Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

DepthOfCoverage run time 4.6 days?

balterbalter Portland OregonMember

Very new to bioinformatics tools here.

I'm running DepthOfCoverage with a list of 30 bam files 1 to 2 GB each on a (rat) reference genome ~ 1.8 GB. My terminal window is taunting me with :

INFO  16:29:24,523 ProgressMeter -      1:74214637   7.4203136E7     2.9 h       2.3 m        2.6%     4.6 d       4.5 d
INFO  16:30:24,525 ProgressMeter -      1:74636521   7.462912E7     2.9 h       2.3 m        2.6%     4.6 d       4.5 d
INFO  16:31:24,526 ProgressMeter -      1:75031737   7.5022336E7     2.9 h       2.3 m        2.6%     4.6 d       4.5 d
INFO  16:32:24,528 ProgressMeter -      1:75443037   7.5431936E7     2.9 h       2.3 m        2.6%     4.6 d       4.5 d
INFO  16:33:24,530 ProgressMeter -      1:75854037   7.5841536E7     2.9 h       2.3 m        2.6%     4.6 d       4.5 d
INFO  16:34:24,532 ProgressMeter -      1:76272821   7.626752E7     3.0 h       2.3 m        2.7%     4.6 d       4.5 d
INFO  16:35:24,533 ProgressMeter -      1:76708805   7.6693504E7     3.0 h       2.3 m        2.7%     4.6 d       4.5 d

This is how I ran it:

java -jar $GATK \
`  `-T DepthOfCoverage \
`  `-R $REF_GENOME \
`  `-o depth.txt \
`  `-I input.list \
`  `--outputFormat csv

Is that just how long it should take?

Answers

Sign In or Register to comment.