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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

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