Dear all,

[Szymon]

I have a following question regarding the set_targets.sh usage.

I have run the following comand on my server after loading the Clark module in the bath script

set_targets.sh $DB_PATH_VIRAL viruses --species

After 10 hours I get the following output from the tail command:

Downloading done. Uncompressing files... 

Viruses sequences downloaded!

Re-building viruses.fileToAccssnTaxID

Loading accession number of all files... done (10012)

Loading merged Tax ID... done

Retrieving taxonomy ID for each file... done (10003 files were successfully mapped, and 9 unidentified).

viruses: Retrieving taxonomy nodes for each sequence based on taxon ID...

Loading nodes of taxonomy tree... done.

Retrieving lineage for each sequence...

After a few hours it did not go anywhere forward

The program seems to be stuck at that point.

For my server config I am using 120GB RAM and 24 threads available.

What can be the reason of such a behavior?

Best regards,

Szymon

[Rachid]

Hi Szymon,

Thank you for reporting this issue!

This is not normal behavior. Let's see, when did you install CLARK and when did you execute this run (set_targets.sh $DB_PATH_VIRAL viruses --species) ?

I wonder if the taxonomy info is not up-to-date, in that case, I'd recommend to execute "updateTaxonomy.sh" and try again.

Best,

Rachid