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SPAdes Genome Assembler
http://ablab.github.io/spades/
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Stuck and segmentation fault #722

Open liangzhengjiao opened 3 years ago

liangzhengjiao commented 3 years ago

hi,@asl

my command is
'metaspades.py -1 SRR9033753.rmhost.clean.1.fq.gz -2 SRR9033753.rmhost.clean.2.fq.gz -t 20 -o output' when I run it by SPAdes-3.14.1, the task stuck when Processing reverse paired-end reads. 0:00:39.478 2G / 2G INFO K-mer Counting (kmer_data.cpp : 312) Processing ./SRR9033753.rmhost.clean.1.fq 0:09:55.001 2G / 2G INFO K-mer Counting (kmer_data.cpp : 321) Processed 10455463 reads 0:09:55.001 2G / 2G INFO K-mer Counting (kmer_data.cpp : 312) Processing ./SRR9033753/SRR9033753.rmhost.clean.2.fq

when I run it by SPAdes-3.15.2, "The program was terminated by segmentation fault" occuring when Processing reverse paired-end reads. 0:00:59.245 1302M / 1302M INFO K-mer Counting (kmer_data.cpp : 315) Processing ./SRR9033753/SRR9033753.rmhost.clean.1.fq.gz 0:08:34.135 1302M / 1491M INFO K-mer Counting (kmer_data.cpp : 324) Processed 10455463 reads 0:08:34.135 1302M / 1491M INFO K-mer Counting (kmer_data.cpp : 315) Processing ./SRR9033753/SRR9033753.rmhost.clean.2.fq.gz The program was terminated by segmentation fault === Stack Trace === [0x40b828] [0x40b956]

thanks!

asl commented 3 years ago

Will you please attach your params.txt and spades.log files as you were instructed in the error message?

liangzhengjiao commented 3 years ago

Here are my log files spades.log params.txt Thanks for your prompt reply!

asl commented 3 years ago

Ok, does the assembly finish if you'd use --only-assembler option in addition to yours?

liangzhengjiao commented 3 years ago

Yes, it works! Plus --only-assemble option can accomplish assembly. So, does the 'read error correction' process introduce conflicts to the pipeline?

asl commented 3 years ago

No, there are no "conflicts". Likely the problem will be solve if you'd compile SPAdes for the host machine instead of using pre-built binaries.

GeoMicroSoares commented 3 years ago

Hey @asl , not quite the same for me here. Also weirder because while SPAdes runs normally for one of my samples, for the other (separate run) it hangs at K-mer Counting (kmer_data.cpp). This is occurring for both a binary and a compiled version of SPAdes and the sample runs fully with --only-assemble. All this running version 3.15.2.

What information can I provide to get some help with this?

skchronicles commented 2 years ago

Hey @asl,

I am also running into the same issue as well. Is there any update on this problem? One sample sample out of a larger set is also failing.

I am running metaspades in a docker image I built that is using the pre-compiled binaries.

Here is the content of the log file:

Command line: /opt2/SPAdes-3.15.4-Linux/bin/metaspades.py   -t  32  -m  64  -1  /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R1.trim.host_removed.fastq.gz  -/gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R2.trim.host_removed.fastq.gz -o  /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/metaspades   

System information:
  SPAdes version: 3.15.4
  Python version: 3.8.10
  OS: Linux-3.10.0-1160.66.1.el7.x86_64-x86_64-with-glibc2.29

Output dir: /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/metaspades
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: ['/gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R1.trim.host_removed.fastq.gz']
      right reads: ['/gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R2.trim.host_removed.fastq.gz']
      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: [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: /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/metaspades/tmp
  Threads: 32
  Memory limit (in Gb): 64

======= SPAdes pipeline started. Log can be found here: /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/metaspades/spades.log

/gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R1.trim.host_removed.fastq.gz: max reads length: 151
/gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R2.trim.host_removed.fastq.gz: max reads length: 151

Reads length: 151

===== Before start started. 

===== Read error correction started. 

===== Read error correction started. 

== Running: /opt2/SPAdes-3.15.4-Linux/bin/spades-hammer /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/metaspades/corrected/configs/config.info

  0:00:00.000     1M / 12M   INFO    General                 (main.cpp                  :  75)   Starting BayesHammer, built from refs/heads/spades_3.15.4, git revision 1a5332e5608a073a9d28a6d0e30836f38dcc5613
  0:00:00.016     1M / 12M   INFO    General                 (main.cpp                  :  76)   Loading config from /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/metaspades/corrected/configs/config.info
  0:00:00.029     1M / 12M   INFO    General                 (main.cpp                  :  78)   Maximum # of threads to use (adjusted due to OMP capabilities): 32
  0:00:00.046     1M / 12M   INFO    General                 (memory_limit.cpp          :  54)   Memory limit set to 64 Gb
  0:00:00.058     1M / 12M   INFO    General                 (main.cpp                  :  86)   Trying to determine PHRED offset
  0:00:00.064     1M / 12M   INFO    General                 (main.cpp                  :  92)   Determined value is 33
  0:00:00.076     1M / 12M   INFO    General                 (hammer_tools.cpp          :  38)   Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
  0:00:00.088     1M / 12M   INFO    General                 (main.cpp                  : 113)   Size of aux. kmer data 24 bytes
     === ITERATION 0 begins ===
  0:00:00.101     1M / 12M   INFO   K-mer Counting           (kmer_data.cpp             : 283)   Estimating k-mer count
  0:00:00.168   513M / 581M  INFO   K-mer Counting           (kmer_data.cpp             : 288)   Processing /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R1.trim.host_removed.fastq.gz
  0:00:02.472   513M / 637M  INFO   K-mer Counting           (kmer_data.cpp             : 297)   Processed 612152 reads
  0:00:02.484   513M / 637M  INFO   K-mer Counting           (kmer_data.cpp             : 288)   Processing /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R2.trim.host_removed.fastq.gz
  0:00:04.768   513M / 637M  INFO   K-mer Counting           (kmer_data.cpp             : 297)   Processed 1224304 reads
  0:00:04.781   513M / 637M  INFO   K-mer Counting           (kmer_data.cpp             : 302)   Total 1224304 reads processed
  0:00:05.930   513M / 637M  INFO   K-mer Counting           (kmer_data.cpp             : 305)   Estimated 30674495 distinct kmers
  0:00:05.943     1M / 637M  INFO   K-mer Counting           (kmer_data.cpp             : 309)   Filtering singleton k-mers
  0:00:05.949    85M / 637M  INFO   K-mer Counting           (kmer_data.cpp             : 315)   Processing /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R1.trim.host_removed.fastq.gz
  0:00:20.264    85M / 637M  INFO   K-mer Counting           (kmer_data.cpp             : 324)   Processed 612152 reads
  0:00:20.265    85M / 637M  INFO   K-mer Counting           (kmer_data.cpp             : 315)   Processing /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/trim/17249_noHg38.R2.trim.host_removed.fastq.gz
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
The program was terminated by segmentation fault
=== Stack Trace ===
=== Stack Trace ===
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x421e29]
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x423956]
/lib/x86_64-linux-gnu/libc.so.6(+0x430c0) [0x7fb65a91b0c0]
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x4a40db]
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x44f6ca]
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x5c93ee]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x8609) [0x7fb65aad2609]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x7fb65a9f7163]
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x421e29]
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x423956]
/lib/x86_64-linux-gnu/libc.so.6(+0x430c0) [0x7fb65a91b0c0]
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x4a40db]
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x44f6ca]
/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer() [0x5c93ee]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x8609) [0x7fb65aad2609]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x7fb65a9f7163]
The program was terminated by segmentation fault
=== Stack Trace ===

== Error ==  system call for: "['/opt2/SPAdes-3.15.4-Linux/bin/spades-hammer', '/gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/metaspades/corrected/configs/config.info']" finished abnormally, OS return value: 1
None

In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.

SPAdes log can be found here: /gs1/RTS/NextGen/ActiveProjects/NGS_Munster_CustomSeqCap/Kwe_Hendra_PROJECTS/Final_HEV/Metavirs/outs_test/17249_noHg38/metaspades/spades.log
lauren-mak commented 2 years ago

I also have this problem! Error correction runs perfectly with 11/12 samples but for some reason, it hangs on the one specific sample, namely R2 of the sample's paired gzipped FastQs. I'm running v3.14.1 installed from conda.

jorondo1 commented 2 years ago

We have the same problem with metaSpades here, where some (but not all) our larger samples output the following error : 

  1:54:42.987  2599M / 2819M INFO   K-mer Counting           (kmer_data.cpp             : 315)   Processing /out/GQ39/GQ39_paired_sorted_2.fastq
The program was terminated by segmentation fault
=== Stack Trace ===
/miniconda3/envs/metawrap-env/bin/spades-hammer(+0x1ddac) [0x55bc7323adac]
/miniconda3/envs/metawrap-env/bin/spades-hammer(+0x1e2ac) [0x55bc7323b2ac]
/lib/x86_64-linux-gnu/libc.so.6(+0x43090) [0x2b3bc87af090]
/miniconda3/envs/metawrap-env/bin/spades-hammer(+0x9a719) [0x55bc732b7719]
/miniconda3/envs/metawrap-env/bin/spades-hammer(+0x5210b) [0x55bc7326f10b]
/miniconda3/envs/metawrap-env/bin/spades-hammer(+0x5224e) [0x55bc7326f24e]
/miniconda3/envs/metawrap-env/bin/../lib/libgomp.so.1(+0x177f0) [0x2b3bc870c7f0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x8609) [0x2b3bc8751609]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x2b3bc888b133]
== Error ==  system call for: "['/miniconda3/envs/metawrap-env/bin/spades-hammer', '/out/assembly/metaspades/corrected/configs/config.info']" finished abnormally, OS return value: 1
None

Any idea what might be happening?


System information:
  SPAdes version: 3.15.4
  Python version: 2.7.15
  OS: Linux-3.10.0-1160.62.1.el7.x86_64-x86_64-with-debian-bullseye-sid
Dataset parameters:
  Metagenomic mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/out/GQ39/GQ39_paired_sorted_1.fastq']
      right reads: ['/out/GQ39/GQ39_paired_sorted_2.fastq']
      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: [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: /out/assembly/metaspades.tmp
  Threads: 48
  Memory limit (in Gb): 251