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.
MuTect repeatedly hangs
I have tried running MuTect on about 10 samples a number of times each now. MuTect seems to randomly hang at different times while processing, and makes no further progress until the process hits the cluster wall time and is killed. This is with MuTect 1.1.4 downloaded last week.
The hang does not occur at the same point for a given sample each time it is run. Three of ten samples finished and didn't hang.
Here is an example of the parameters I'm passing to MuTect:
INFO 10:18:50,248 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-25-g2a68eab, Compiled 2012/11/08 10:30:02
INFO 17:57:57,086 HelpFormatter - Program Args: --analysis_type MuTect --reference_sequence hg19_wRandomsNew.fa --cosmic CosmicCodingMuts_v66_20130725.sorted.chr.vcf --dbsnp dbsnp_132_b37.leftAligned.chr.vcf --input_file:normal NJ_DIPG_O6N.t30l30.realigned.markdup.sorted.fixmate.final.bam --input_file:tumor NJ_DIPG_06T.t30l30.realigned.markdup.sorted.fixmate.final.bam --out NJ_DIPG_06.call_stats.out -log NJ_DIPG_06.mutect.log --num_threads 4
This process ran for 1hr20 before it stopped producing output, and it was killed after 24 hrs. Here is the end of the output it produced:
INFO 11:37:37,628 ProgressMeter - chr2:129339397 3.79e+08 78.6 m 12.5 s 12.2% 10.7 h 9.4 h
INFO 11:37:40,454 MuTect - [MUTECTOR] Processed -1915761945 reads in 6153 ms
INFO 11:37:43,393 MuTect - [MUTECTOR] Inspected 828000 potential candidates
INFO 11:37:48,253 MuTect - [MUTECTOR] Processed -1914761944 reads in 7799 ms
INFO 11:37:55,192 MuTect - [MUTECTOR] Inspected 829000 potential candidates
INFO 11:37:56,187 MuTect - [MUTECTOR] Processed -1913761940 reads in 7934 ms
INFO 11:38:00,243 MuTect - [MUTECTOR] Processed -1912761494 reads in 4056 ms
INFO 11:38:02,117 MuTect - [MUTECTOR] Processed -1911761112 reads in 1874 ms
INFO 11:38:03,337 MuTect - [MUTECTOR] Processed -1910761108 reads in 1220 ms
INFO 11:38:04,319 MuTect - [MUTECTOR] Inspected 830000 potential candidates
INFO 11:38:05,288 MuTect - [MUTECTOR] Processed -1909761095 reads in 1951 ms
INFO 11:38:18,352 ProgressMeter - chr2:130940745 3.80e+08 79.2 m 12.5 s 12.3% 10.8 h 9.5 h
INFO 11:38:19,105 MuTect - [MUTECTOR] Processed -1908760932 reads in 13817 ms
I'm not sure how to get MuTect to run completely. Any thoughts what could be causing this? Let me know if there's more data I could provide to help figure it out.