Not writing output files but still says 'Success!'

[haleyhallowell]

Hi Stephen,

So sorry for the back to back issue requests. After your fix i was able to download the toolkit (and dependencies) and database easily (thanks!!). I ran the uhgv-toolkit in the following way:

uhgv-tools classify -i ../mappings/final_vOTUs_dedup.fna -o uhgv -d /home/hhallow1/scratch4-jsuez1/shared_databases/UHGV/uhgv-db-v0.4/ -t 10

Looking at the uhgv output directory, i am only seeing a directory called tmp. Looking further into the log file, this is what i am seeing:

UHGV-tools v0.0.1: classify

[1/10] Reading input sequences [2/10] Reading database sequences [3/10] Calculating nucleotide similarity with blastn [4/10] Identifying genes using prodigal-gv [5/10] Performing self alignment [6/10] Aligning proteins to database [7/10] Calculating amino acid similarity scores

Success! Elapsed time (s): 564.79 Peak RAM usage (GB): 7.6

For reference, this is what the database directory look like:

genomes.fna genomes.nhr genomes.not genomes.nto proteins.faa genomes.log genomes.nin genomes.nsq genome_taxonomy.tsv proteins.log genomes.ndb genomes.njs genomes.ntf proteins.dmnd viral_cluster_info.tsv

Any insight into this? Thanks!

[snayfach]

Apologies, I forgot to uncomment a few lines of code, and should be fixed now - can you try again?

[haleyhallowell]

worked perfectly!! Thanks!