[Error] when "[6] Add new genomes to VHM database..." - feature to ignore non-fasta files (or directories) in --fna_dir

[Josue Rodriguez]

I was trying to run the command to add additional genomes to the iPHoP database as follows:

iphop add_to_db --fna_dir ./genomes --gtdb_dir ./GTDB-tk_results/ --db_dir ./Sept_2021_pub_rw --num_threads 20 --out_dir ./new_iphop_db --debug

The job would run steps [1] through [5] just fine, but then would hang on step [6]:

Loading custom packages...
Load existing database
Running Host Db building function

Job would eventually just time out with no error. Looked into the head node and found:

read(4, xx, ##) = -1 EISDIR (Is a directory)

Turns out that --fna_dir had two folders within that which were not in .fasta format. The program did not know how to skip or address these, and so it was stalling at that point. Removing the folders within --fna_dir resolved the issue.

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Request to either 1) Have iPHoP ignore non-fasta files in a dir (or skip other dirs), or 2) output an error that would be more easy to debug for others.

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Love the tool- and thanks for the help troubleshooting!

[Simon Roux]

Thanks for reporting it, and glad you found the solution ! :-)

[Simon Roux]

On hold until preparing the next release, where this should be corrected as suggested.