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  • PacBio SmrtAnalysis on AWS

    Hi,

    I am having some issues processing pacbio data on AWS. I am trying to use the PacBioToCA module to correct PacBio subreads with illumina reads. I have made an illumina.frg file ok, and using this command for correcting:

    /opt/smrtanalysis/analysis/bin/wgs-7.0/Linux-amd64/bin/pacBioToCA -l ec_pacbio_ren -s pacbio.spec -t 16 -length 500 -partitions 200 -fastq /opt/smrtanalysis/common/inputs_dropbox/renilla_filtered_subread_fastq.fastq illumina.frg >run.out 2>&1

    But, i am getting this error in my run.out file

    Any advice?

    Thanks~
    Running with 16 threads and 200 partitions
    Starting correction...
    CA: /opt/smrtanalysis-1.3.3/analysis/bin/wgs-7.0/Linux-amd64/bin
    AMOS:/opt/smrtanalysis/analysis/bin
    ----------------------------------------START Fri Aug 5 18:27:16 2016
    /opt/smrtanalysis-1.3.3/analysis/bin/wgs-7.0/Linux-amd64/bin/fastqToCA -libraryname PacBio -type sanger -innie -technology pacbio -reads /opt/smrtanalysis/common/inputs_dropbox/renilla_filtered_subread_fastq.fastq > /opt/smrtanalysis/common/jobs//ec_pacbio_ren.frg
    ----------------------------------------END Fri Aug 5 18:27:16 2016 (0 seconds)
    ----------------------------------------START Fri Aug 5 18:27:16 2016
    /opt/smrtanalysis-1.3.3/analysis/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d tempec_pacbio_ren "sge = -V -S /bin/sh -sync y" sgePropagateHold=corAsm stopAfter=initialStoreBuilding illumina.frg /opt/smrtanalysis/common/jobs//ec_pacbio_ren.frg
    ----------------------------------------START Fri Aug 5 18:27:16 2016
    qsub -V -S /bin/sh -sync y -pe smp 16 -cwd -N "rCA_asm" -j y -o /opt/smrtanalysis/common/jobs/tempec_pacbio_ren/runCA.sge.out.00 /opt/smrtanalysis/common/jobs/tempec_pacbio_ren/runCA.sge.out.00.sh
    sh: qsub: not found
    ----------------------------------------END Fri Aug 5 18:27:16 2016 (0 seconds)
    ERROR: Failed with signal 127
    ================================================================================

    runCA failed.

    ----------------------------------------
    Stack trace:

    at /opt/smrtanalysis-1.3.3/analysis/bin/wgs-7.0/Linux-amd64/bin/runCA line 1237
    main::caFailure('Failed to submit script.\x{a}') called at /opt/smrtanalysis-1.3.3/analysis/bin/wgs-7.0/Linux-amd64/bin/runCA line 1214
    main::submitScript(undef) called at /opt/smrtanalysis-1.3.3/analysis/bin/wgs-7.0/Linux-amd64/bin/runCA line 5870

    ----------------------------------------
    Failure message:

    Failed to submit script.


    ----------------------------------------END Fri Aug 5 18:27:16 2016 (0 seconds)
    Failed to execute /opt/smrtanalysis-1.3.3/analysis/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d tempec_pacbio_ren "sge = -V -S /bin/sh -sync y" sgePropagateHold=corAsm stopAfter=initialStoreBuilding illumina.frg /opt/smrtanalysis/common/jobs//ec_pacbio_ren.frg[/FONT][/SIZE][/SIZE][/SIZE]

  • #2
    sh: qsub: not found


    This indicates that the SGE binaries are not in your $PATH.

    I'm assuming you're trying to run it locally on an AWS server, and not through SGE.

    Try setting the option `useGrid=0` in your config file to tell it to run locally.
    Last edited by gconcepcion; 08-05-2016, 12:29 PM.

    Comment


    • #3
      What's the experiment? How old is the data you are looking at? The version of SMRT Analysis you are using is extremely old "/opt/smrtanalysis-1.3.3/" and out of date.

      Comment

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