Can not run ClinSV in Singularity

[weizhousjtu]

Dear Andre,

I installed Singularity by root and download clinsv.sif, refdata and NA12878_v0.9.bam as suggested. Then I run the following code:

$singularity run clinsv.sif \ -i "$input_path/*.bam" \ -ref $refdata_path \ -p $Out_path/project_folder The error is :

error exist status != 0 (512), please check /home/zhouwei/zhou_data/WGS/CHD_Trio_WGS//project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.e for more information

I check the 'bigwig.createWigs.FR05812606.e' file and found

`

• export PATH=/opt/clinsv/bin:/opt/clinsv/bin:/opt/clinsv/root/bin:/bin/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
• PATH=/opt/clinsv/bin:/opt/clinsv/bin:/opt/clinsv/root/bin:/bin/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
• cd /home/project_folder/alignments/FR05812606/bw/
• sort -k2,2nr /home/RefData/reference/b37/clinsv/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta.fai
• awk '{print $1":1-"$2}'
• xargs -P 15 -t '-i{}' perl /opt/clinsv/clinSV/scripts/bam2wig.pl 1 q0 '{}' /home/project_folder/alignments/FR05812606/bw/tmp/FR05812606.q0 /home/RefData/reference/b37/clinsv/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta /home//project_folder/alignments/FR05812606/FR05812606.bam sort: open failed: /home/clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta.fai: No such file or directory `

However, it worked when I run: sort -k2,2nr /home//clinsv/refdata-b37/genome/human_g1k_v37_decoy.fasta.fai

I noticed that

export PATH=/opt/clinsv/bin

However, my "clinsv.sif" file and Singularity file is not located in that path.

Does this cause the error? How do I set the corrected path of clinsv?

Thank you!

LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.2.1511 (Core) Release: 7.2.1511