Fusioncatcher build fails

[apeltzer]

Description of the bug

Command used and terminal output

nextflow run nf-core/rnafusion -r master -profile bi,XXX (this is a singularity profile), without home mounting.

Relevant files

No response

System information

No response

[apeltzer]

@fmalmeida FYI

[rannick]

I suspect it has to do with the home mounting. Fusioncatcher does a lot of explicit path coding that could be affected. Can you test with a standard singularity mount?

[apeltzer]

Yes, I can give it a try (y)

[apeltzer]

Hm still doesnt work I fear.

a.) STARfusion build error:
nhmmscan --noali --cut_ga --dfamtblout /tmp/BRphdvSPd7 --cpu=24 homo_sapiens_dfam.hmm ref_annot.cdsplus.fa
Error, cmd: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile homo_sapiens_dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 24 died with ret 6400 No such file or directory at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/../lib/Pipeliner.pm line 186.
Pipeliner::run(Pipeliner=HASH(0x5589ff7c0788)) called at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/dfam_repeat_masker.pl line 84
b.) Fusion Report

c.) Fusion Catcher Build: (also fails with 127 exit code, not fond -- I have to check thats the problem there still).

cc @fmalmeida FYI

[rannick]

Trying to reproduce, but with dev. I manage to run fusion-report, I would assume your error there is due to a access problem. Are you providing the correct cosmic username and password (quiagen ones)?

[apeltzer]

Trying to reproduce, but with dev. I manage to run fusion-report, I would assume your error there is due to a access problem. Are you providing the correct cosmic username and password (quiagen ones)?

Yes, and I already checked that they are accurate (and they are)... :-(