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  • Error in Trinity - Chrysalis: ReadsToTranscripts

    Hello,

    I am running trinity to perform some de novo assemblies and everything was doing ok. Now I am facing a really weird problem that is making the trinity die everytime.

    Processing reads:
    reading another 10000000... done. Read 5427877 reads.

    libgomp: Out of memory allocating 1456 bytes
    COMMAND: /home/user/oliveira/Assemblers/trinityrnaseq_r20131110/Chrysalis/ReadsToTranscripts -i both.fa -f /scratch/trinity_test_4a/chrysalis/bundled_iworm_contigs.fasta -t 1 -o /scratch/trinity_test_4a/chrysalis -max_mem_reads 10000000
    Died with exit code 256
    That is the problem, and it is quite weird because it looks like it is a memory problem, but I already performed some assemblies with bigger datasets and this problem never happened. Someone knows what is happening? Someone already faced this same problem? I will really appreciate some help, because I have no idea how to solve this.

    Best regards,
    André
    Last edited by aloliveira; 02-02-2014, 03:19 AM. Reason: Problem solved.

  • #2
    More informations about the error.

    COMMAND: /home/user/oliveira/Assemblers/trinityrnaseq_r20131110/Chrysalis/ReadsToTranscripts -i both.fa -f /scratch/trinity_test_4a/chrysalis/bundled_iworm_contigs.fasta -t 8 -o /scratch/trinity_test_4a/chrysalis -max_mem_reads 10000000
    Died with exit code 256
    Exiting.
    core file size (blocks, -c) 0
    data seg size (kbytes, -d) unlimited
    scheduling priority (-e) 0
    file size (blocks, -f) unlimited
    pending signals (-i) 386252
    max locked memory (kbytes, -l) 64
    max memory size (kbytes, -m) unlimited
    open files (-n) 1024
    pipe size (512 bytes, -p) 8
    POSIX message queues (bytes, -q) 819200
    real-time priority (-r) 0
    stack size (kbytes, -s) 8192
    cpu time (seconds, -t) unlimited
    max user processes (-u) 1024
    virtual memory (kbytes, -v) unlimited
    file locks (-x) unlimited

    Error, the Chrysalis process failed:
    Error, cmd: /home/user/oliveira/Assemblers/trinityrnaseq_r20131110/Chrysalis/Chrysalis -i both.fa -iworm /scratch/trinity_test_4a/inchworm.K25.L25.DS.fa -o /scratch/trinity_test_4a/chrysalis -cpu 8 -min_glue 2 -min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48 -min 200 -dist 500 -max_reads 200000 -sort_buffer_size 48G -max_mem_reads 10000000 -paired -reads_for_pairs both.fa -butterfly /home/user/oliveira/Assemblers/trinityrnaseq_r20131110/Butterfly/Butterfly.jar 2>&1 died with ret 65280 at ./Trinity.pl line 1793.

    at ./Trinity.pl line 1322.
    main::run_chrysalis('/scratch/trinity_test_4a/inchworm.K25.L25.DS.fa', 'both.fa', 200, 500, undef, 'both.fa') called at ./Trinity.pl line 1136

    Comment


    • #3
      So, I just solved the problem changing the chrysalis parameter -max_mem_reads to a lower value.

      Comment

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