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sanger-pathogens / circlator

A tool to circularize genome assemblies
http://sanger-pathogens.github.io/circlator/
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Problem with option gnuplotTested=true when calling canu #149

Open guibar opened 5 years ago

guibar commented 5 years ago

When running circlator with version 1.8 of canu, the execution fails because circlator call canu with the following command:

canu -useGrid=false gnuplotTested=true -assemble genomeSize=0.1m -d /root/lhs91/LHS91-pacbio/outcirc/03.assemble -p canu -pacbio-corrected /root/lhs91/LHS91-pacbio/outcirc/02.bam2reads.fastaq

and the parameter gnuplotTested=true is invalid for canu. Is there a workaround for this?

Thanks,

splaisan commented 5 years ago

same here

The following command failed with exit code 1
canu -useGrid=false gnuplotTested=true -assemble genomeSize=0.1m 
-d /data2/gridion_data/2741/circlator_ont_canu-out/03.assemble 
-p canu -nanopore-corrected /data2/gridion_data/2741/circlator_ont_canu-out/02.bam2reads.fasta
ERROR:  Parameter 'gnuplotTested' is not known.
maxgmarin commented 5 years ago

Same here.

The following command that Circlator submitted fails for the same reason (Using Canu 1.8).

The following command failed with exit code 1
canu -useGrid=false gnuplotTested=true -assemble genomeSize=0.1m -d /n/data1/hms/dbmi/farhat/mm774/Projects/PacBio_Evaluation_Project/AnalysisPipelineOutput/PacmanPipeV2_ENA_T1/output/ERX3451130/pacbio/circlator/03.assemble -p canu -pacbio-corrected /n/data1/hms/dbmi/farhat/mm774/Projects/PacBio_Evaluation_Project/AnalysisPipelineOutput/PacmanPipeV2_ENA_T1/output/ERX3451130/pacbio/circlator/02.bam2reads.fasta

Giving the following error:

ERROR:  Parameter 'gnuplotTested' is not known.
ilnamkang commented 5 years ago

I experienced the same error and solved it by editing one file in the install directory.

The file is "assemble.py" located in "/usr/local/lib/python3.4/dist-packages/circlator" on my system.

Delete a line 'gnuplotTested=true' from the file. In my case, the line number was 86.

I wish this trick would work for others.

EricDeveaud commented 5 years ago

since canu 1.8 gnuplotTested disapeared see: from canu/1.8 Changelog

Option 'gnuplotTested' was removed. Failure to find or run gnuplot is now handled automagically. Issues #1084 and #1129.