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Syed Murtuza Baker
Apr 25, 2017, 1:47:11 PM4/25/17
to CLARK Users
Hello,
I ran classify_metagenome and it is running for two days in my cluster, the last output that it gave is
CLARK version 1.2.3 (UCR CS&E. Copyright 2013-2016 Rachid Ounit, roun...@cs.ucr.edu)
The program did not find the database files for the provided settings and reference sequences. The program will build them.
Starting the creation of the database of targets specific 21-mers from input files...
Progress report: (2/5)
Is there any chance that it got stuck on something?
Best Regards,
Syed
I ran classify_metagenome and it is running for two days in my cluster, the last output that it gave is
CLARK version 1.2.3 (UCR CS&E. Copyright 2013-2016 Rachid Ounit, roun...@cs.ucr.edu)
The program did not find the database files for the provided settings and reference sequences. The program will build them.
Starting the creation of the database of targets specific 21-mers from input files...
Progress report: (2/5)
Is there any chance that it got stuck on something?
Best Regards,
Syed
Rachid
Apr 27, 2017, 9:32:30 AM4/27/17
to CLARK Users
Hello Syed,
Please let us know how much RAM available your cluster has. It seems the program became slow because it can not find enough space in memory and probably is swapping between disk and RAM?
I believe you should be able to request a cluster dedicated for RAM-intensive jobs (~150GB for the database creation).
Cheers,
Rachid
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