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cancerit / ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
http://cancerit.github.io/ascatNgs/
GNU Affero General Public License v3.0
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A permanen error in running ascatNgs #82

Closed beginner984 closed 5 years ago

beginner984 commented 5 years ago

Sorry, whatever I am trying my script being terminated by this 

-bash-4.1$ singularity exec /local/containers/dockstore-cgpwgs-2.0.1.simg ascat.pl -o /temp/hgig/fi1d18/copyca/ -t /temp/hgig/fi1d18/Oesophageal/1631_WTSI-OESO_121_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-OESO_121_1pre.dupmarked.bam -n /temp/hgig/fi1d18/Oesophageal/1631_WTSI-OESO_005_b/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-OESO_005_b.dupmarked.bam -r /temp/hgig/fi1d18/hs37d5.fa -sg /temp/hgig/fi1d18/reference/SnpGcCorrections.tsv -g XX -pr WGS
Executing: /opt/wtsi-cgp/bin/ascat.pl -o /temp/hgig/fi1d18/copyca/ -t /temp/hgig/fi1d18/Oesophageal/1631_WTSI-OESO_121_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-OESO_121_1pre.dupmarked.bam -n /temp/hgig/fi1d18/Oesophageal/1631_WTSI-OESO_005_b/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-OESO_005_b.dupmarked.bam -r /temp/hgig/fi1d18/hs37d5.fa -sg /temp/hgig/fi1d18/reference/SnpGcCorrections.tsv -g XX -pr WGS
Option 'tumour' (/temp/hgig/fi1d18/Oesophageal/1631_WTSI-OESO_121_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-OESO_121_1pre.dupmarked.bam) should be an existing file.
-bash-4.1$

Saying Option 'tumour' should be an existing file while I have defined that

Any help please?

Thank you

keiranmraine commented 5 years ago

How is your singularity configured? By default the container can't see filesystems you don't explicitly mount/bind.

Something like the following should work:

singularity exec \
--bind /temp/hgig/fi1d18/Oesophageal:/var/spool/inputs:ro \
--bind /temp/hgig/fi1d18:/var/spool/other:rw \
/local/containers/dockstore-cgpwgs-2.0.1.simg ascat.pl \
-o /var/spool/other/copyca \
-t /var/spool/inputs/1631_WTSI-OESO_121_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-OESO_121_1pre.dupmarked.bam \
-n /var/spool/inputs/1631_WTSI-OESO_005_b/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-OESO_005_b.dupmarked.bam \
-r /var/spool/other/hs37d5.fa \
-sg /var/spool/other/reference/SnpGcCorrections.tsv \
-g XX -pr WGS

I'd very much recommend you move all reference files into a folder so they can be mounted readonly (like I have for the inputs).

There's a clear example here:

https://github.com/cancerit/dockstore-cgpmap#singularity

The easiest way to test what you can see is by just using ls instead of the ascat.pl comand:

singularity exec /local/containers/dockstore-cgpwgs-2.0.1.simg ls \
/temp/hgig/fi1d18/Oesophageal/1631_WTSI-OESO_121_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-OESO_121_1pre.dupmarked.bam

Then try:

singularity exec \
--bind
--bind /temp/hgig/fi1d18/Oesophageal:/var/spool/inputs:ro \
/local/containers/dockstore-cgpwgs-2.0.1.simg ls \
/var/spool/inputs/1631_WTSI-OESO_121_1pre/mapped_sample/HUMAN_1000Genomes_hs37d5_genomic_WTSI-OESO_121_1pre.dupmarked.bam

I'm going to close this as it appears to be a usage issue.