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`tb-profiler update_tbdb --match_ref` fails

Open schorlton-bugseq opened this issue 3 months ago • 1 comments

On v6.2.0, I run: tb-profiler update_tbdb --match_ref myref.fna

I get:

ValueError: Command Failed:
/bin/bash -c set -o pipefail; tb-profiler create_db --prefix tbdb --csv mutations.csv --watchlist watchlist.csv --rules rules.txt --match_ref /test/tbdb/myref.fna --load

...

File "pysam/libcfaidx.pyx", line 121, in pysam.libcfaidx.FastaFile.__cinit__
  File "pysam/libcfaidx.pyx", line 153, in pysam.libcfaidx.FastaFile._open
OSError: file `/test/tbdb/myref.fna` not found

It looks like it's looking for the ref in tbdb dir and not the parent where it is located.

Thanks for your help and tool!

schorlton-bugseq avatar Mar 26 '24 19:03 schorlton-bugseq