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KCCG / ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
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wigToBigWig error #34

Closed gneedle1 closed 2 months ago

gneedle1 commented 2 years ago

When running, the program kills during wigToBigWig in the bigwig.q0.patient.sh step. The error is:

wigToBigWig /app/project_folder/alignments/patient/bw/tmp/patient.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/patient/bw/patient.q0.bw /app/project_folder/alignments/patient/bw/sh/bigwig.q0.patient.sh: line 7: 4593 Killed wigToBigWig /app/project_folder/alignments/patient/bw/tmp/patient.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/patient/bw/patient.q0.bw

J-Bradlee commented 2 years ago

Do you mind if you can cat and share the script found at project_folder/alignments/patient/bw/sh/bigwig.q0.patient.sh . Change "project_folder" to the name of the folder you defined when you set the project_folder environment variable: project_folder=$PWD/{name of folder you made to be project folder} .

Just so we can verify why its breaking on line 7.

gneedle1 commented 2 years ago

set -e -x -o pipefail

export PATH=/app/clinsv/bin:$PATH

cd /app/project_folder/alignments/patient/bw/ wigToBigWig /app/project_folder/alignments/patient/bw/tmp/patient.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_f>## checking the content of bw... bigWigToWig /app/project_folder/alignments/patient/bw/patient.q0.bw stdout | wc -l > /app/project_folder/alignments/patient/bw/patient.q0.bw.test wclTest=$(cat /app/project_folder/alignments/patient/bw/patient.q0.bw.test) if [ $wclTest -eq 3220490784 ]; then echo "bw size == 3220490784 OK "; else echo "bs size $wclTest != 3220490784, bw potentially truncated"; exit 111; fi

rm /app/project_folder/alignments/patient/bw/tmp/patient.q0.wig

J-Bradlee commented 2 years ago

Sorry for the late reply. I have recived this error before, I think your OS might of shut wigToBigWig down, this can happen if ClinSV starts taking up too much ram. Are you sure that there is over 60 gb of ram available?

gneedle1 commented 2 years ago

oh shoot, not at the moment. I will free up space and try again!

J-Bradlee commented 2 years ago

Cool try again with more ram and let me know if it fixed it