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]
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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