Comments (6)
That should be the only change - just add the -R '...' to the end of the string. Or, pass this in through gridEngineMemoryOption="-M MEMORY -R '...'" on the canu command line (or specfile) and leave the code unmodified.
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Thanks! I'm giving the gridEngineMemoryOption a go. Got an error first
time up which may have been down to threaded jobs running on multiple
hosts (adding span [hosts=1] to the -R option).
As an aside, the link to the gzipped 25X subset FASTQ E. coli reads from
the readthedoces page throws a 404 error (using curl to get the unzipped
file works fine).
Best regards,
Martin
On Tue, 5 Jan 2016, brianwalenz wrote:
That should be the only change - just add the -R '...' to the end of the string. Or, pass this in through
gridEngineMemoryOption="-M MEMORY -R '...'" on the canu command line (or specfile) and leave the code unmodified.—
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Hi again,
Setting gridEngineMemoryOption on the command line is working but my jobs are still failing. This time with a non-existent job array after the first job runs. It looks like the gridEngineHoldOption setting is causing problems. I've tried changing this on the command line but I'm not sure exactly what the format needs to be. I think the issue is that numended requires the job ID and the -w check is using job name?
I've attached the output file.
Thanks,
Martin
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Yep, now you're in the untested code based on LSF documentation since we don't have a system to test on. The LSF documentation claims that done, ended, etc take either job name or job id but it might be the case that numended doesn't follow this behavior. You can try modifying
src/pipelines/canu/Execution.pm, line 803 from:
if (uc(getGlobal("gridEngine")) eq "PBS" || uc(getGlobal("gridEngine")) eq "SLURM"){
to
if (uc(getGlobal("gridEngine")) eq "PBS" || uc(getGlobal("gridEngine")) eq "SLURM" || uc(getGlobal("gridEngine") eq "LSF"){
and see if that makes the holds valid. However, there would still be untested LSF code in terms of job restarts/resumes.
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This fix worked for me: #39
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And that was just merged in commit 7b16f2f. Thanks!
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Related Issues (20)
- Bogart Failed, Unknown Options Error HOT 2
- ERROR: Invalid command line option 'barcode06.fastq.gz'. Did you forget quotes around options with spaces? HOT 7
- Correction step parameters HOT 1
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- some canu contigs are in reverse HOT 4
- Runing canu in conda environment in HPC, which one is the assembly contig file I that I should get? HOT 3
- Bogart BestOverlapGraph::removeLopsidedEdges HOT 1
- About the memory space and script HOT 2
- how to get only one contig by setting the parameter? HOT 2
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- Will Canu read correction reduce true variation for strain-typing ONT reads? HOT 2
- no Corrected reads created HOT 7
- how to regenerate the readNames.txt HOT 2
- Question: parameters for better quality data HOT 1
- Error: Could not establish configuration source HOT 1
- How much storage space is required for the assembly of a large genome species? HOT 1
- reads overlap file HOT 1
- Possible problem with consensus step HOT 1
- sqStoreCreate failed. Failed with exit code 1. (rc=256) HOT 4
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