[INFO][WGSCoveragePlotter]no valid chromosome was found in

[jolvany]

Verify

• if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue
• the version of java

Subject of the issue

The wgscoverageplotter is throwing an error I don't know how to remedy, and that makes no sense logically because the fasta file is normal and has a .dict file.

from the log:

[INFO][WGSCoveragePlotter]no valid chromosome was found in /directory/PlasmoDB-51_Pfalciparum3D7_Genome.fasta [INFO][Launcher]wgscoverageplotter Exited with failure (-1)

Your environment

• version of jvarkit - your Readme says Feb 2019
• version of java -openjdk version "1.8.0_322"
• the value of ${JAVA_HOME}- nothing comes up
• which OS - Red Hat Enterprise Linux Server v 7.9

Steps to reproduce

I have a sorted and indexed .bam file with the reads from an alignment to the above mentioned fasta file I downloaded and assembled the package following the steps on https://lindenb.github.io/jvarkit/WGSCoveragePlotter.html I used the following command java -jar dist/wgscoverageplotter.jar --dimension 1500x500 -C -1 --clip -R /directory/PlasmoDB-51_Pfalciparum3D7_Genome.fasta /directory/full_falciparum_sorted.bam --include-contig-regex "PF.*" --percentile median > /directory/pf_coverage.svg

The first error it threw said that I was missing a .dict file for the fasta file, so I generated one with samtools dict, with the following

samtools dict PlasmoDB-51_Pfalciparum3D7_Genome.fasta > PlasmoDB-51_Pfalciparum3D7_Genome.dict

then reran and got the above error

Expected behaviour

I should have a .svg with 16 chr with the corresponding coverage

Actual behaviour

Failed the .svg generation with error above

[jolvany]

Never mind I think it was not understanding the chromosome names properly because of certain things appended to the header line and it was skipping them. Removed the --include-contig-regex "PF.*" and it seems to potentially be working.