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SPAdes Genome Assembler
http://ablab.github.io/spades/
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err code: -6 v3.11.1 #57

Closed cistarsa closed 6 years ago

cistarsa commented 6 years ago

Hello. I'm attempting to run a hybrid assembly with test input on a HTC cluster, I've ran SPAdes v3.11.1 a few times already on this cluster without nanopore and two sets of trusted contigs, so perhaps that is contributing to the failure. 

Command line: ./spades.py   -m  50  --pe1-1 /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec_180bp_male_1CLEAN.fq  --pe1-2 /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec_180bp_male_2CLEAN.fq  --pe2-1 /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec_500bp_male_1_CLEAN.fq --pe2-2 /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec_500bp_male_2_CLEAN.fq --mp1-1 /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec3Kb_male_1_CLEAN.fq    --mp1-2 /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec3Kb_male_2_CLEAN.fq    --only-assembler    -t  2   -k  37,59,71,85,97  --trusted-contigs   /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/Ldec_redundans_on_alpaths_contigs_genome_reduced.fa --trusted-contigs   /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Redundans_jelly.out.fasta  --nanopore  /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Minion.fq  -o  /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Hybrid_Assembly1222    

System information:
  SPAdes version: 3.11.1
  Python version: 2.7.5
  OS: Linux-3.10.0-693.5.2.el7.centos.plus.x86_64-x86_64-with-centos-7.4.1708-Core

Output dir: /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Hybrid_Assembly1222
Mode: ONLY assembling (without read error correction)
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: mate-pairs
      orientation: rf
      left reads: ['/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec3Kb_male_1_CLEAN.fq']
      right reads: ['/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec3Kb_male_2_CLEAN.fq']
      interlaced reads: not specified
      single reads: not specified
    Library number: 2, library type: paired-end
      orientation: fr
      left reads: ['/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec_180bp_male_1CLEAN.fq']
      right reads: ['/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec_180bp_male_2CLEAN.fq']
      interlaced reads: not specified
      single reads: not specified
    Library number: 3, library type: paired-end
      orientation: fr
      left reads: ['/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec_500bp_male_1_CLEAN.fq']
      right reads: ['/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Ldec_500bp_male_2_CLEAN.fq']
      interlaced reads: not specified
      single reads: not specified
    Library number: 4, library type: nanopore
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Minion.fq']
    Library number: 5, library type: trusted-contigs
      left reads: not specified
      right reads: not specified
      interlaced reads: not specified
      single reads: ['/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/Ldec_redundans_on_alpaths_contigs_genome_reduced.fa', '/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Redundans_jelly.out.fasta']
Assembly parameters:
  k: [37, 59, 71, 85, 97]
  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: /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Hybrid_Assembly1222/tmp
  Threads: 2
  Memory limit (in Gb): 50

======= SPAdes pipeline started. Log can be found here: /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Hybrid_Assembly1222/spades.log

== Processing additional contigs (/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Redundans_jelly.out.fasta): changing Ns to As and splitting by continues (>= 10) Ns fragments (results are in /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Hybrid_Assembly1222/split_input directory)

===== Assembling started.

== Running assembler: K37

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  76)   Loading config from /var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Hybrid_Assembly1222/K37/configs/config.info
  0:00:00.000     4M / 4M    INFO    General                 (memory_limit.hpp          :  51)   Memory limit set to 50 Gb
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  89)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum k-mer length: 128
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  91)   Assembling dataset (/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Hybrid_Assembly1222/dataset.info) with K=37
  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
  0:00:00.001     4M / 4M    INFO    General                 (construction.cpp          :  57)   Trusted contigs will be used in graph construction
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  84)   Converting reads to binary format for library #1 (takes a while)
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  85)   Converting paired reads
  0:00:00.106    68M / 100M  INFO    General                 (binary_converter.hpp      : 159)   3 reads written
  0:00:00.113     4M / 100M  INFO    General                 (read_converter.hpp        :  94)   Converting single reads
  0:00:00.326   132M / 196M  INFO    General                 (binary_converter.hpp      : 159)   0 reads written
  0:00:00.341     4M / 196M  INFO    General                 (read_converter.hpp        :  84)   Converting reads to binary format for library #2 (takes a while)
  0:00:00.341     4M / 196M  INFO    General                 (read_converter.hpp        :  85)   Converting paired reads
=== Stack Trace ===
[0x40c26a]
[0x572533]
[0x41d6b3]
[0x421c4a]
[0x42aaef]
[0x42af97]
[0x41f799]
[0x434f45]
[0x435efb]
[0x470958]
[0x470ceb]
[0x69a48d]
[0x541c71]
[0x40a0ee]
[0x402e62]
[0x7b1ef0]
[0x408f2d]
spades: /spades/src/common/io/reads/single_read.hpp:218: void io::SingleRead::Init(): Assertion `seq_.size() == qual_.size()' failed.

== Error ==  system call for: "['/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/spades', '/var/lib/condor/execute/slot1/dir_18130/SPAdes-3.11.1-Linux/bin/head_Hybrid_Assembly1222/K37/configs/config.info']" finished abnormally, err code: -6

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.
asl commented 6 years ago

Hello

Thank you for your interest in SPAdes.

It seems that your paired-end reads are corrupted - the length of sequence line for some read is not equal to the length of quality line, so they are not valid FASTQ.

Also, your mate pair dataset seem to contain only 3 reads which also looks very strange.