ClinSV issue

Question

[Jordi]

Hi,

I am testing ClinSV on a Ubuntu 20.04 VM. I pulled the docker image and tried to run the following command:

sudo docker run kccg/clinsv -r all -i $PWD/WGS/*.bam -ref $PWD/WGS/Reference_hg19/hg19.fa -p $PWD/test_run

The script seems to start correctly, but stops right away at the first task. This is the console output I get:

##############################################
####                ClinSV                ####
##############################################
# 15/03/2022 08:40:29

# clinsv dir: /app/clinsv
# projectDir: /media/analyst/Data/test_run
# sampleInfoFile: /media/analyst/Data/test_run/sampleInfo.txt 
# name stem: test_run
# lumpyBatchSize: 15
# genome reference: /media/analyst/Data/WGS/Reference_hg19/hg19.fa
# run steps: all
# number input bams: 1

# Create sample info file from bam files ...
ln -s  /media/analyst/Data/test_run/alignments//.bam

Unfortunately there are no error messages nor any hints as to what may be wrong. Any idea where the problem may lie?

Thanks for your help.

[Charles R.]

Did you ever find a answer to this?