Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.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.

Computataion time per one million records,is varying in different modules of GATK 4

Hi GATK Team,

While computing RevertedSAM , Markilluminaadapter and SamtoFastq Module there is an inconsistency in processing time for each 1 million records. For Instance in the below segments RevertedSAM, Markilluminaadapter and SamtoFastq module are taking processing time of 4 , 7 and 85 seconds respectively.

Kindly suggest a solution and reason why its so slow in SamtoFastq module and faster in other two mentioned modules of GATK 4.

RevertedSAM taking 4s
INFO 2019-07-29 11:08:23 RevertSam Reverted 764,000,000 records. Elapsed time: 00:54:44s. Time for last 1,000,000: 4s. Last read position: /
INFO 2019-07-29 11:08:27 RevertSam Reverted 765,000,000 records. Elapsed time: 00:54:48s. Time for last 1,000,000: 4s. Last read position: /
INFO 2019-07-29 11:08:32 RevertSam Reverted 766,000,000 records. Elapsed time: 00:54:53s. Time for last 1,000,000: 4s. Last read position: /
INFO 2019-07-29 11:08:36 RevertSam Reverted 767,000,000 records. Elapsed time: 00:54:57s. Time for last 1,000,000: 4s. Last read position: /
INFO 2019-07-29 11:08:40 RevertSam Reverted 768,000,000 records. Elapsed time: 00:55:01s. Time for last 1,000,000: 4s. Last read position: /
INFO 2019-07-29 11:08:44 RevertSam Reverted 769,000,000 records. Elapsed time: 00:55:05s. Time for last 1,000,000: 4s. Last read position: /

MarkIlluminaadapter taking 7s
INFO 2019-07-29 11:40:03 MarkIlluminaAdapters Read 80,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 7s. Last read position: /
INFO 2019-07-29 11:40:07 MarkIlluminaAdapters Read 73,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 7s. Last read position: /
INFO 2019-07-29 11:40:10 MarkIlluminaAdapters Read 81,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 7s. Last read position: /
INFO 2019-07-29 11:40:15 MarkIlluminaAdapters Read 74,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 7s. Last read position: /

SAMToFASTQ taking 85s
INFO 2019-07-31 22:35:11 SamToFastq Processed 422,000,000 records. Elapsed time: 10:04:22s. Time for last 1,000,000: 85s. Last read position: /
INFO 2019-07-31 22:35:47 SamToFastq Processed 425,000,000 records. Elapsed time: 10:04:58s. Time for last 1,000,000: 85s. Last read position: /
INFO 2019-07-31 22:36:36 SamToFastq Processed 423,000,000 records. Elapsed time: 10:05:47s. Time for last 1,000,000: 85s. Last read position: /
INFO 2019-07-31 22:37:13 SamToFastq Processed 426,000,000 records. Elapsed time: 10:06:24s. Time for last 1,000,000: 85s. Last read position: /

Tagged:

Answers

Sign In or Register to comment.