Is this a known issue or is it just my own system?
Command line: /usr/local/bin/spades.py --meta --pe1-1 /Users/mars/Desktop/spades_single_end/fastq/R1.fastq --pe1-2 /Users/mars/Desktop/spades_single_end/fastq/R2.fastq -o /Users/mars/Desktop/spades_single_end/fastq/metaspades_output
System information:
SPAdes version: 3.10.1
Python version: 2.7.13
OS: Darwin-16.4.0-x86_64-i386-64bit
Output dir: /Users/mars/Desktop/spades_single_end/fastq/metaspades_output
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/Users/mars/Desktop/spades_single_end/fastq/R1.fastq']
right reads: ['/Users/mars/Desktop/spades_single_end/fastq/R2.fastq']
interlaced reads: not specified
single reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed (with gzip)
Assembly parameters:
k: [21, 33, 55]
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: /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/tmp
Threads: 16
Memory limit (in Gb): 250
Command line: /usr/local/bin/spades.py --meta --pe1-1 /Users/mars/Desktop/spades_single_end/fastq/R1.fastq --pe1-2 /Users/mars/Desktop/spades_single_end/fastq/R2.fastq -o /Users/mars/Desktop/spades_single_end/fastq/metaspades_output
System information:
SPAdes version: 3.10.1
Python version: 2.7.13
OS: Darwin-16.4.0-x86_64-i386-64bit
Output dir: /Users/mars/Desktop/spades_single_end/fastq/metaspades_output
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/Users/mars/Desktop/spades_single_end/fastq/R1.fastq']
right reads: ['/Users/mars/Desktop/spades_single_end/fastq/R2.fastq']
interlaced reads: not specified
single reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed (with gzip)
Assembly parameters:
k: [21, 33, 55]
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: /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/tmp
Threads: 16
Memory limit (in Gb): 250
======= SPAdes pipeline started. Log can be found here: /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/spades.log
===== Read error correction started.
== Running read error correction tool: /usr/local/Cellar/spades/3.10.1/bin/hammer /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/corrected/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 83) Starting BayesHammer, built from N/A, git revision N/A
0:00:00.000 4M / 4M INFO General (main.cpp : 84) Loading config from /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/corrected/configs/config.info
0:00:00.001 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 250 Gb
0:00:00.001 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset
0:00:00.002 4M / 4M INFO General (main.cpp : 99) Determined value is 33
0:00:00.002 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.002 4M / 4M INFO General (main.cpp : 120) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.002 4M / 4M INFO K-mer Counting (kmer_data.cpp : 282) Estimating k-mer count
0:00:00.064 132M / 132M INFO K-mer Counting (kmer_data.cpp : 287) Processing /Users/mars/Desktop/spades_single_end/fastq/R1.fastq
0:00:52.307 160M / 160M INFO K-mer Counting (kmer_data.cpp : 296) Processed 17262970 reads
0:00:52.307 160M / 160M INFO K-mer Counting (kmer_data.cpp : 287) Processing /Users/mars/Desktop/spades_single_end/fastq/R2.fastq
0:01:53.443 160M / 160M INFO K-mer Counting (kmer_data.cpp : 296) Processed 34525940 reads
0:01:53.443 160M / 160M INFO K-mer Counting (kmer_data.cpp : 301) Total 34525940 reads processed
0:01:53.814 160M / 160M INFO K-mer Counting (kmer_data.cpp : 308) Estimated 241188234 distinct kmers
0:01:53.828 32M / 160M INFO K-mer Counting (kmer_data.cpp : 313) Filtering singleton k-mers
0:01:54.150 724M / 724M INFO K-mer Counting (kmer_data.cpp : 319) Processing /Users/mars/Desktop/spades_single_end/fastq/R1.fastq
0:04:27.200 724M / 724M INFO K-mer Counting (kmer_data.cpp : 328) Processed 17262970 reads
0:04:27.200 724M / 724M INFO K-mer Counting (kmer_data.cpp : 319) Processing /Users/mars/Desktop/spades_single_end/fastq/R2.fastq
0:07:02.500 724M / 724M INFO K-mer Counting (kmer_data.cpp : 328) Processed 34525940 reads
0:07:02.500 724M / 724M INFO K-mer Counting (kmer_data.cpp : 333) Total 34525940 reads processed
0:07:02.500 724M / 724M INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index
0:07:02.500 724M / 724M INFO K-mer Splitting (kmer_data.cpp : 91) Splitting kmer instances into 128 buckets. This might take a while.
0:07:02.500 724M / 724M INFO General (file_limit.hpp : 30) Open file limit set to 256
0:07:02.500 724M / 724M INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 10.3872 Gb
0:07:02.500 724M / 724M INFO General (kmer_index_builder.hpp : 116) Using cell size of 524288
0:07:02.501 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /Users/mars/Desktop/spades_single_end/fastq/R1.fastq
0:07:44.102 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 3636514 reads
0:08:25.846 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 7281705 reads
0:09:08.302 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 10907241 reads
0:09:53.044 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 14540365 reads
0:10:31.197 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 17262970 reads
0:10:31.197 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 98) Processing /Users/mars/Desktop/spades_single_end/fastq/R2.fastq
0:10:54.579 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 19253383 reads
0:11:21.035 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 21251668 reads
0:11:46.696 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 23275865 reads
0:12:12.916 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 25323869 reads
0:12:35.470 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 27337193 reads
0:14:15.936 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 108) Processed 34525940 reads
0:14:15.936 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 113) Total 34525940 reads processed
0:14:16.584 724M / 8G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting.
0:14:32.137 724M / 8G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 49672548 kmers in total.
0:14:32.138 724M / 8G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets.
0:14:32.570 724M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices
0:14:37.942 724M / 8G INFO General (kmer_index_builder.hpp : 276) Merging final buckets.
0:14:38.326 724M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 16229096 bytes occupied (2.61377 bits per kmer).
0:14:38.390 32M / 8G INFO K-mer Counting (kmer_data.cpp : 359) Arranging kmers in hash map order
0:14:43.033 792M / 8G INFO General (main.cpp : 155) Clustering Hamming graph.
0:17:16.522 792M / 8G INFO General (main.cpp : 162) Extracting clusters
0:17:41.626 792M / 8G INFO General (main.cpp : 174) Clustering done. Total clusters: 12605166
0:17:41.668 412M / 8G INFO K-mer Counting (kmer_data.cpp : 381) Collecting K-mer information, this takes a while.
0:17:42.425 1G / 8G INFO K-mer Counting (kmer_data.cpp : 387) Processing /Users/mars/Desktop/spades_single_end/fastq/R1.fastq
0:25:28.606 1G / 8G INFO K-mer Counting (kmer_data.cpp : 387) Processing /Users/mars/Desktop/spades_single_end/fastq/R2.fastq
0:31:56.721 1G / 8G INFO K-mer Counting (kmer_data.cpp : 394) Collection done, postprocessing.
0:31:57.263 1G / 8G INFO K-mer Counting (kmer_data.cpp : 408) There are 49672548 kmers in total. Among them 2096018 (4.21967%) are singletons.
0:31:57.264 1G / 8G INFO General (main.cpp : 180) Subclustering Hamming graph
0:33:17.836 1G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 226 non-read kmers were generated.
0:33:17.836 1G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics:
0:33:17.836 1G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 7304888. Among them 5557790 (76.0832%) are good
0:33:17.836 1G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 344751. Among them 344001 (99.7825%) are good
0:33:17.836 1G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 5838504. Among them 5706857 (97.7452%) are good
0:33:17.836 1G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 7.25687 kmers
0:33:17.836 1G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.16659
0:33:17.836 1G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 11608648
0:33:17.836 1G / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: 4,4
0:33:17.847 1G / 8G INFO General (main.cpp : 185) Finished clustering.
0:33:17.847 1G / 8G INFO General (main.cpp : 204) Starting solid k-mers expansion in 8 threads.
0:36:38.764 1G / 8G INFO General (main.cpp : 225) Solid k-mers iteration 0 produced 2627006 new k-mers.
0:39:50.894 1G / 8G INFO General (main.cpp : 225) Solid k-mers iteration 1 produced 551044 new k-mers.
0:42:59.502 1G / 8G INFO General (main.cpp : 225) Solid k-mers iteration 2 produced 11722 new k-mers.
0:46:12.313 1G / 8G INFO General (main.cpp : 225) Solid k-mers iteration 3 produced 877 new k-mers.
0:49:14.087 1G / 8G INFO General (main.cpp : 225) Solid k-mers iteration 4 produced 96 new k-mers.
0:52:16.169 1G / 8G INFO General (main.cpp : 225) Solid k-mers iteration 5 produced 6 new k-mers.
0:52:16.170 1G / 8G INFO General (main.cpp : 229) Solid k-mers finalized
0:52:16.170 1G / 8G INFO General (hammer_tools.cpp : 211) Starting read correction in 8 threads.
0:52:16.170 1G / 8G INFO General (hammer_tools.cpp : 222) Correcting pair of reads: /Users/mars/Desktop/spades_single_end/fastq/R1.fastq and /Users/mars/Desktop/spades_single_end/fastq/R2.fastq
0:52:18.238 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 0 of 800000 reads.
0:52:31.709 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0
0:52:34.225 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 0
0:52:35.749 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 1 of 800000 reads.
0:52:49.156 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 1
0:52:51.347 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 1
0:52:52.849 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 2 of 800000 reads.
0:53:06.493 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 2
0:53:08.673 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 2
0:53:10.174 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 3 of 800000 reads.
0:53:23.408 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 3
0:53:25.593 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 3
0:53:27.097 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 4 of 800000 reads.
0:53:40.841 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 4
0:53:43.015 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 4
0:53:44.501 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 5 of 800000 reads.
0:53:58.065 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 5
0:54:00.237 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 5
0:54:01.754 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 6 of 800000 reads.
0:54:15.639 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 6
0:54:17.845 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 6
0:54:19.360 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 7 of 800000 reads.
0:54:32.769 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 7
0:54:34.937 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 7
0:54:36.457 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 8 of 800000 reads.
0:54:50.710 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 8
0:54:52.844 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 8
0:54:54.372 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 9 of 800000 reads.
0:55:08.741 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 9
0:55:10.914 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 9
0:55:12.413 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 10 of 800000 reads.
0:55:26.369 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 10
0:55:28.525 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 10
0:55:30.010 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 11 of 800000 reads.
0:55:43.282 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 11
0:55:45.414 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 11
0:55:46.910 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 12 of 800000 reads.
0:56:00.087 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 12
0:56:02.279 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 12
0:56:03.822 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 13 of 800000 reads.
0:56:17.640 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 13
0:56:19.807 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 13
0:56:21.321 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 14 of 800000 reads.
0:56:35.051 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 14
0:56:37.195 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 14
0:56:38.709 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 15 of 800000 reads.
0:56:51.090 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 15
0:56:53.193 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 15
0:56:54.718 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 16 of 800000 reads.
0:57:07.045 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 16
0:57:09.204 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 16
0:57:10.688 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 17 of 800000 reads.
0:57:22.746 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 17
0:57:24.886 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 17
0:57:26.397 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 18 of 800000 reads.
0:57:39.180 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 18
0:57:41.323 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 18
0:57:42.825 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 19 of 800000 reads.
0:57:55.794 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 19
0:57:57.923 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 19
0:57:59.420 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 20 of 800000 reads.
0:58:12.749 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 20
0:58:14.970 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 20
0:58:15.832 2G / 8G INFO General (hammer_tools.cpp : 166) Prepared batch 21 of 462970 reads.
0:58:23.314 2G / 8G INFO General (hammer_tools.cpp : 175) Processed batch 21
0:58:24.554 2G / 8G INFO General (hammer_tools.cpp : 185) Written batch 21
0:58:25.129 1G / 8G INFO General (hammer_tools.cpp : 270) Correction done. Changed 7972253 bases in 4231994 reads.
0:58:25.129 1G / 8G INFO General (hammer_tools.cpp : 271) Failed to correct 53443 bases out of 2933572997.
0:58:25.259 32M / 8G INFO General (main.cpp : 262) Saving corrected dataset description to /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/corrected/corrected.yaml
0:58:25.262 32M / 8G INFO General (main.cpp : 269) All done. Exiting.
== Compressing corrected reads (with gzip)
== Dataset description file was created: /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/corrected/corrected.yaml
===== Read error correction finished.
===== Assembling started.
== Running assembler: K21
0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/K21/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/K21/configs/mda_mode.info
0:00:00.000 4M / 4M INFO General (main.cpp : 75) Loading config from /Users/mars/Desktop/spades_single_end/fastq/metaspades_output/K21/configs/meta_mode.info
0:00:00.000 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 250 Gb
0:00:00.000 4M / 4M INFO General (main.cpp : 88) Starting SPAdes, built from N/A, git revision N/A
0:00:00.000 4M / 4M INFO General (main.cpp : 89) Maximum k-mer length: 128
0:00:00.000 4M / 4M INFO General (main.cpp : 90) Assembling dataset (/Users/mars/Desktop/spades_single_end/fastq/metaspades_output/dataset.info) with K=21
0:00:00.000 4M / 4M INFO General (launch.hpp : 51) SPAdes started
0:00:00.000 4M / 4M INFO General (launch.hpp : 58) Starting from stage: construction
0:00:00.000 4M / 4M INFO General (launch.hpp : 61) Two-step RR enabled: 0
0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 126) STAGE == Construction
0:00:00.000 4M / 4M INFO General (read_converter.hpp : 84) Converting reads to binary format for library #0 (takes a while)
0:00:00.000 4M / 4M INFO General (read_converter.hpp : 85) Converting paired reads
0:00:00.170 76M / 76M INFO General (binary_converter.hpp : 139) 16384 reads processed
0:00:00.285 84M / 84M INFO General (binary_converter.hpp : 139) 32768 reads processed
0:00:00.522 100M / 100M INFO General (binary_converter.hpp : 139) 65536 reads processed
0:00:01.012 132M / 132M INFO General (binary_converter.hpp : 139) 131072 reads processed
0:00:01.975 200M / 200M INFO General (binary_converter.hpp : 139) 262144 reads processed
0:00:04.129 240M / 240M INFO General (binary_converter.hpp : 139) 524288 reads processed
0:00:08.432 268M / 268M INFO General (binary_converter.hpp : 139) 1048576 reads processed
0:00:16.662 272M / 276M INFO General (binary_converter.hpp : 139) 2097152 reads processed
0:00:33.577 276M / 276M INFO General (binary_converter.hpp : 139) 4194304 reads processed
0:01:07.809 272M / 280M INFO General (binary_converter.hpp : 139) 8388608 reads processed
0:02:15.197 268M / 280M INFO General (binary_converter.hpp : 139) 16777216 reads processed
0:02:17.302 236M / 280M INFO General (binary_converter.hpp : 159) 17037115 reads written
0:02:17.536 4M / 280M INFO General (read_converter.hpp : 94) Converting single reads
0:02:17.687 136M / 280M INFO General (binary_converter.hpp : 139) 16384 reads processed
0:02:17.740 140M / 280M INFO General (binary_converter.hpp : 139) 32768 reads processed
0:02:17.846 148M / 280M INFO General (binary_converter.hpp : 139) 65536 reads processed
0:02:18.055 164M / 280M INFO General (binary_converter.hpp : 139) 131072 reads processed
0:02:18.428 184M / 280M INFO General (binary_converter.hpp : 159) 205439 reads written
0:02:18.556 4M / 280M INFO General (graph_construction.hpp : 120) Constructing DeBruijn graph for k=21
0:02:18.556 4M / 280M INFO General (kmer_splitters.hpp : 129) Splitting kmer instances into 64 buckets. This might take a while.
0:02:18.556 4M / 280M INFO General (file_limit.hpp : 30) Open file limit set to 256
0:02:18.556 4M / 280M INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 10.4165 Gb
0:02:18.556 4M / 280M INFO General (kmer_index_builder.hpp : 116) Using cell size of 1048576
0:02:39.440 6G / 6G INFO General (kmer_splitters.hpp : 153) Processed 11804580 reads
0:03:00.695 6G / 6G INFO General (kmer_splitters.hpp : 153) Processed 23708251 reads
0:03:22.223 6G / 6G INFO General (kmer_splitters.hpp : 153) Processed 35691964 reads
0:03:43.328 6G / 6G INFO General (kmer_splitters.hpp : 153) Processed 47533456 reads
0:04:05.050 6G / 6G INFO General (kmer_splitters.hpp : 153) Processed 59439178 reads
0:04:21.389 6G / 6G INFO General (kmer_splitters.hpp : 153) Processed 68559338 reads
0:04:21.389 6G / 6G INFO General (kmer_splitters.hpp : 159) Adding contigs from previous K
0:04:21.626 32M / 6G INFO General (kmer_splitters.hpp : 172) Used 68559338 reads. Maximum read length 85
0:04:21.626 32M / 6G INFO General (kmer_splitters.hpp : 173) Average read length 84.9954
0:04:21.626 32M / 6G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting.
0:04:26.046 32M / 6G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 45935316 kmers in total.
0:04:26.046 32M / 6G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets.
0:04:26.428 32M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index
0:04:26.428 32M / 6G INFO General (kmer_splitters.hpp : 285) Splitting kmer instances into 128 buckets. This might take a while.
0:04:26.428 32M / 6G INFO General (file_limit.hpp : 30) Open file limit set to 256
0:04:26.428 32M / 6G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 10.4154 Gb
0:04:26.428 32M / 6G INFO General (kmer_index_builder.hpp : 116) Using cell size of 524288
0:04:41.306 8G / 8G INFO General (kmer_splitters.hpp : 304) Processed 45935316 kmers
0:04:41.306 8G / 8G INFO General (kmer_splitters.hpp : 309) Used 45935316 kmers.
0:04:41.373 32M / 8G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting.
0:04:43.859 32M / 8G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 44558213 kmers in total.
0:04:43.859 32M / 8G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets.
0:04:44.232 32M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices
0:04:47.465 32M / 8G INFO General (kmer_index_builder.hpp : 276) Merging final buckets.
0:04:47.788 32M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 14558136 bytes occupied (2.61377 bits per kmer).
0:04:47.816 76M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 85) Building k-mer extensions from k+1-mers
0:04:56.526 76M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 89) Building k-mer extensions from k+1-mers finished.
0:04:56.527 76M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping
0:05:16.064 76M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 14791162 22-mers were removed by early tip clipper
0:05:16.064 76M / 8G INFO General (graph_construction.hpp : 136) Condensing graph
0:05:16.064 76M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 340) Extracting unbranching paths
0:05:47.284 864M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths finished. 7287052 sequences extracted
0:05:51.743 864M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 313) Collecting perfect loops
0:06:02.601 864M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 329) Collecting perfect loops finished. 72 loops collected
0:06:06.431 1G / 8G INFO General (graph_construction.hpp : 141) Building index with from graph
0:06:06.431 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 428) Building kmer index
0:06:06.431 1G / 8G INFO General (kmer_splitters.hpp : 214) Splitting kmer instances into 16 buckets. This might take a while.
0:06:06.431 1G / 8G INFO General (file_limit.hpp : 30) Open file limit set to 256
0:06:06.431 1G / 8G INFO General (kmer_index_builder.hpp : 108) Memory available for splitting buffers: 82.8607 Gb
0:06:06.431 1G / 8G INFO General (kmer_index_builder.hpp : 116) Using cell size of 4194304
0:06:13.796 1G / 8G INFO General (kmer_splitters.hpp : 225) Processed 7287124 edges
0:06:13.796 1G / 8G INFO General (kmer_splitters.hpp : 230) Used 7287124 sequences.
0:06:13.816 1G / 8G INFO General (kmer_index_builder.hpp : 252) Starting k-mer counting.
0:06:19.147 1G / 8G INFO General (kmer_index_builder.hpp : 258) K-mer counting done. There are 31144154 kmers in total.
0:06:19.147 1G / 8G INFO General (kmer_index_builder.hpp : 260) Merging temporary buckets.
0:06:19.401 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 437) Building perfect hash indices
0:06:28.047 1G / 8G INFO General (kmer_index_builder.hpp : 276) Merging final buckets.
0:06:28.247 1G / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 483) Index built. Total 10175528 bytes occupied (2.61379 bits per kmer).
0:06:28.827 2G / 8G INFO General (edge_index_builders.hpp : 27) Collecting k-mer coverage information from graph, this takes a while.
0:06:31.463 2G / 8G INFO General (edge_index.hpp : 91) Index refilled
0:06:31.535 2G / 8G INFO General (graph_construction.hpp : 173) Filling coverage index
0:06:31.535 2G / 8G INFO General (edge_index_builders.hpp : 105) Collecting k-mer coverage information from reads, this takes a while.
0:11:02.962 2G / 8G INFO General (graph_construction.hpp : 175) Filling coverage and flanking coverage from index
0:11:07.552 2G / 8G INFO General (construction.cpp : 30) Figured out: read length = 85
0:11:07.552 2G / 8G INFO StageManager (stage.cpp : 126) STAGE == EC Threshold Finding
0:11:15.903 2G / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 25
0:11:15.904 2G / 8G INFO General (genomic_info_filler.cpp : 104) Average edge coverage: 69.9561
0:11:15.904 2G / 8G INFO General (genomic_info_filler.cpp : 105) Graph threshold: 115
0:11:21.318 2G / 8G INFO General (genomic_info_filler.cpp : 147) EC coverage threshold value was calculated as 69.9561
0:11:21.318 2G / 8G INFO General (genomic_info_filler.cpp : 148) Trusted kmer low bound: 0
0:11:21.318 2G / 8G INFO StageManager (stage.cpp : 126) STAGE == Simplification
0:11:21.381 1G / 8G INFO General (simplification.cpp : 380) Graph simplification started
0:11:21.382 1G / 8G INFO General (simplification.cpp : 76) PROCEDURE == InitialCleaning
0:11:21.382 1G / 8G INFO General (graph_simplification.hpp : 645) Flanking coverage based disconnection disabled
0:11:21.382 1G / 8G INFO General (simplification.cpp : 349) Running Self conjugate edge remover
0:11:21.670 1G / 8G INFO General (simplification.cpp : 351) Triggered 0 times
0:11:21.670 1G / 8G INFO General (simplification.cpp : 349) Running Initial isolated edge remover
0:11:22.185 1G / 8G INFO General (simplification.cpp : 351) Triggered 17442 times
0:11:22.185 1G / 8G INFO General (simplification.cpp : 349) Running Initial tip clipper
0:11:23.784 1G / 8G INFO General (simplification.cpp : 351) Triggered 62685 times
0:11:23.784 1G / 8G INFO General (simplification.cpp : 349) Running Initial ec remover
0:11:24.303 1G / 8G INFO General (simplification.cpp : 351) Triggered 0 times
0:11:24.331 1G / 8G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:11:24.331 1G / 8G INFO General (simplification.cpp : 403) PROCEDURE == Simplification cycle, iteration 1
0:11:24.331 1G / 8G INFO General (simplification.cpp : 349) Running Tip clipper
0:11:24.884 1G / 8G INFO General (simplification.cpp : 351) Triggered 2053 times
0:11:24.884 1G / 8G INFO General (simplification.cpp : 349) Running Bulge remover
0:15:46.949 1G / 8G INFO General (simplification.cpp : 351) Triggered 63838 times
0:15:46.950 1G / 8G INFO General (simplification.cpp : 349) Running Low coverage edge remover
0:15:49.233 1G / 8G INFO General (simplification.cpp : 351) Triggered 0 times
0:15:49.233 1G / 8G INFO General (simplification.cpp : 403) PROCEDURE == Simplification cycle, iteration 2
0:15:49.233 1G / 8G INFO General (simplification.cpp : 349) Running Tip clipper
0:15:49.645 1G / 8G INFO General (simplification.cpp : 351) Triggered 1069 times
0:15:49.645 1G / 8G INFO General (simplification.cpp : 349) Running Bulge remover
0:15:49.723 1G / 8G INFO General (simplification.cpp : 351) Triggered 29 times
0:15:49.723 1G / 8G INFO General (simplification.cpp : 349) Running Low coverage edge remover
0:16:47.286 1G / 8G INFO General (simplification.cpp : 351) Triggered 1062524 times
0:16:47.286 1G / 8G INFO General (simplification.cpp : 403) PROCEDURE == Simplification cycle, iteration 3
0:16:47.286 1G / 8G INFO General (simplification.cpp : 349) Running Tip clipper
0:16:48.026 1G / 8G INFO General (simplification.cpp : 351) Triggered 9374 times
0:16:48.026 1G / 8G INFO General (simplification.cpp : 349) Running Bulge remover
0:17:27.471 1G / 8G INFO General (simplification.cpp : 351) Triggered 54962 times
0:17:27.471 1G / 8G INFO General (simplification.cpp : 349) Running Low coverage edge remover
0:17:32.639 1G / 8G INFO General (simplification.cpp : 351) Triggered 83619 times
0:17:32.639 1G / 8G INFO General (simplification.cpp : 403) PROCEDURE == Simplification cycle, iteration 4
0:17:32.639 1G / 8G INFO General (simplification.cpp : 349) Running Tip clipper
0:17:32.787 1G / 8G INFO General (simplification.cpp : 351) Triggered 382 times
0:17:32.787 1G / 8G INFO General (simplification.cpp : 349) Running Bulge remover
0:17:44.333 1G / 8G INFO General (simplification.cpp : 351) Triggered 7856 times
0:17:44.333 1G / 8G INFO General (simplification.cpp : 349) Running Low coverage edge remover
0:17:44.334 1G / 8G INFO General (simplification.cpp : 351) Triggered 11 times
0:17:44.334 1G / 8G INFO General (simplification.cpp : 403) PROCEDURE == Simplification cycle, iteration 5
0:17:44.334 1G / 8G INFO General (simplification.cpp : 349) Running Tip clipper
0:17:44.358 1G / 8G INFO General (simplification.cpp : 351) Triggered 6 times
0:17:44.358 1G / 8G INFO General (simplification.cpp : 349) Running Bulge remover
0:17:44.365 1G / 8G INFO General (simplification.cpp : 351) Triggered 2 times
0:17:44.365 1G / 8G INFO General (simplification.cpp : 349) Running Low coverage edge remover
0:17:44.365 1G / 8G INFO General (simplification.cpp : 351) Triggered 0 times
0:17:44.365 1G / 8G INFO General (simplification.cpp : 403) PROCEDURE == Simplification cycle, iteration 6
0:17:44.365 1G / 8G INFO General (simplification.cpp : 349) Running Tip clipper
0:17:44.365 1G / 8G INFO General (simplification.cpp : 351) Triggered 0 times
0:17:44.365 1G / 8G INFO General (simplification.cpp : 349) Running Bulge remover
0:17:44.365 1G / 8G INFO General (simplification.cpp : 351) Triggered 0 times
0:17:44.365 1G / 8G INFO General (simplification.cpp : 349) Running Low coverage edge remover
0:17:44.365 1G / 8G INFO General (simplification.cpp : 351) Triggered 0 times
0:17:44.365 1G / 8G INFO General (simplification.cpp : 162) PROCEDURE == Post simplification
0:17:44.365 1G / 8G INFO General (graph_simplification.hpp : 617) Creating parallel br instance
0:17:44.365 1G / 8G INFO General (simplification.cpp : 294) Iteration 0
0:17:44.365 1G / 8G INFO General (simplification.cpp : 349) Running Relative coverage component remover
0:17:55.094 1016M / 8G INFO General (simplification.cpp : 351) Triggered 74153 times
0:17:55.094 1016M / 8G INFO General (simplification.cpp : 349) Running Disconnecting edges with relatively low coverage
== Error == system call for: "['/usr/local/Cellar/spades/3.10.1/bin/spades', '/Users/mars/Desktop/spades_single_end/fastq/metaspades_output/K21/configs/config.info', '/Users/mars/Desktop/spades_single_end/fastq/metaspades_output/K21/configs/mda_mode.info', '/Users/mars/Desktop/spades_single_end/fastq/metaspades_output/K21/configs/meta_mode.info']" finished abnormally, err code: -10
In case you have troubles running SPAdes, you can write to [email protected]
Please provide us with params.txt and spades.log files from the output directory.