 287307272 bytes occupied (3.70984 bits per kmer).
0:19:46.300 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
0:20:16.332 1G / 18G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
0:20:16.336 1G / 18G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph
0:20:16.384 1G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths
0:21:02.555 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 29257634 sequences extracted
0:21:24.651 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops
0:21:36.857 2G / 18G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 181 loops collected
0:21:56.563 10G / 18G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM)
0:21:56.563 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:21:56.563 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:22:15.216 10G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 286355778 bytes occupied (3.71021 bits per kmer).
0:22:16.662 12G / 18G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while.
0:36:51.163 12G / 18G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM
0:37:11.492 12G / 18G INFO General (construction.cpp : 464) Processed 32000000 edges
0:37:26.230 12G / 18G INFO General (construction.cpp : 464) Processed 58515078 edges
0:37:29.090 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding
0:38:27.039 9G / 18G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 39
0:38:27.043 9G / 18G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 113.812
0:38:27.043 9G / 18G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 1070
0:38:27.862 9G / 18G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 113.812
0:38:27.862 9G / 18G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0
0:38:27.862 9G / 18G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
0:38:27.862 9G / 18G INFO General (graph_pack.hpp : 101) Index refill
0:38:27.862 9G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:38:27.862 9G / 18G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
0:38:27.863 9G / 18G INFO General (file_limit.hpp : 32) Open file limit set to 65535
0:38:27.863 9G / 18G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.45479 Gb
0:38:27.863 9G / 18G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536
0:38:46.674 26G / 27G INFO General (edge_index_builders.hpp : 77) Processed 58515078 edges
0:38:46.675 26G / 27G INFO General (edge_index_builders.hpp : 82) Used 58515078 sequences.
0:38:47.608 9G / 27G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
0:38:52.599 9G / 27G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 617444092 kmers in total.
0:38:52.599 9G / 27G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
0:39:01.983 9G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
0:39:29.459 9G / 27G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
0:41:26.701 9G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 286318272 bytes occupied (3.70972 bits per kmer).
0:41:34.686 23G / 27G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
0:41:59.969 23G / 27G INFO General (edge_index.hpp : 92) Index refilled
0:41:59.971 23G / 27G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:43:04.022 26G / 27G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:44:17.568 26G / 27G INFO General (gap_closer.cpp : 138) Used 47754126 paired reads
0:44:17.568 26G / 27G INFO General (gap_closer.cpp : 140) Merging paired indices
0:44:29.699 23G / 27G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:46:30.754 23G / 27G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 8641 gaps after checking 99864 candidates
0:46:37.744 23G / 27G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:47:36.497 26G / 27G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:48:00.495 26G / 27G INFO General (gap_closer.cpp : 138) Used 139945158 paired reads
0:48:00.495 26G / 27G INFO General (gap_closer.cpp : 140) Merging paired indices
0:48:12.969 23G / 27G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:50:12.357 23G / 27G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 13500 gaps after checking 163550 candidates
0:50:20.626 23G / 27G INFO General (gap_closer.cpp : 159) Preparing shift maps
0:51:20.225 26G / 27G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
0:51:43.112 26G / 27G INFO General (gap_closer.cpp : 138) Used 31883074 paired reads
0:51:43.112 26G / 27G INFO General (gap_closer.cpp : 140) Merging paired indices
0:51:55.118 23G / 27G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
0:53:54.990 23G / 27G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 13488 gaps after checking 151850 candidates
0:54:03.249 23G / 27G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification
0:54:04.601 9G / 27G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
0:54:04.601 9G / 27G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled
0:54:04.601 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
0:54:07.371 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times
0:54:07.371 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges
0:54:07.371 9G / 27G INFO General (simplification.cpp : 76) Removing short polyAT
0:55:01.566 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 136494 times
0:55:01.566 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges
0:55:03.921 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times
0:55:03.921 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
0:55:54.413 9G / 27G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 4360105 times
0:55:54.413 9G / 27G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections
0:57:30.069 9G / 27G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 17/1578/86
0:57:30.070 9G / 27G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 0/145/434
0:57:30.576 9G / 27G INFO StageManager (stage.cpp : 132) STAGE == Simplification
0:57:30.576 9G / 27G INFO General (simplification.cpp : 357) Graph simplification started
0:57:30.576 9G / 27G INFO General (graph_simplification.hpp : 641) Creating parallel br instance
0:57:30.576 9G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
0:57:30.576 9G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1
0:57:30.576 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
0:58:42.610 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4468812 times
0:58:42.610 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
0:59:00.211 9G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1004507 times
0:59:00.211 9G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:12:51.383 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1605502 times
1:12:51.383 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:12:54.867 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2828 times
1:12:54.867 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:12:56.727 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 5146 times
1:12:56.728 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:12:57.722 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 686 times
1:12:57.722 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:12:57.729 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times
1:12:57.729 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:12:57.731 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times
1:12:57.731 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:12:57.732 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times
1:12:57.732 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:12:57.732 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:12:57.732 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:12:57.732 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:12:57.732 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:12:57.732 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:12:57.732 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:13:02.677 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:14:48.152 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1465614 times
1:14:48.152 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2
1:14:48.152 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:14:51.290 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 41549 times
1:14:51.290 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:14:53.747 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 30879 times
1:14:53.747 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:16:22.655 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 113271 times
1:16:22.656 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:16:23.052 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 83 times
1:16:23.052 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:16:23.294 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:16:23.294 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:16:23.303 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8 times
1:16:23.303 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:16:23.303 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:16:23.303 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:16:23.303 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:16:23.303 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:16:23.303 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:16:23.303 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:16:25.032 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:16:29.235 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 71200 times
1:16:29.236 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3
1:16:29.236 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:16:30.530 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6085 times
1:16:30.530 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:16:31.298 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 774 times
1:16:31.298 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:16:44.110 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 12180 times
1:16:44.110 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:16:44.166 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times
1:16:44.166 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:16:44.209 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:16:45.434 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:16:46.578 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 22934 times
1:16:46.578 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4
1:16:46.578 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:16:47.611 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1697 times
1:16:47.611 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:16:48.374 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 87 times
1:16:48.374 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:16:54.554 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4011 times
1:16:54.554 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:16:54.573 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times
1:16:54.573 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:16:54.588 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:16:55.489 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:16:56.014 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11346 times
1:16:56.015 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5
1:16:56.015 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:16:57.001 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 707 times
1:16:57.001 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:16:57.809 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 11 times
1:16:57.809 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:02.261 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1819 times
1:17:02.261 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:02.271 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:17:02.271 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:02.278 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:02.278 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:02.278 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:17:02.278 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:17:03.100 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:17:03.389 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6983 times
1:17:03.389 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6
1:17:03.389 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:04.137 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 397 times
1:17:04.137 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:04.813 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 6 times
1:17:04.814 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:08.155 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1113 times
1:17:08.155 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:08.162 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:17:08.162 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:08.166 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:08.166 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:08.166 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:17:08.166 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:17:09.197 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:17:09.401 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4735 times
1:17:09.401 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7
1:17:09.401 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:10.193 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 240 times
1:17:10.193 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:10.929 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 2 times
1:17:10.929 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:13.750 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 694 times
1:17:13.750 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:13.754 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:17:13.754 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:13.756 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:13.756 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:13.756 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:17:13.756 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:17:14.474 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:17:14.610 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3443 times
1:17:14.610 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8
1:17:14.610 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:15.350 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 148 times
1:17:15.351 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:16.059 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 1 times
1:17:16.059 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:19.131 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 514 times
1:17:19.131 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:19.135 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:17:19.135 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:19.137 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:19.137 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:19.137 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:17:19.137 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:17:20.030 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:17:20.136 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2519 times
1:17:20.136 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9
1:17:20.136 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:20.951 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 105 times
1:17:20.952 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:21.660 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:21.661 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:23.994 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 337 times
1:17:23.994 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:23.995 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:17:23.995 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:23.997 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:23.997 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:23.997 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:17:23.997 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:17:24.635 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:17:24.723 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2081 times
1:17:24.723 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10
1:17:24.723 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:25.428 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 76 times
1:17:25.428 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:26.114 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:26.115 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:28.714 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 257 times
1:17:28.714 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:28.716 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:17:28.716 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:28.717 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:28.717 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:28.717 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:17:28.717 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:17:29.548 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:17:29.624 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1637 times
1:17:29.624 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11
1:17:29.624 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:30.390 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 68 times
1:17:30.391 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:31.144 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:31.144 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:33.495 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 217 times
1:17:33.495 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:33.496 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:17:33.496 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:33.497 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:33.497 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:33.497 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:17:33.497 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:17:34.166 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:17:34.167 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times
1:17:34.168 16G / 27G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 12
1:17:34.168 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:17:34.168 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:17:34.169 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper
1:17:34.169 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times
1:17:34.169 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:17:34.170 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:17:34.170 16G / 27G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
1:17:34.170 16G / 27G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1
1:17:34.171 16G / 27G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
1:17:34.171 16G / 27G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer
1:17:34.172 16G / 27G INFO General (graph_pack.hpp : 101) Index refill
1:17:34.172 16G / 27G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
1:17:34.172 16G / 27G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
1:17:34.173 16G / 27G INFO General (file_limit.hpp : 32) Open file limit set to 65535
1:17:34.174 16G / 27G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.3761 Gb
1:17:34.174 16G / 27G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536
1:17:42.339 34G / 34G INFO General (edge_index_builders.hpp : 77) Processed 7783244 edges
1:17:42.340 34G / 34G INFO General (edge_index_builders.hpp : 82) Used 7783244 sequences.
1:17:42.856 16G / 34G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
1:17:45.781 16G / 34G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 316973855 kmers in total.
1:17:45.781 16G / 34G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
1:17:50.356 16G / 34G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
1:18:01.506 17G / 34G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
1:18:50.184 17G / 34G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 146996044 bytes occupied (3.70999 bits per kmer).
1:18:56.453 24G / 34G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
1:19:06.749 24G / 34G INFO General (edge_index.hpp : 92) Index refilled
1:19:06.750 24G / 34G INFO General (gap_closer.cpp : 159) Preparing shift maps
1:19:22.000 25G / 34G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
1:20:33.517 25G / 34G INFO General (gap_closer.cpp : 138) Used 47754126 paired reads
1:20:33.518 25G / 34G INFO General (gap_closer.cpp : 140) Merging paired indices
1:20:37.566 24G / 34G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
1:20:55.304 24G / 34G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 2143 gaps after checking 50647 candidates
1:21:00.778 24G / 34G INFO General (gap_closer.cpp : 159) Preparing shift maps
1:21:14.754 25G / 34G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
1:21:42.045 25G / 34G INFO General (gap_closer.cpp : 138) Used 139945158 paired reads
1:21:42.046 25G / 34G INFO General (gap_closer.cpp : 140) Merging paired indices
1:21:45.286 24G / 34G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
1:22:05.397 24G / 34G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 2826 gaps after checking 53611 candidates
1:22:08.627 24G / 34G INFO General (gap_closer.cpp : 159) Preparing shift maps
1:22:26.540 25G / 34G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while)
1:22:48.976 25G / 34G INFO General (gap_closer.cpp : 138) Used 31883074 paired reads
1:22:48.976 25G / 34G INFO General (gap_closer.cpp : 140) Merging paired indices
1:22:53.359 24G / 34G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps
1:23:11.965 24G / 34G INFO GapCloser (gap_closer.cpp : 380) Closing short gaps complete: filled 2110 gaps after checking 137173 candidates
1:23:15.562 24G / 34G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup
1:23:15.562 24G / 34G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification
1:23:15.562 24G / 34G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled
1:23:15.562 24G / 34G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled
1:23:15.562 24G / 34G INFO General (graph_simplification.hpp : 641) Creating parallel br instance
1:23:15.562 24G / 34G INFO General (graph_simplification.hpp : 641) Creating parallel br instance
1:23:15.562 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover
1:23:19.016 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 5655 times
1:23:19.016 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:24:55.420 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 197764 times
1:24:55.420 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
1:25:49.247 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 6256 times
1:25:49.248 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:25:50.496 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 313 times
1:25:50.496 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
1:26:57.095 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 94437 times
1:26:57.095 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:27:07.905 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3699 times
1:27:07.905 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
1:27:09.764 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
1:27:09.764 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
1:27:10.708 24G / 34G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 1521 times
1:27:10.708 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover
1:27:12.369 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 1310 times
1:27:12.369 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:27:13.537 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 261 times
1:27:13.537 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
1:27:47.491 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 295 times
1:27:47.491 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:27:48.561 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5 times
1:27:48.562 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
1:27:49.566 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 386 times
1:27:49.566 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:27:51.309 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 120 times
1:27:51.309 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
1:27:52.587 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
1:27:52.587 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
1:27:53.268 24G / 34G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 6 times
1:27:53.269 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover
1:27:53.275 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 4 times
1:27:53.275 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:27:53.923 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 3 times
1:27:53.923 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
1:28:25.499 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 4 times
1:28:25.499 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:28:25.503 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:28:25.503 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
1:28:25.509 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 4 times
1:28:25.509 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:28:25.519 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times
1:28:25.519 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
1:28:25.521 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
1:28:25.521 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
1:28:25.521 24G / 34G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times
1:28:25.521 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover
1:28:25.521 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times
1:28:25.521 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover
1:28:26.614 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times
1:28:26.615 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover
1:28:58.845 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times
1:28:58.845 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
1:28:58.845 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
1:28:58.845 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper
1:28:58.845 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times
1:28:58.845 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
1:28:58.846 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
1:28:58.846 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover
1:28:58.846 24G / 34G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times
1:28:58.846 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips
1:28:58.846 24G / 34G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times
1:28:58.846 24G / 34G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges
1:29:09.863 24G / 34G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges
1:31:46.630 23G / 34G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 2632468 times
1:31:46.631 23G / 34G INFO General (simplification.cpp : 470) Counting average coverage
1:31:48.561 23G / 34G INFO General (simplification.cpp : 476) Average coverage = 439.681
1:31:48.561 23G / 34G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction
1:31:48.561 23G / 34G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 177776507 kmers to process
1:35:02.538 23G / 34G INFO General (graph_pack.hpp : 111) Normalizing done
2:14:51.311 111G / 111G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions
2:21:00.735 26G / 111G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed
2:21:09.670 23G / 111G INFO General (mismatch_correction.cpp : 27) Corrected 19398 nucleotides
2:21:09.675 23G / 111G INFO StageManager (stage.cpp : 132) STAGE == Strand-specific Edge Spliting
2:21:09.675 23G / 111G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 178881615 kmers to process
2:24:09.284 23G / 111G INFO General (graph_pack.hpp : 111) Normalizing done
2:24:09.284 23G / 111G INFO General (ss_edge_split.cpp : 38) Running strand-specific edge splitter only for library # 0
2:24:11.029 23G / 111G INFO General (ss_edge_split.cpp : 46) Selecting usual mapper
2:24:41.246 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:24:41.403 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:24:41.516 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:24:41.625 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:24:41.734 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:24:41.846 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:24:42.483 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:24:43.999 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:24:48.529 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:24:58.630 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:25:17.737 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
2:25:52.651 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
2:26:59.913 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 134400000 reads
2:29:13.330 24G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 268600000 reads
2:30:57.835 24G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 379387101 reads processed
2:30:59.548 17G / 111G INFO SSCoverage (ss_coverage.hpp : 292) Detecting split positions
2:30:59.652 17G / 111G INFO SSCoverage (ss_coverage.hpp : 302) Splitting edges
2:30:59.688 17G / 111G INFO SSCoverage (ss_coverage.hpp : 306) Total edges splits performed 2166
2:31:03.182 16G / 111G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
2:31:03.188 16G / 111G INFO General (contig_output_stage.cpp : 45) Writing GFA to /DATA/markop/Pcitri_rnaspades_alldata/output//K49/assembly_graph_with_scaffolds.gfa
2:31:08.138 16G / 111G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades_alldata/output//K49/before_rr.fasta
2:31:12.935 16G / 111G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /DATA/markop/Pcitri_rnaspades_alldata/output//K49/assembly_graph.fastg
2:31:27.181 16G / 111G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades_alldata/output//K49/final_contigs.fasta
2:31:31.539 16G / 111G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting
2:31:45.894 16G / 111G INFO General (graph_pack.hpp : 101) Index refill
2:31:45.894 16G / 111G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
2:31:45.894 16G / 111G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
2:31:45.895 16G / 111G INFO General (file_limit.hpp : 32) Open file limit set to 65535
2:31:45.895 16G / 111G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.38037 Gb
2:31:45.895 16G / 111G INFO General (kmer_splitters.hpp : 97) Using cell size of 65536
2:31:49.809 34G / 111G INFO General (edge_index_builders.hpp : 77) Processed 1208220 edges
2:31:49.809 34G / 111G INFO General (edge_index_builders.hpp : 82) Used 1208220 sequences.
2:31:50.111 16G / 111G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
2:31:52.204 16G / 111G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 157521861 kmers in total.
2:31:52.204 16G / 111G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
2:31:54.565 16G / 111G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
2:32:00.091 16G / 111G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
2:32:14.523 16G / 111G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 73051112 bytes occupied (3.71002 bits per kmer).
2:32:17.126 20G / 111G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.
2:32:22.161 20G / 111G INFO General (edge_index.hpp : 92) Index refilled
2:32:22.161 20G / 111G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 178881615 kmers to process
2:32:22.161 20G / 111G INFO General (graph_pack.hpp : 111) Normalizing done
2:32:22.892 20G / 111G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 719
2:32:22.892 20G / 111G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0
2:32:22.892 20G / 111G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)
2:32:23.253 20G / 111G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
2:32:33.704 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:32:33.774 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:32:33.836 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:32:33.898 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:32:33.961 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:32:33.999 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:32:34.290 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:32:34.784 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:32:44.572 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:32:55.891 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:33:25.587 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
2:33:45.409 20G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 47754126 reads processed
2:33:47.007 20G / 111G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit)
2:33:47.007 20G / 111G INFO General (pair_info_count.cpp : 213) 7722858 paired reads (16.1721% of all) aligned to long edges
2:33:47.050 20G / 111G INFO General (pair_info_count.cpp : 357) Insert size = 385.829, deviation = 124.99, left quantile = 199, right quantile = 530, read length = 391
2:33:47.050 20G / 111G WARN General (pair_info_count.cpp : 361) Estimated mean insert size 385.829 is very small compared to read length 391
2:33:47.050 20G / 111G INFO General (pair_info_count.cpp : 386) Mapping library #0
2:33:47.050 20G / 111G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while)
2:33:47.050 20G / 111G INFO General (pair_info_count.cpp : 289) Left insert size quantile 199, right insert size quantile 530, filtering threshold 0, rounding threshold 0
2:33:47.059 20G / 111G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
2:34:20.946 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:34:20.950 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:34:21.024 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:34:21.037 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:34:21.079 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:34:21.233 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:34:21.991 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:34:23.661 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:34:54.279 20G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:35:37.538 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:38:11.000 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
2:39:49.507 21G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 47754126 reads processed
2:39:49.795 21G / 111G INFO General (pair_info_count.cpp : 395) Mapping single reads of library #0
2:39:49.795 21G / 111G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well
2:39:49.795 21G / 111G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
2:39:56.007 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:39:56.024 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:39:56.040 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:39:56.054 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:39:56.072 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:39:56.084 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:39:56.151 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:39:56.355 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:40:02.515 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:40:09.115 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:40:28.028 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
2:41:00.060 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
2:42:03.243 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 134400000 reads
2:44:15.692 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 268600000 reads
2:45:52.994 21G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 379387101 reads processed
2:45:53.245 21G / 111G INFO General (pair_info_count.cpp : 397) Total paths obtained from single reads: 0
2:45:53.245 21G / 111G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #1
2:45:53.245 21G / 111G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)
2:45:53.607 22G / 111G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
2:45:57.623 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:45:57.670 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:45:57.704 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:45:57.750 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:45:57.799 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:45:57.835 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:45:58.083 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:45:58.499 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:46:01.083 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:46:05.769 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:46:15.784 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
2:46:35.504 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
2:47:13.722 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 134400000 reads
2:47:17.192 22G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 139945158 reads processed
2:47:18.804 22G / 111G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit)
2:47:18.804 22G / 111G INFO General (pair_info_count.cpp : 213) 23517933 paired reads (16.8051% of all) aligned to long edges
2:47:18.857 21G / 111G INFO General (pair_info_count.cpp : 357) Insert size = 164.579, deviation = 46.9004, left quantile = 113, right quantile = 228, read length = 91
2:47:18.857 21G / 111G INFO General (pair_info_count.cpp : 386) Mapping library #1
2:47:18.857 21G / 111G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while)
2:47:18.857 21G / 111G INFO General (pair_info_count.cpp : 289) Left insert size quantile 113, right insert size quantile 228, filtering threshold 0, rounding threshold 0
2:47:18.866 21G / 111G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
2:47:23.217 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:47:23.218 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:47:23.218 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:47:23.218 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:47:23.218 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:47:23.219 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:47:23.219 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:47:23.220 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:47:27.491 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:47:31.635 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:47:44.483 21G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
2:48:05.421 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
2:48:46.450 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 134400000 reads
2:48:49.788 22G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 139945158 reads processed
2:48:50.026 22G / 111G INFO General (pair_info_count.cpp : 395) Mapping single reads of library #1
2:48:50.026 22G / 111G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well
2:48:50.026 22G / 111G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
2:48:53.877 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:48:53.900 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:48:53.923 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:48:53.945 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:48:53.967 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:48:53.985 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:48:54.137 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:48:54.441 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:48:57.479 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:49:02.016 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:49:13.031 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
2:49:33.056 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
2:50:12.890 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 134400000 reads
2:51:34.426 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 268600000 reads
2:51:49.346 22G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 293363170 reads processed
2:51:49.567 22G / 111G INFO General (pair_info_count.cpp : 397) Total paths obtained from single reads: 0
2:51:49.567 22G / 111G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #2
2:51:49.567 22G / 111G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)
2:51:49.955 22G / 111G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
2:51:54.982 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:51:55.040 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:51:55.096 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:51:55.135 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:51:55.168 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:51:55.193 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:51:55.361 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:51:55.873 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:52:00.387 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:52:06.245 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:52:18.024 22G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 31883074 reads processed
2:52:19.627 22G / 111G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit)
2:52:19.628 22G / 111G INFO General (pair_info_count.cpp : 213) 5781026 paired reads (18.132% of all) aligned to long edges
2:52:19.671 22G / 111G INFO General (pair_info_count.cpp : 357) Insert size = 251.904, deviation = 63.6816, left quantile = 165, right quantile = 326, read length = 241
2:52:19.671 22G / 111G WARN General (pair_info_count.cpp : 361) Estimated mean insert size 251.904 is very small compared to read length 241
2:52:19.671 22G / 111G INFO General (pair_info_count.cpp : 386) Mapping library #2
2:52:19.671 22G / 111G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while)
2:52:19.671 22G / 111G INFO General (pair_info_count.cpp : 289) Left insert size quantile 165, right insert size quantile 326, filtering threshold 0, rounding threshold 0
2:52:19.681 22G / 111G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
2:52:25.240 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:52:25.246 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:52:25.248 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:52:25.254 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:52:25.254 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:52:25.261 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:52:25.270 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:52:25.370 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:52:30.908 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:52:36.744 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:52:48.774 22G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 31883074 reads processed
2:52:49.035 22G / 111G INFO General (pair_info_count.cpp : 395) Mapping single reads of library #2
2:52:49.035 22G / 111G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well
2:52:49.035 22G / 111G INFO General (pair_info_count.cpp : 39) Selecting usual mapper
2:52:54.159 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 200000 reads
2:52:54.189 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 400000 reads
2:52:54.213 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 600000 reads
2:52:54.224 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 800000 reads
2:52:54.237 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1000000 reads
2:52:54.255 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 1200000 reads
2:52:54.352 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 2200000 reads
2:52:54.576 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 4200000 reads
2:52:59.413 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 8400000 reads
2:53:04.876 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 16800000 reads
2:53:19.945 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 33600000 reads
2:53:45.948 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 67200000 reads
2:54:37.827 22G / 111G INFO General (sequence_mapper_notifier.h: 80) Processed 134400000 reads
2:55:41.679 22G / 111G INFO General (sequence_mapper_notifier.h: 98) Total 234037667 reads processed
2:55:41.795 22G / 111G INFO General (pair_info_count.cpp : 397) Total paths obtained from single reads: 0
2:55:41.795 22G / 111G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation
2:55:41.795 22G / 111G INFO General (distance_estimation.cpp : 173) Processing library #0
2:55:41.795 22G / 111G INFO General (distance_estimation.cpp : 149) Weight Filter Done
2:55:41.801 22G / 111G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator
2:59:24.697 23G / 111G INFO General (distance_estimation.cpp : 34) Filtering info
2:59:24.697 23G / 111G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 68682816
2:59:51.290 23G / 111G INFO General (pair_info_filters.hpp : 263) Done filtering
2:59:51.306 23G / 111G INFO General (distance_estimation.cpp : 156) Refining clustered pair information
2:59:53.915 23G / 111G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished
2:59:53.915 23G / 111G INFO General (distance_estimation.cpp : 160) Improving paired information
3:00:31.518 23G / 111G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 2380516; contradictional = 302
3:01:26.480 24G / 111G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 700447; contradictional = 12
3:01:26.480 24G / 111G INFO General (distance_estimation.cpp : 173) Processing library #1
3:01:26.480 24G / 111G INFO General (distance_estimation.cpp : 149) Weight Filter Done
3:01:26.480 24G / 111G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator
3:01:32.523 24G / 111G INFO General (distance_estimation.cpp : 34) Filtering info
3:01:32.523 24G / 111G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2285798
3:01:34.960 24G / 111G INFO General (pair_info_filters.hpp : 263) Done filtering
3:01:34.964 24G / 111G INFO General (distance_estimation.cpp : 156) Refining clustered pair information
3:01:35.527 24G / 111G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished
3:01:35.527 24G / 111G INFO General (distance_estimation.cpp : 160) Improving paired information
3:01:40.677 24G / 111G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 206158; contradictional = 62
3:01:49.580 24G / 111G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 142882; contradictional = 0
3:01:49.580 24G / 111G INFO General (distance_estimation.cpp : 173) Processing library #2
3:01:49.580 24G / 111G INFO General (distance_estimation.cpp : 149) Weight Filter Done
3:01:49.580 24G / 111G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator
3:02:11.669 24G / 111G INFO General (distance_estimation.cpp : 34) Filtering info
3:02:11.669 24G / 111G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 4895127
3:02:15.318 24G / 111G INFO General (pair_info_filters.hpp : 263) Done filtering
3:02:15.324 24G / 111G INFO General (distance_estimation.cpp : 156) Refining clustered pair information
3:02:16.132 24G / 111G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished
3:02:16.132 24G / 111G INFO General (distance_estimation.cpp : 160) Improving paired information
3:02:27.481 24G / 111G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 643408; contradictional = 92
3:02:42.495 24G / 111G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 212163; contradictional = 8
3:02:42.495 24G / 111G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving
3:05:09.145 24G / 111G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving
3:05:09.151 24G / 111G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started
3:05:14.507 26G / 111G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000
3:05:18.406 26G / 111G INFO General (extenders_logic.cpp : 475) Using 3 paired-end libraries
3:05:18.406 26G / 111G INFO General (extenders_logic.cpp : 476) Using 3 paired-end scaffolding libraries
3:05:18.406 26G / 111G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries
3:05:18.406 26G / 111G INFO General (launcher.cpp : 420) Total number of extenders is 15
3:05:18.406 26G / 111G INFO General (path_extender.hpp : 885) Processed 0 paths from 600043 (0%)
3:05:19.079 26G / 111G INFO General (path_extender.hpp : 883) Processed 128 paths from 600043 (0%)
3:05:19.606 26G / 111G INFO General (path_extender.hpp : 883) Processed 256 paths from 600043 (0%)
3:05:20.669 26G / 111G INFO General (path_extender.hpp : 883) Processed 512 paths from 600043 (0%)
3:05:23.579 26G / 111G INFO General (path_extender.hpp : 883) Processed 1024 paths from 600043 (0%)
3:05:27.602 26G / 111G INFO General (path_extender.hpp : 883) Processed 2048 paths from 600043 (0%)
3:05:35.313 26G / 111G INFO General (path_extender.hpp : 883) Processed 4096 paths from 600043 (0%)
3:05:55.294 26G / 111G INFO General (path_extender.hpp : 883) Processed 8192 paths from 600043 (1%)
3:06:17.254 26G / 111G INFO General (path_extender.hpp : 883) Processed 16384 paths from 600043 (2%)
3:06:55.726 27G / 111G INFO General (path_extender.hpp : 883) Processed 32768 paths from 600043 (5%)
3:07:43.416 27G / 111G INFO General (path_extender.hpp : 885) Processed 60005 paths from 600043 (10%)
3:07:51.560 27G / 111G INFO General (path_extender.hpp : 883) Processed 65536 paths from 600043 (10%)
3:09:00.077 28G / 111G INFO General (path_extender.hpp : 885) Processed 120010 paths from 600043 (20%)
3:09:16.610 28G / 111G INFO General (path_extender.hpp : 883) Processed 131072 paths from 600043 (21%)
3:10:55.450 28G / 111G INFO General (path_extender.hpp : 885) Processed 180015 paths from 600043 (30%)
3:13:30.211 29G / 111G INFO General (path_extender.hpp : 885) Processed 240020 paths from 600043 (40%)
3:14:11.048 29G / 111G INFO General (path_extender.hpp : 883) Processed 262144 paths from 600043 (43%)
3:15:17.886 30G / 111G INFO General (path_extender.hpp : 885) Processed 300025 paths from 600043 (50%)
3:16:52.474 30G / 111G INFO General (path_extender.hpp : 885) Processed 360030 paths from 600043 (60%)
3:17:46.774 30G / 111G INFO General (path_extender.hpp : 885) Processed 420035 paths from 600043 (70%)
3:18:53.876 31G / 111G INFO General (path_extender.hpp : 885) Processed 480040 paths from 600043 (80%)
3:19:10.085 31G / 111G INFO General (path_extender.hpp : 883) Processed 524288 paths from 600043 (87%)
3:19:18.143 31G / 111G INFO General (path_extender.hpp : 885) Processed 540045 paths from 600043 (90%)
3:19:31.551 31G / 111G INFO General (launcher.cpp : 234) Finalizing paths
3:19:31.551 31G / 111G INFO General (launcher.cpp : 236) Deduplicating paths
3:19:36.958 31G / 111G INFO General (launcher.cpp : 240) Paths deduplicated
3:19:36.958 31G / 111G INFO General (launcher.cpp : 247) Overlaps will not be removed
3:19:39.418 31G / 111G INFO General (launcher.cpp : 257) Paths finalized
3:19:39.418 31G / 111G INFO General (launcher.cpp : 427) Closing gaps in paths
3:19:41.859 31G / 111G INFO General (launcher.cpp : 455) Gap closing completed
3:19:43.671 31G / 111G INFO General (launcher.cpp : 286) Traversing tandem repeats
3:19:49.600 31G / 111G INFO General (launcher.cpp : 296) Traversed 67 loops
3:19:49.600 31G / 111G INFO General (launcher.cpp : 234) Finalizing paths
3:19:49.600 31G / 111G INFO General (launcher.cpp : 236) Deduplicating paths
3:19:52.449 31G / 111G INFO General (launcher.cpp : 240) Paths deduplicated
3:19:52.449 31G / 111G INFO General (launcher.cpp : 247) Overlaps will not be removed
3:19:53.755 31G / 111G INFO General (launcher.cpp : 257) Paths finalized
3:19:53.755 31G / 111G INFO General (launcher.cpp : 525) Paths will be printed according to strand-specific coverage
3:19:54.543 31G / 111G INFO General (launcher.cpp : 466) Finalizing paths - hard
3:19:55.460 33G / 111G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 537
3:19:55.460 33G / 111G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 537
3:19:55.460 33G / 111G INFO General (launcher.cpp : 281) Length cutoff: 537
3:19:55.628 32G / 111G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 733
3:19:55.628 32G / 111G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 733
3:19:55.628 32G / 111G INFO General (launcher.cpp : 281) Length cutoff: 733
3:19:55.661 32G / 111G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 733
3:19:55.661 32G / 111G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 733
3:19:55.661 32G / 111G INFO General (launcher.cpp : 281) Length cutoff: 733
3:20:03.756 31G / 111G INFO General (launcher.cpp : 466) Finalizing paths - soft
3:20:04.662 33G / 111G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 361
3:20:04.662 33G / 111G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 361
3:20:04.662 33G / 111G INFO General (launcher.cpp : 281) Length cutoff: 361
3:20:04.811 32G / 111G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 537
3:20:04.811 32G / 111G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 537
3:20:04.811 32G / 111G INFO General (launcher.cpp : 281) Length cutoff: 537
3:20:04.854 32G / 111G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 420
3:20:04.854 32G / 111G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 420
3:20:04.854 32G / 111G INFO General (launcher.cpp : 281) Length cutoff: 420
3:20:13.945 31G / 111G INFO General (launcher.cpp : 474) Finalizing main paths
3:20:13.945 31G / 111G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 459
3:20:13.945 31G / 111G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 459
3:20:13.945 31G / 111G INFO General (launcher.cpp : 281) Length cutoff: 459
3:20:14.125 31G / 111G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 576
3:20:14.125 31G / 111G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 576
3:20:14.125 31G / 111G INFO General (launcher.cpp : 281) Length cutoff: 576
3:20:14.173 31G / 111G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 537
3:20:14.173 31G / 111G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 537
3:20:14.173 31G / 111G INFO General (launcher.cpp : 281) Length cutoff: 537
3:20:14.374 31G / 111G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished
3:20:29.160 25G / 111G INFO StageManager (stage.cpp : 132) STAGE == Contig Output
3:20:29.161 25G / 111G INFO General (contig_output_stage.cpp : 45) Writing GFA to /DATA/markop/Pcitri_rnaspades_alldata/output//K49/assembly_graph_with_scaffolds.gfa
3:20:33.657 25G / 111G INFO General (contig_output.hpp : 22) Outputting contigs to /DATA/markop/Pcitri_rnaspades_alldata/output//K49/before_rr.fasta
3:20:38.353 25G / 111G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /DATA/markop/Pcitri_rnaspades_alldata/output//K49/assembly_graph.fastg
3:20:52.899 25G / 111G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /DATA/markop/Pcitri_rnaspades_alldata/output//K49/transcripts.paths
3:21:04.766 25G / 111G INFO General (launch.hpp : 151) SPAdes finished
3:23:29.819 208M / 111G INFO General (main.cpp : 109) Assembling time: 3 hours 23 minutes 29 seconds
===== Assembling finished. Used k-mer sizes: 29, 49
* Assembled transcripts are in /DATA/markop/Pcitri_rnaspades_alldata/output/transcripts.fasta
* Paths in the assembly graph corresponding to the transcripts are in /DATA/markop/Pcitri_rnaspades_alldata/output/transcripts.paths
* Hard filtered transcripts are in /DATA/markop/Pcitri_rnaspades_alldata/output/hard_filtered_transcripts.fasta
* Soft filtered transcripts are in /DATA/markop/Pcitri_rnaspades_alldata/output/soft_filtered_transcripts.fasta
* Assembly graph is in /DATA/markop/Pcitri_rnaspades_alldata/output/assembly_graph.fastg
* Assembly graph in GFA format is in /DATA/markop/Pcitri_rnaspades_alldata/output/assembly_graph_with_scaffolds.gfa
======= SPAdes pipeline finished WITH WARNINGS!
=== Error correction and assembling warnings:
* 2:33:47.050 20G / 111G WARN General (pair_info_count.cpp : 361) Estimated mean insert size 385.829 is very small compared to read length 391
* 2:52:19.671 22G / 111G WARN General (pair_info_count.cpp : 361) Estimated mean insert size 251.904 is very small compared to read length 241
======= Warnings saved to /DATA/markop/Pcitri_rnaspades_alldata/output/warnings.log
SPAdes log can be found here: /DATA/markop/Pcitri_rnaspades_alldata/output/spades.log
Thank you for using SPAdes!
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Created: 16th May 2022 at 11:58
Last updated: 6th Nov 2024 at 15:27
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Version History
Version 1 (earliest) Created 16th May 2022 at 11:58 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
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Advanced Projects list for this Document with search and filtering
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
Advanced Studies list for this Document with search and filtering
Short Name: P4_Pcitri_tr2 Description: Study of P. citri transcriptome data from SUSPHIRE and mealybug.org RNA-Seq datasets Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T31_mealybug
Assays: _A_01_assembly2-rnaSPAdes, _A_02_assembly2-IPS, _A_03_mapAs2ToGenome-STAR, _A_04_mapReadsToAs2-STAR, _A_05_As2_tr_limmaDE-R, _S_P4_Pcitri_tr2-files
Advanced Assays list for this Document with search and filtering
Short Name: 01_assembly2-rnaSPAdes Assay Class: DRY Assay Type: rnaSPAdes Title: P citri de-novo transcriptome assembly 2 Description: P citri de-novo transcriptome assembly using SUSPHIRE and mealybug.org RNA-seq datasets pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_Pcitri_tr2
