bigwig.q0.xxx errors out run ends

[tollecr]

When you run the docker version, v1.0:

docker pull mrbradley2/clinsv:v1.0

sampleInfo.txt: NG130ECKCK rg lb /app/input/NG130ECKCK.bam

I also had to make links to the bam files within the alignments\NG130ECKCK folder so that bigwig.createWigs.NG130ECKCK.sh could mostly run.

It errors out and if you run it again it always ends at the same place:

docker run --platform linux/amd64 -v $refdata_path:/app/ref-data
-v $project_folder:/app/project_folder
-v $input_path:/app/input
--entrypoint "perl" mrbradley2/clinsv:v1.0 /app/clinsv/bin/clinsv
-r all
-p /app/project_folder
-i "/app/input/*.bam"
-ref /app/ref-data/refdata-b38 \

End of the output obtained:

OK # job bigwig, createWigs, NG130ECKCK ran successfully (exit=0) -> skip : /app/project_folder/alignments/NG130ECKCK/bw/sh/bigwig.createWigs.NG130ECKCK.sh

executing: sh /app/project_folder/alignments/NG130ECKCK/bw/sh/bigwig.q0.NG130ECKCK.sh &> /app/project_folder/alignments/NG130ECKCK/bw/sh/bigwig.q0.NG130ECKCK.e ...

finished after (hh:mm:ss): 00:01:56

exist status: 35072

See the file /app/project_folder/alignments/NG130ECKCK/bw/sh/bigwig.q0.NG130ECKCK.e below:

***** error exist status != 0 (35072), please check /app/project_folder/alignments/NG130ECKCK/bw/sh/bigwig.q0.NG130ECKCK.e for more information

/app/project_folder/alignments/NG130ECKCK/bw/sh/bigwig.q0.NG130ECKCK.e :

• export PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
• PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
• cd /app/project_folder/alignments/NG130ECKCK/bw/
• wigToBigWig /app/project_folder/alignments/NG130ECKCK/bw/tmp/NG130ECKCK.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/NG130ECKCK/bw/NG130ECKCK.q0.bw /app/project_folder/alignments/NG130ECKCK/bw/sh/bigwig.q0.NG130ECKCK.sh: line 7: 36 Killed wigToBigWig /app/project_folder/alignments/NG130ECKCK/bw/tmp/NG130ECKCK.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/NG130ECKCK/bw/NG130ECKCK.q0.bw

issues listed as #58 and #53 don't help solve the issue. As #58 states I believe there are path issues here. Not sure how to solve them. You do need to correct the README, v1.0.0 doesn't exist:

docker pull mrbradley2/clinsv:v1.0

This could be very useful to many if you could get it working for the community/beginners.