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Old 08-05-2016, 10:30 AM   #1
quattrinia
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Location: Philadelphia

Join Date: Jun 2013
Posts: 5
Default 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]
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Old 08-05-2016, 12:24 PM   #2
gconcepcion
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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 at 12:29 PM.
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Old 08-12-2016, 12:10 PM   #3
rhall
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Join Date: Aug 2012
Posts: 322
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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.
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