[BUG] bowtie database not found
bernt-matthias opened this issue · 1 comments
Describe the bug
I'm getting
No MetaPhlAn BowTie2 database found (--index option)!
Expecting location bowtie2db
when calling metaphlan as follows:
metaphlan ... --bowtie2db '/gpfs1/data/galaxy_server/galaxy/tool-data/metaphlan/data/mpa_v30_CHOCOPhlAn_201901/' --index 'mpa_v30_CHOCOPhlAn_201901' ...
The folder content is tree /gpfs1/data/galaxy_server/galaxy/tool-data/metaphlan/data/mpa_v30_CHOCOPhlAn_201901/
/gpfs1/data/galaxy_server/galaxy/tool-data/metaphlan/data/mpa_v30_CHOCOPhlAn_201901/
├── mpa_v30_CHOCOPhlAn_201901.1.bt2
├── mpa_v30_CHOCOPhlAn_201901.2.bt2
├── mpa_v30_CHOCOPhlAn_201901.3.bt2
├── mpa_v30_CHOCOPhlAn_201901.4.bt2
├── mpa_v30_CHOCOPhlAn_201901.fna.bz2
├── mpa_v30_CHOCOPhlAn_201901.md5
├── mpa_v30_CHOCOPhlAn_201901.pkl
├── mpa_v30_CHOCOPhlAn_201901.rev.1.bt2
├── mpa_v30_CHOCOPhlAn_201901.rev.2.bt2
└── mpa_v30_CHOCOPhlAn_201901.tar
I guess this is because
MetaPhlAn/metaphlan/metaphlan.py
Line 367 in 6c50424
mpa_v30_CHOCOPhlAn_201901.bt2
is available and irgnores the possibility of mpa_v30_CHOCOPhlAn_201901.1.bt2
.
Or do the bowtie indices be constructed in a different way?
To Reproduce
See above
Screenshots
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Platform (please complete the following information):
This is for the latest Galaxy tool version
Additional context
NA
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