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  • Trintiy with Bowtie2 or Bowtie1

    Dear all,

    I run Trinity to assemble 100bp PE HiSeq2000 data (2x100M reads) on a 256GB RAM cluster with this setting:

    Code:
    perl Trinity.pl --seqType fq --JM 240G --left Seq_1.fq  --right Seq_2.fq --single single.fq --output /path/to/output --CPU 6 --min_contig_length 150
    I constantly get the following error message:

    Code:
    -------------------
    ---- Chrysalis ----
    -------------------
    
    mkdir: cannot create directory `/usr/users/xxx/Gm/Trinity/Assembled/chrysalis': File exists
    CMD: ln -sf /home/xxx/xxx/Gm/Trinity/Assembled/inchworm.K25.L25.DS.fa target.fa 
    Warning, bowtie-build output already exists and will be re-used: target.fa*
    CMD: bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead  -f target single.fa > bowtie.out
    Error: Could not allocate ChunkPool of 536870912 bytes
    terminate called after throwing an instance of 'int'
    sh: line 1:  2534 Aborted                 (core dumped) bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead -f target single.fa > bowtie.out
    COMMAND: bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead  -f target single.fa > bowtie.out
    Died with exit code 34304
    Exiting.
    core file size          (blocks, -c) unlimited
    data seg size           (kbytes, -d) unlimited
    scheduling priority             (-e) 0
    file size               (blocks, -f) unlimited
    pending signals                 (-i) 2067510
    max locked memory       (kbytes, -l) unlimited
    max memory size         (kbytes, -m) unlimited
    open files                      (-n) 65536
    pipe size            (512 bytes, -p) 8
    POSIX message queues     (bytes, -q) 819200
    real-time priority              (-r) 0
    stack size              (kbytes, -s) unlimited
    cpu time               (seconds, -t) unlimited
    max user processes              (-u) 2067510
    virtual memory          (kbytes, -v) unlimited
    file locks                      (-x) unlimited
    
    Error, the Chrysalis process failed:
    Error, cmd: /home/xxx/xxx/Programme/trinityrnaseq_r2013-02-25/Chrysalis/Chrysalis -i single.fa -iworm /home/xxx/xxx/Gm/Trinity/Assembled/inchworm.K25.L25.DS.fa -o /usr/users/xxx/Gm/Trinity/Assembled/chrysalis -cpu 6  -min_glue 2 -min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48  -min 150 -dist 500 -max_reads 200000  -sort_buffer_size 240G -max_mem_reads 1000000  -paired  -reads_for_pairs single.fa  -butterfly /home/xxx/xxx/Programme/trinityrnaseq_r2013-02-25/Butterfly/Butterfly.jar  2>&1  died with ret 65280 at Trinity.pl line 1476.
    
     at Trinity.pl line 1101
    	main::run_chrysalis('/home/xxx/xxx/Gm/Trinity/Assembled/inchworm.K25.L25.DS.fa', 'single.fa', 150, 500, undef, 'single.fa') called at Trinity.pl line 930
    Any idea what is goin wrong there? I have both Bowtie and Bowtie2 installed. Is Trinty able to use Bowtie2?

    Any suggestions are high appreciated.
    Thanks in advance.

  • #2
    This may not be the cause of the error but I think that in your command line you should not give --left --right and --single parameters. Instead the single reads should be added to the left reads. You may get a quicker answer about the error from the trinity mailing list.

    Comment


    • #3
      Answered, or being tried to be answered, via the Trinity mailing list. We think that Nico's bowtie may be 32-bit instead of 64-bit (which of course has a big effect on memory -- which is what a "could not allocate" message refers to.) We've asked Nico to check his bowtie version.

      If I may make a plug, like other program's mailing list (e.g., Mira) the Trinity mailing list is active and the developers chime in frequently. If anyone is using Trinity but is not on the mailing list then I suggest joining it.

      Comment


      • #4
        Thanks for all the help! It was actually the bowtie version (I have now clue why compilation of bowtie source on a 464bit machine results in a 32bit version, but ....).

        Comment

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