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oschwengers / referenceseeker

Rapid determination of appropriate reference genomes.
https://doi.org/10.21105/joss.01994
GNU General Public License v3.0
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<NA/> is being added to the start of file path #19

Closed Rob-murphys closed 3 years ago

Rob-murphys commented 3 years ago

Describe the bug NA/ is being added to the start of file path resulting it it not being added to database

Input: referenceseeker_db import --db /home/people/robmur/ku_00014/data/termitomyces/referenceSeeker_db/termitomyces --genome /home/people/robmur/ku_00014/data/termitomyces/sequences/D53_scaffolds.fasta

Output: ERROR: could not import genome (NA//home/people/robmur/ku_00014/data/termitomyces/sequences/D53_scaffolds.fasta) into database (/home/people/robmur/ku_00014/data/termitomyces/referenceSeeker_db/termitomyces)!

Proof file exists:

(base) [robmur@g-12-l0002 phylogeny]$ ll /home/people/robmur/ku_00014/data/termitomyces/sequences/D53_scaffolds.fasta
-rw-rw-r-- 1 robmur ku_00014 196777164 Apr 21 11:00 /home/people/robmur/ku_00014/data/termitomyces/sequences/D53_scaffolds.fasta

The organism name is being added to the front of the --genome file path. It seems this is only added in the error report but not during the actual import so I am none the wiser as to what the actual issue is.

The sequence does seems to be getting added to the database under the name of the first record in the fasta file. Looks like it is in the mash or tsv creation steps then maybe?

oschwengers commented 3 years ago

Hi @Lamm-a , thanks for reporting this issue. I've fixed a couple of minor issues and added some more CI tests to cover these better. A new release v1.7.3 is on its way: https://github.com/oschwengers/referenceseeker/releases/tag/v1.7.3 I'll let you know when it is available via Bioconda.

oschwengers commented 3 years ago

@Lamm-a the new version v1.7.3 is now available via conda. Could you please try it again with the new version?

Rob-murphys commented 3 years ago

@oschwengers Awesome thank you ! I will give it a go then let you know, in a couple of hours unfortunatly as I am in the wet lab today.

Rob-murphys commented 3 years ago

@oschwengers issue fixed. The genomes now successfully imported. Both the .msh and .tsv are now populated.