Hi guys,
I use mutct2 to do somatic variant calls, and got this ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions? I searched the forum and found people got similar errors before when doing UnifiedGenotyper or HaplotypeCaller. Now I got this from running mutetc2. What's strange is that some of my samples went through mutect2 successfully. I am doing a analysis of 14 samples and so far 1 succeeded and 1 got the error, the rest are still running or in queue
Any suggestion?
Thanks a lot for the help!
Ying
sean@honey03 mutectOut]$ more 12-BI_S12.mutect_log
INFO 10:13:01,304 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:13:01,312 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 10:13:01,313 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 10:13:01,313 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 10:13:01,318 HelpFormatter - Program Args: -nct 8 -T MuTect2 -R /data02/sean/refGenome/mgp/REL-1505-SNPs_Indels/GRCm38_68.fa -I:tumor /data02/sean/BI_Mouse_Exo
me/12-BI_S12_fixmate_sorted_Dedup_merged_realign_recal_merged.bam -I:normal /data02/sean/BI_Mouse_Exome/BI_control_S15_S16_merged.bam --dbsnp /data02/sean/
refGenome/mgp/REL-1505-SNPs_Indels/mgp.v5.merged.indels.snps_all.dbSNP142.rsIDonly.sorted.C57BL_6NJ.vcf -o /data02/sean/BI_Mouse_Exome/mutectOut/12-BI_S12_somati
c.vcf
INFO 10:13:01,326 HelpFormatter - Executing as sean@honey on Linux 2.6.32-431.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_12_10_15_14-b00.
INFO 10:13:01,326 HelpFormatter - Date/Time: 2016/02/03 10:13:01
INFO 10:13:01,326 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:13:01,327 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:13:01,588 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:13:01,804 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 10:13:01,815 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 10:13:01,937 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
INFO 10:13:02,419 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 8 CPU thread(s) for each of 1 data thread(s), of 48 processors available on this
machine
INFO 10:13:02,636 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
INFO 10:13:03,402 GenomeAnalysisEngine - Done preparing for traversal
INFO 10:13:03,403 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 10:13:03,403 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 10:13:03,404 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
INFO 10:13:03,568 MuTect2 - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
INFO 10:13:03,570 PairHMM - Performance profiling for PairHMM is disabled because HaplotypeCaller is being run with multiple threads (-nct>1) option
Profiling is enabled only when running in single thread mode
Using AVX accelerated implementation of PairHMM
INFO 10:13:12,307 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
INFO 10:13:12,308 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
INFO 10:13:33,410 ProgressMeter - 1:4347420 0.0 30.0 s 49.6 w 0.2% 5.2 h 5.2 h
INFO 10:14:03,413 ProgressMeter - 1:4889805 0.0 60.0 s 99.2 w 0.2% 9.3 h 9.3 h
INFO 10:14:33,415 ProgressMeter - 1:6248751 0.0 90.0 s 148.8 w 0.2% 10.9 h 10.9 h
......
......
......
INFO 15:12:07,667 ProgressMeter - 2:35036630 1.263075341E9 29.0 h 82.0 s 47.5% 61.0 h 32.0 h
INFO 15:13:07,669 ProgressMeter - 2:35293870 1.263075341E9 29.0 h 82.0 s 47.5% 61.0 h 32.0 h
INFO 15:13:11,896 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the requested coordinate is not covered by the read. Too many deletions?
at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:474)
at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:420)
at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:411)
at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(ReadClipper.java:543)
at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesLeftTail(ReadClipper.java:177)
at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:408)
at org.broadinstitute.gatk.utils.clipping.ReadClipper.hardClipAdaptorSequence(ReadClipper.java:411)
at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.finalizeActiveRegion(MuTect2.java:1179)
at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.assembleReads(MuTect2.java:1123)
at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:535)
at org.broadinstitute.gatk.tools.walkers.cancer.m2.MuTect2.map(MuTect2.java:175)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions?
ERROR ------------------------------------------------------------------------------------------
[sean@honey03 mutectOut]$