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  • Trinity error in both.fa

    Hi!

    I am using Trinity (r2014-07-17) for de novo assembly of RNA-seq data (100bp PE). I have 12 samples and 9 of them have successfully completed, however 3 fail early on in the program.

    For these samples, the error message I get is:
    HTML Code:
    Monday, April 13, 2015: 15:18:53	CMD: mkdir -p /brashear/mlim/Trinityfiles/trinityResults/CGML001B/chrysalis
    CMD finished (0 seconds)
    Converting input files. (in parallel)Monday, April 13, 2015: 15:18:54	CMD: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001B_trinity_left.fq >> left.fa 2> /brashear/mlim/Trinityfiles/CGML001B_trinity_left.fq.readcount 
    Monday, April 13, 2015: 15:18:54	CMD: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001B_trinity_right.fq >> right.fa 2> /brashear/mlim/Trinityfiles/CGML001B_trinity_right.fq.readcount 
    CMD finished (62 seconds)
    Thread 1 terminated abnormally: Error, cmd: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001B_trinity_left.fq >> left.fa 2> /brashear/mlim/Trinityfiles/CGML001B_trinity_left.fq.readcount  died with ret 256 at /usr/local/packages/trinity/r2014-07-17/Trinity line 1990.
    Use of uninitialized value in array dereference at /usr/local/packages/trinity/r2014-07-17/Trinity line 1171.
    Error prepping sequences. at /usr/local/packages/trinity/r2014-07-17/Trinity line 1175.
    For reference, when it works, I get:
    HTML Code:
    Wednesday, April 8, 2015: 18:40:33	CMD: mkdir -p /brashear/mlim/Trinityfiles/trinityResults/CGML001A/chrysalis
    CMD finished (0 seconds)
    Converting input files. (in parallel)Wednesday, April 8, 2015: 18:40:33	CMD: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001A_trinity_left.fq >> left.fa 2> /brashear/mlim/Trinityfiles/CGML001A_trinity_left.fq.readcount 
    Wednesday, April 8, 2015: 18:40:33	CMD: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001A_trinity_right.fq >> right.fa 2> /brashear/mlim/Trinityfiles/CGML001A_trinity_right.fq.readcount 
    CMD finished (47 seconds)
    CMD finished (49 seconds)
    Done converting input files.Wednesday, April 8, 2015: 18:41:22	CMD: cat left.fa right.fa > both.fa
    CMD finished (21 seconds)
    Has anyone gotten these errors before? I'd appreciate any suggestions!
    Thanks!!

  • #2
    This loos like input problem. Check if your fastq files for 3 fails are in correct format.

    Comment

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