Non zero existing of scatngs

Question

[zizigolu]

Hi,

I am trying to use scatngs for copy number calling

https://github.com/cancerit/ascatNgs

But nothing happens and asking for tumor while tumor already defined, have you used this tool at all?

-bash-4.1$ singularity exec /local/containers/dockstore-cgpwgs-2.0.1.simg ascat.pl -o POUT/result -t ASCEX/tumor.bam -n ASCEX/normal.bam -r REF/hs37d5.fa -sg REF/SnpGcCorrections.tsv -g XX -pr WGS 
Executing: /opt/wtsi-cgp/bin/ascat.pl -o POUT/result -t ASCEX/tumor.bam -n ASCEX/normal.bam -r REF/hs37d5.fa -sg REF/SnpGcCorrections.tsv -g XX -pr WGS
Option 'tumour' (/scratch/ASCEX/tumor.bam) should be an existing file.

Answer 1

[GenoMax]

Is that file path available within singularity? Is /scratch/ASCEX/tumor.bam real full path to that file?

[zizigolu]

Thank you

-bash-4.1$ cd /home/local/containers/
-bash-4.1$ ls
Singularity  dockstore-cgpwgs-2.0.1.simg
-bash-4.1$

I have tried with full path though without export :(

-bash-4.1$ module load singularity/2.6.0
-bash-4.1$ export SINGULARITY_BINDPATH=/scratch

-bash-4.1$ singularity exec /local/containers/dockstore-cgpwgs-2.0.1.simg ascat.pl -h
Usage:
    ascat.pl [options]

      Please define as many of the parameters as possible

      Required parameters

        -outdir       -o    Folder to output result to.
        -tumour       -t    Tumour BAM/CRAM file
        -normal       -n    Normal BAM/CRAM file
        -reference    -r    Reference fasta
        -snp_gc       -sg   Snp GC correction file
        -protocol     -pr   Sequencing protocol (e.g. WGS, WXS)
        -gender       -g    Sample gender (XX, XY, L)
                              For XX/XY see '-gc'
                              When 'L' see '-l'


      Other
        -help         -h    Brief help message
        -man          -m    Full documentation.
        -version      -v    Ascat version number

-bash-4.1$

[GenoMax]

I assume /scratch is present on host and you are binding it in singularity? Is ASCEX a directory under /scratch? Is /scratch/ASCEX/tumor.bam real full path to that file on your OS?

[zizigolu]

You were alright, I should bind temp to

-bash-4.1$ export SINGULARITY_BINDPATH=/temp

But I am not able to understand the logic behind that :(

[GenoMax]

https://www.sylabs.io/guides/3.1/user-guide/bind_paths_and_mounts.html#user-defined-bind-paths

You still have not answered this: Is /scratch/ASCEX/tumor.bam real full path to that file?

[zizigolu]

Sorry I did not use export and used the full path because I am not sure if /scratch/ASCEX/tumor.bam is real full path to that file

-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/tumor.bam -n /temp/hgig/fi1d18/Oesophageal/normal.bam -r /temp/hgig/fi1d18/hs37d5.fa -sg /temp/hgig/fi1d18/reference/SnpGcCorrections.tsv -g L -pr WGS
Executing: /opt/wtsi-cgp/bin/ascat.pl -o /temp/hgig/fi1d18/copyca/ -t /temp/hgig/fi1d18/Oesophageal/tumor.bam -n /temp/hgig/fi1d18/Oesophageal/normal.bam -r /temp/hgig/fi1d18/hs37d5.fa -sg /temp/hgig/fi1d18/reference/SnpGcCorrections.tsv -g L -pr WGS
Reading locis
Done reading locis

Thank you for helping, without your mentioning about path I would wander for days without any clue