Bernt Guldbrandtsen
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Activity overview
Latest activity by Bernt Guldbrandtsen-
Bernt Guldbrandtsen commented,
HI Tiff, Thank you again for your reply. With version 4.1.8.1 and the new option added, the import proceeds at about 1.5 MB per second running against the NFS file server. A thing that puzzles me i...
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Bernt Guldbrandtsen commented,
Dear Tiff, Thank you for your reply, and sorry for the very slow response. As before (for consistency), I'm testing with version gatk-4.1.6.0. For reference, the command line is listed at the botto...
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Bernt Guldbrandtsen commented,
Hi Tiffany, Thank you! Our sysadmin moved the relevant files to a different file server (zfs, ssd, 10 Gb network), usually never breaks a sweat under heavy load. I tried a job allocating 23 (virtua...
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Bernt Guldbrandtsen commented,
Hi Tiffany Miller, Thank you for your reply. The other threads do not help solve this. Parallelization does not seem to do the trick. In the first seconds according to "top", the java process does ...
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Bernt Guldbrandtsen commented,
Hi Samuel, I have tried various sets of values. The amounts of memory, I have tried did not seem to make a difference for speed. The current batch of jobs runs with jopt="-Xmx10g -Xms5g" Currentl...
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Bernt Guldbrandtsen commented,
Hello again, now the first batch of 50 samples has finished for the shortest autosome (BTA25). It took 36 hours. That means the total time to import the shortest autosome is going to take about two...
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Bernt Guldbrandtsen commented,
Hi Tiffany, Thank you for your reply. 1. To check, I increased Xms to 200g. 2. I don't understand the latter part of the comment. I'm running a GenomicsDBImport. Given 29 autosomes, the X, the MT ...
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Bernt Guldbrandtsen commented,
Hi Tiffany, Thank you for the link. I looked through it, and it says GATK should be able to run in parallel. However, GATK-4.1.4.1 upon initialization says: "20:33:38.220 WARN GenomicsDBImport - Ge...
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Bernt Guldbrandtsen created a post,
Strategy for buildling GenomicsDB
Hello, Until now, I have stuck with GATK 3.8, as I haven't found a good strategy to build a GenomicsDB for use with GATK 4. I have a substantial number of germline GVCF files which work fine with ...