[Errno 2] No such file or directory: 'gtdbtk_outdir/gtdbtk_bac120_markers_summary.tsv'

[ZhihaoXie]

When I run gtdbtk classify_wf, it error message below:

[2018-03-07 10:42:06] INFO: GTDB-Tk v0.0.3
[2018-03-07 10:42:06] INFO: gtdbtk classify_wf --genome_dir ./test1/ --out_dir gtdbtk_outdir -x fa --min_perc_aa 50 --prefix metabat --cpus 12
[2018-03-07 10:42:06] WARNING: Results are still being validated and taxonomic assignments may be incorrect! Use at your own risk!
[2018-03-07 10:42:06] INFO: Identifying markers in 1 genomes with 12 threads.
[2018-03-07 10:42:06] INFO: Running Prodigal to identify genes.
==> Finished processing 1 of 1 (100.0%) genomes.
[2018-03-07 10:42:18] INFO: Identifying TIGRfam protein families.
==> Finished processing 1 of 1 (100.0%) genomes.
[2018-03-07 10:42:26] INFO: Identifying Pfam protein families.
==> Finished processing 1 of 1 (100.0%) genomes.
[2018-03-07 10:42:28] INFO: Done.
[2018-03-07 10:42:28] INFO: Aligning markers in 1 genomes with 12 threads.
[2018-03-07 10:42:28] ERROR: [Errno 2] No such file or directory: 'gtdbtk_outdir/gtdbtk_bac120_markers_summary.tsv'
[2018-03-07 10:42:28] ERROR: GTDB-Tk has encountered an error.
[2018-03-07 10:42:28] INFO: Done.
[2018-03-07 10:42:28] INFO: Done.

As you known, the --prefix param didn't work. And then, I change "--prefix metabat" to " --prefix gtdbtk", it work good. So，maybe it's a bug. And GTDB-Tk need mash, but there is no mention in the README.md file of this repository. Thanks.

[pchaumeil]

Dear Zhihao,

Thanks for your feedback. Both the prefix issue and the mash dependency requirement have been fixed in gtdbtk v0.0.4b1 ( https://pypi.python.org/pypi/gtdbtk/0.0.4b1 )

Regards, Pierre

[ZhihaoXie]

@Pierre Thanks for your work. Thanks.