Hi,
First, sorry if it's a duplicate question. I have looked for solution, but didn't find.
I have 8 exomes data from 4 patient: normal and tumor.
I ran MuTect2 (in GTAK 3.7) in normal/tumor mode, and it works well.
But now, I would like to generate a Panel of Normal.
Here the log:
INFO 16:48:48,998 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:48:49,000 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 16:48:49,001 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 16:48:49,001 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 16:48:49,001 HelpFormatter - [Mon Apr 03 16:48:48 CEST 2017] Executing on Linux 4.4.0-62-generic amd64
INFO 16:48:49,001 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13
INFO 16:48:49,004 HelpFormatter - Program Args: -T MuTect2 -nct 2 -R /media/raid/genomic_DB//hg19/hg19.fasta -I:normal bam/WES_8N.sorted.dedup.recalib.bam -L /media/raid/genomic_DB//hg19/bed/hg19_Gene_table.bed --dbsnp /media/raid/genomic_DB//hg19/GATK_bundle/dbsnp_138.hg19.vcf --cosmic /media/raid/genomic_DB//hg19/GATK_bundle/Cosmic.hg19.vcf --artifact_detection_mode -o var/WES_8_N.vcf
INFO 16:48:49,007 HelpFormatter - Executing as aatkinson@umr910-pfg-ws2 on Linux 4.4.0-62-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13.
INFO 16:48:49,007 HelpFormatter - Date/Time: 2017/04/03 16:48:48
INFO 16:48:49,008 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:48:49,008 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:48:49,023 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:48:49,133 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 16:48:49,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:48:49,160 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 16:48:50,273 IntervalUtils - Processing 1325431593 bp from intervals
INFO 16:48:50,285 MicroScheduler - Running the GATK in parallel mode with 2 total threads, 2 CPU thread(s) for each of 1 data thread(s), of 56 processors available on this machine
INFO 16:48:50,340 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 16:48:50,465 GenomeAnalysisEngine - Done preparing for traversal
INFO 16:48:50,466 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 16:48:50,466 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 16:48:50,466 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
INFO 16:48:50,532 MuTect2 - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
INFO 16:48:50,533 PairHMM - Performance profiling for PairHMM is disabled because the program is being run with multiple threads (-nct>1) option
Profiling is enabled only when running in single thread mode
INFO 16:49:20,470 ProgressMeter - chr1:14958958 5.97786178E8 30.0 s 0.0 s 0.6% 82.1 m 81.6 m
INFO 16:49:50,473 ProgressMeter - chr1:26627596 2.516091919E9 60.0 s 0.0 s 1.1% 88.4 m 87.4 m
INFO 16:50:20,474 ProgressMeter - chr1:42766671 6.139828701E9 90.0 s 0.0 s 1.7% 85.9 m 84.4 m
INFO 16:50:50,476 ProgressMeter - chr1:62963628 1.0743175026E10 120.0 s 0.0 s 2.7% 73.3 m 71.3 m
INFO 16:51:20,478 ProgressMeter - chr1:91817153 1.5892962774E10 2.5 m 0.0 s 3.8% 66.3 m 63.8 m
INFO 16:51:50,480 ProgressMeter - chr1:117093107 2.5856520721E10 3.0 m 0.0 s 4.6% 65.4 m 62.4 m
INFO 16:52:20,482 ProgressMeter - chr1:156181686 4.2774755347E10 3.5 m 0.0 s 5.3% 65.5 m 62.0 m
INFO 16:52:50,484 ProgressMeter - chr1:178832743 5.9965019186E10 4.0 m 0.0 s 6.2% 64.3 m 60.3 m
INFO 16:53:20,486 ProgressMeter - chr1:205910763 7.6568008961E10 4.5 m 0.0 s 7.1% 63.5 m 59.0 m
INFO 16:53:50,487 ProgressMeter - chr1:231612271 9.5039378738E10 5.0 m 0.0 s 8.1% 62.0 m 57.0 m
INFO 16:54:20,489 ProgressMeter - chr2:10978103 1.08452450175E11 5.5 m 0.0 s 9.1% 60.2 m 54.7 m
...
...
*MuTect2 running, without any warnings, so I delete lines to keep message shorter*
...
...
INFO 18:55:50,952 ProgressMeter - chrX:76856153 6.28621417292E11 2.1 h 0.0 s 97.8% 2.2 h 2.8 m
INFO 18:56:20,953 ProgressMeter - chrX:76877471 6.28621417292E11 2.1 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 18:56:50,954 ProgressMeter - chrX:76893542 6.28621417292E11 2.1 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 18:57:20,956 ProgressMeter - chrX:76906228 6.28621417292E11 2.1 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 18:57:50,958 ProgressMeter - chrX:76917364 6.28621417292E11 2.2 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 18:58:20,959 ProgressMeter - chrX:76927855 6.28621417292E11 2.2 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 18:58:50,961 ProgressMeter - chrX:76937585 6.28621417292E11 2.2 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 18:59:20,962 ProgressMeter - chrX:76946451 6.28621417292E11 2.2 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 18:59:50,964 ProgressMeter - chrX:76954953 6.28621417292E11 2.2 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 19:00:20,965 ProgressMeter - chrX:76963009 6.28621417292E11 2.2 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 19:00:50,966 ProgressMeter - chrX:76970682 6.28621417292E11 2.2 h 0.0 s 97.8% 2.2 h 2.9 m
INFO 19:01:20,967 ProgressMeter - chrX:118733701 6.34550108037E11 2.2 h 0.0 s 98.9% 2.2 h 92.0 s
Using AVX accelerated implementation of PairHMM
INFO 19:01:44,249 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
INFO 19:01:44,249 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
INFO 19:01:44,250 MuTect2 - Ran local assembly on 0 active regions
INFO 19:01:44,252 ProgressMeter - done 6.48115744256E11 2.2 h 0.0 s 100.0% 2.2 h 0.0 s
INFO 19:01:44,253 ProgressMeter - Total runtime 7973.79 secs, 132.90 min, 2.21 hours
INFO 19:01:44,253 MicroScheduler - 386106 reads were filtered out during the traversal out of approximately 105750521 total reads (0.37%)
INFO 19:01:44,253 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 19:01:44,253 MicroScheduler - -> 371854 reads (0.35% of total) failing DuplicateReadFilter
INFO 19:01:44,253 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 19:01:44,254 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 19:01:44,254 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 19:01:44,254 MicroScheduler - -> 14252 reads (0.01% of total) failing NotPrimaryAlignmentFilter
INFO 19:01:44,254 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
------------------------------------------------------------------------------------------
Done. There were no warn messages.
------------------------------------------------------------------------------------------
At the end, I have a vcf without any variant, only header appear.
I have looked for solutions, and it seems I have the same problem like here:
1. http://gatkforums.broadinstitute.org/gatk/discussion/6085/generating-pool-of-normal
2. https://gatkforums.broadinstitute.org/wdl/discussion/6690/mutect2-tumor-only-mode-empty-vcfs
As in previous post, I read the same strange info in my log:
INFO 19:01:44,250 MuTect2 - Ran local assembly on 0 active regions
So I have tried a nightly build, as recommended in previous post:
INFO 16:09:07,202 HelpFormatter - ---------------------------------------------------------------------------------------------
INFO 16:09:07,204 HelpFormatter - The Genome Analysis Toolkit (GATK) vnightly-2017-04-04-g34bd8a3, Compiled 2017/04/04 00:01:14
INFO 16:09:07,204 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 16:09:07,204 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 16:09:07,204 HelpFormatter - [Tue Apr 04 16:09:07 CEST 2017] Executing on Linux 4.4.0-62-generic amd64
INFO 16:09:07,204 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13
INFO 16:09:07,208 HelpFormatter - Program Args: -T MuTect2 -nct 2 -R /media/raid/genomic_DB//hg19/hg19.fasta -I:normal bam/WES_26N.sorted.dedup.recalib.bam -L /media/raid/genomic_DB//hg19/bed/hg19_Gene_table.bed --dbsnp /media/raid/genomic_DB//hg19/GATK_bundle/dbsnp_138.hg19.vcf --cosmic /media/raid/genomic_DB//hg19/GATK_bundle/Cosmic.hg19.vcf --artifact_detection_mode -o var/WES_26_N.vcf
INFO 16:09:07,210 HelpFormatter - Executing as aatkinson@umr910-pfg-ws2 on Linux 4.4.0-62-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13.
INFO 16:09:07,210 HelpFormatter - Date/Time: 2017/04/04 16:09:07
INFO 16:09:07,210 HelpFormatter - ---------------------------------------------------------------------------------------------
INFO 16:09:07,210 HelpFormatter - ---------------------------------------------------------------------------------------------
INFO 16:09:07,225 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:09:07,340 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 16:09:07,346 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:09:07,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 16:09:08,334 IntervalUtils - Processing 1325431593 bp from intervals
INFO 16:09:08,346 MicroScheduler - Running the GATK in parallel mode with 2 total threads, 2 CPU thread(s) for each of 1 data thread(s), of 56 processors available on this machine
INFO 16:09:08,399 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 16:09:08,539 GenomeAnalysisEngine - Done preparing for traversal
INFO 16:09:08,540 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 16:09:08,540 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 16:09:08,542 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
INFO 16:09:08,610 MuTect2 - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
INFO 16:09:08,611 PairHMM - Performance profiling for PairHMM is disabled because the program is being run with multiple threads (-nct>1) option
Profiling is enabled only when running in single thread mode
INFO 16:09:38,546 ProgressMeter - chr1:16563659 7.97486694E8 30.0 s 0.0 s 0.7% 71.0 m 70.5 m
INFO 16:10:08,547 ProgressMeter - chr1:36384738 4.675477702E9 60.0 s 0.0 s 1.5% 66.7 m 65.7 m
INFO 16:10:38,549 ProgressMeter - chr1:65120499 1.1110499512E10 90.0 s 0.0 s 2.8% 53.0 m 51.5 m
INFO 16:11:08,551 ProgressMeter - chr1:108509208 1.9618437838E10 120.0 s 0.0 s 4.3% 46.9 m 44.9 m
...
...
again, I delete some lines without warnings to keep shorter
...
...
INFO 18:07:38,969 ProgressMeter - chrX:76944672 6.28621417292E11 118.5 m 0.0 s 97.8% 2.0 h 2.7 m
INFO 18:08:08,970 ProgressMeter - chrX:76953314 6.28621417292E11 119.0 m 0.0 s 97.8% 2.0 h 2.7 m
INFO 18:08:38,971 ProgressMeter - chrX:76961411 6.28621417292E11 119.5 m 0.0 s 97.8% 2.0 h 2.7 m
INFO 18:09:08,973 ProgressMeter - chrX:76968843 6.28621417292E11 120.0 m 0.0 s 97.8% 2.0 h 2.7 m
INFO 18:09:38,974 ProgressMeter - chrX:113099932 6.33515778237E11 2.0 h 0.0 s 98.7% 2.0 h 93.0 s
Using AVX accelerated implementation of PairHMM
INFO 18:10:00,807 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
INFO 18:10:00,808 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
INFO 18:10:00,809 MuTect2 - Ran local assembly on 0 active regions
INFO 18:10:00,812 ProgressMeter - done 6.48115744256E11 2.0 h 0.0 s 100.0% 2.0 h 0.0 s
INFO 18:10:00,812 ProgressMeter - Total runtime 7252.27 secs, 120.87 min, 2.01 hours
INFO 18:10:00,813 MicroScheduler - 231969 reads were filtered out during the traversal out of approximately 82616070 total reads (0.28%)
INFO 18:10:00,813 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 18:10:00,813 MicroScheduler - -> 215232 reads (0.26% of total) failing DuplicateReadFilter
INFO 18:10:00,813 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 18:10:00,813 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 18:10:00,813 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 18:10:00,814 MicroScheduler - -> 16737 reads (0.02% of total) failing NotPrimaryAlignmentFilter
INFO 18:10:00,814 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
------------------------------------------------------------------------------------------
Done. There were no warn messages.
------------------------------------------------------------------------------------------
Nightly build doesn't work better.
Not shown here, but I have tried without -L myBedFile.bed, and also without -nct, and I get a empty vcf again.
I don't know what to do/try...