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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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finished abnormally, err code: -15 #319

Open harigowthem opened 5 years ago

harigowthem commented 5 years ago

#This following is the params.txt

Command line: ./../SPAdes-3.13.1-Linux/bin/spades.py --careful -t 20 --pe1-1 /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R1_val_1.fq --pe1-2 /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R2_val_2.fq -o /run/media/user1/storage1/5_hari_g/spades

System information: SPAdes version: 3.13.1 Python version: 2.7.5 OS: Linux-3.10.0-957.10.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core

Output dir: /run/media/user1/storage1/5_hari_g/spades Mode: read error correction and assembling Debug mode is turned OFF

Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R1_val_1.fq'] right reads: ['/run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R2_val_2.fq'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned ON MismatchCorrector will be used Coverage cutoff is turned OFF Other parameters: Dir for temp files: /run/media/user1/storage1/5_hari_g/spades/tmp Threads: 20 Memory limit (in Gb): 250

#The following is spades.log

Command line: ./../SPAdes-3.13.1-Linux/bin/spades.py --careful -t 20 --pe1-1 /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R1_val_1.fq --pe1-2 /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R2_val_2.fq -o /run/media/user1/storage1/5_hari_g/spades

System information: SPAdes version: 3.13.1 Python version: 2.7.5 OS: Linux-3.10.0-957.10.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core

Output dir: /run/media/user1/storage1/5_hari_g/spades Mode: read error correction and assembling Debug mode is turned OFF

Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R1_val_1.fq'] right reads: ['/run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R2_val_2.fq'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned ON MismatchCorrector will be used Coverage cutoff is turned OFF Other parameters: Dir for temp files: /run/media/user1/storage1/5_hari_g/spades/tmp Threads: 20 Memory limit (in Gb): 250

======= SPAdes pipeline started. Log can be found here: /run/media/user1/storage1/5_hari_g/spades/spades.log

===== Read error correction started.

== Running read error correction tool: /run/media/user1/storage1/5_hari_g/SPAdes-3.13.1-Linux/bin/spades-hammer /run/media/user1/storage1/5_hari_g/spades/corrected/configs/config.info

0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.1, git revision 9a9d54db2ff9abaac718155bf74c12ec9464e8ca 0:00:00.001 4M / 4M INFO General (main.cpp : 76) Loading config from /run/media/user1/storage1/5_hari_g/spades/corrected/configs/config.info 0:00:00.001 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 20 0:00:00.002 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 250 Gb 0:00:00.002 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.002 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.003 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.003 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.004 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.004 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 320 files using 20 threads. This might take a while. 0:00:00.004 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.005 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 4.1666 Gb 0:00:00.005 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 209715 0:00:00.084 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R1_val_1.fq 0:00:40.469 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 4382260 reads 0:01:19.149 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 8760059 reads 0:01:57.333 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 12942158 reads 0:02:35.505 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 17338970 reads 0:03:14.727 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 21600330 reads 0:03:52.728 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 25985899 reads 0:04:32.170 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 30341373 reads 0:05:11.669 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 34621077 reads 0:05:51.130 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 39055164 reads 0:06:27.743 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 43358079 reads 0:07:07.165 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 47822439 reads 0:10:14.401 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 69503025 reads 0:19:28.403 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R2_val_2.fq 0:20:08.102 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 138626401 reads 0:38:16.160 11G / 11G INFO K-mer Splitting (kmer_data.cpp : 112) Total 267921958 reads processed 0:38:18.000 80M / 11G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:43:14.462 80M / 11G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2562826166 kmers in total. 0:43:14.462 80M / 11G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:43:48.658 80M / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:46:34.831 1G / 11G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:47:19.942 1G / 11G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1188468318 bytes occupied (3.70987 bits per kmer). 0:47:19.962 1G / 11G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:49:59.003 39G / 39G INFO General (main.cpp : 148) Clustering Hamming graph. 3:30:07.985 39G / 39G INFO General (main.cpp : 155) Extracting clusters 4:03:48.005 39G / 98G INFO General (main.cpp : 167) Clustering done. Total clusters: 1046542006 4:03:51.111 20G / 98G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 4:04:32.070 77G / 98G INFO K-mer Counting (kmer_data.cpp : 382) Processing /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R1_val_1.fq 5:17:44.675 77G / 98G INFO K-mer Counting (kmer_data.cpp : 382) Processing /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC-1_R2_val_2.fq 6:27:27.669 77G / 98G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 6:27:48.152 77G / 98G INFO K-mer Counting (kmer_data.cpp : 403) There are 2562826166 kmers in total. Among them 1300220620 (50.7339%) are singletons. 6:27:48.152 77G / 98G INFO General (main.cpp : 173) Subclustering Hamming graph

== Error == system call for: "['/run/media/user1/storage1/5_hari_g/SPAdes-3.13.1-Linux/bin/spades-hammer', '/run/media/user1/storage1/5_hari_g/spades/corrected/configs/config.info']" finished abnormally, err code: -15

hafizmtalha commented 5 years ago

any help on this error ?

Cynthiavlu commented 4 years ago

I have the same error. Is there a solution for this?

ChristophIrvin commented 4 years ago

I'm also looking for a solution on this same err...

Cynthiavlu commented 4 years ago

Hi @ChristophIrvin,

I was able to keep it running by running it in a shell instead of in a command. I made a .sh script and ran the script.

I hope this helps you!

swiesenfeld0 commented 2 years ago

Did anyone else find a different solution to this? I also get error 15 but the running the command as a script did not help.

neenah13 commented 2 years ago

Yes I have the same error. Was anybody able to sort it out?? I got this error after running the command as a script