drmjc
commented
1 year ago Hi, Thanks for reporting. What is the error message in
${project_dir}/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e
Thanks
On Wed, 15 Mar 2023, 11:32 am mxiong2, @.***> wrote:
Note sure what the error status means. I tried running the default test bam files
refdata_path=/home/mai/Desktop/svclin/clinsv input_path=/home/mai/Desktop/svclin/bam_files project_folder=/home/mai/Desktop/svclin/test_run2
docker run -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 ############################################## ClinSV
############################################## 15/03/2023 03:38:51 clinsv dir: /app/clinsv projectDir: /app/project_folder sampleInfoFile: /app/project_folder/sampleInfo.txt name stem: project_folder lumpyBatchSize: 5 genome reference: /app/ref-data/refdata-b38 run steps: all number input bams: 1 Create sample info file from bam files ...
ln -s /app/input/NA12878_b38.bam /app/project_folder/alignments/FR05812606/FR05812606.bam ln -s /app/input/NA12878_b38.bam.bai /app/project_folder/alignments/FR05812606/FR05812606.bam.bai executing: sh /app/project_folder/alignments/FR05812606/bw/sh/ bigwig.createWigs.FR05812606.sh &> /app/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.e ... Read Sample Info from /app/project_folder/sampleInfo.txt use: FR05812606 H7LH3CCXX_6 /app/input/NA12878_b38.bam 1 samples to process If not, please exit make a copy of sampleInfo.txt, modify it and rerun with -s sampleInfo_mod.txt pointing to the new sample info file. Generate the commands and scripts bigwig lumpy cnvnator annotate prioritize qc Run jobs finished after (hh:mm:ss): 03:55:58 exist status: 0 executing: sh /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh &> /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e ... finished after (hh:mm:ss): 00:10:01 exist status: 35072
*** error exist status != 0 (35072), please check /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e for more information**
@.***:/home/mai/Desktop/svclin#
- 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/FR05812606/bw/
- wigToBigWig /app/project_folder/alignments/FR05812606/bw/tmp/FR05812606.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/FR05812606/bw/FR05812606.q0.bw /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh: line 7: 37060 Killed wigToBigWig /app/project_folder/alignments/FR05812606/bw/tmp/FR05812606.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/FR05812606/bw/FR05812606.q0.bw
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Note sure what the error status means. I tried running the default test bam files
refdata_path=/home/mai/Desktop/svclin/clinsv input_path=/home/mai/Desktop/svclin/bam_files project_folder=/home/mai/Desktop/svclin/test_run2
docker run -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 ##############################################
ClinSV
##############################################
15/03/2023 03:38:51
clinsv dir: /app/clinsv
projectDir: /app/project_folder
sampleInfoFile: /app/project_folder/sampleInfo.txt
name stem: project_folder
lumpyBatchSize: 5
genome reference: /app/ref-data/refdata-b38
run steps: all
number input bams: 1
Create sample info file from bam files ...
ln -s /app/input/NA12878_b38.bam /app/project_folder/alignments/FR05812606/FR05812606.bam ln -s /app/input/NA12878_b38.bam.bai /app/project_folder/alignments/FR05812606/FR05812606.bam.bai
executing: sh /app/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.sh &> /app/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.e ...
Read Sample Info from /app/project_folder/sampleInfo.txt
use: FR05812606 H7LH3CCXX_6 /app/input/NA12878_b38.bam
1 samples to process
If not, please exit make a copy of sampleInfo.txt, modify it and rerun with -s sampleInfo_mod.txt pointing to the new sample info file.
Generate the commands and scripts
bigwig
lumpy
cnvnator
annotate
prioritize
qc
Run jobs
finished after (hh:mm:ss): 03:55:58
exist status: 0
executing: sh /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh &> /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e ...
finished after (hh:mm:ss): 00:10:01
exist status: 35072
*** error exist status != 0 (35072), please check /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e for more information**
root@Ubuntu:/home/mai/Desktop/svclin#