Entering edit mode
5.0 years ago
zizigolu
★
4.3k
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.
Thank you
I have tried with full path though without export :(
I assume
/scratch
is present on host and you are binding it insingularity
? IsASCEX
a directory under/scratch
? Is/scratch/ASCEX/tumor.bam
real full path to that file on your OS?You were alright, I should bind temp to
But I am not able to understand the logic behind that :(
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?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 fileThank you for helping, without your mentioning about path I would wander for days without any clue