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ERROR stack trace

Hi,

I was running GATK BaseRecalibrator and came across "Stack Trace" error after completion of 58.6% . I ran the same command before with another bam file and it ran fine. Both of the bam files were produced using BWA MEM, sorted, indexed, fixed mate information (samtools) and then duplicate removed by PICARD.

My command is as follows:

java -Xmx4g -jar GenomeAnalysisTK.jar \

-T BaseRecalibrator \
-I "$sampleID".GATK.realigned.bam \
-R $humanRefSequence \
-knownSites $humanDbsnpFile \
-o "$sampleID".recal_data.grp

And the output are as follows:

INFO 16:22:06,245 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:22:06,248 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.4-9-g532efad, Compiled 2013/03/19 07:35:36
INFO 16:22:06,248 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 16:22:06,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 16:22:06,252 HelpFormatter - Program Args: -T BaseRecalibrator -I SK-PHP-pool2_S2.GATK.realigned.bam -R /scratch/fr1u11/ACE/REF_GENOME/HG19/b37_karyotypicallySorted/human_g1k_v37.fasta -knownSites /scratch/fr1u11/ACE/dbSNP137/dbsnp_137.b37.vcf -o SK-PHP-pool2_S2.recal_data.grp
INFO 16:22:06,252 HelpFormatter - Date/Time: 2013/04/25 16:22:06
INFO 16:22:06,252 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:22:06,252 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:22:06,317 ArgumentTypeDescriptor - Dynamically determined type of /scratch/fr1u11/ACE/dbSNP137/dbsnp_137.b37.vcf to be VCF
INFO 16:22:06,914 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:22:07,028 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 16:22:07,035 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:22:07,072 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
INFO 16:22:07,109 RMDTrackBuilder - Loading Tribble index from disk for file /scratch/fr1u11/ACE/dbSNP137/dbsnp_137.b37.vcf
INFO 16:22:07,549 GenomeAnalysisEngine - Creating shard strategy for 1 BAM files
INFO 16:22:07,554 GenomeAnalysisEngine - Done creating shard strategy
INFO 16:22:07,555 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 16:22:07,555 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 16:22:07,576 BaseRecalibrator - The covariates being used here:
INFO 16:22:07,576 BaseRecalibrator - ReadGroupCovariate
INFO 16:22:07,576 BaseRecalibrator - QualityScoreCovariate
INFO 16:22:07,576 BaseRecalibrator - ContextCovariate
INFO 16:22:07,576 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
INFO 16:22:07,576 BaseRecalibrator - CycleCovariate
INFO 16:22:07,596 ReadShardBalancer$1 - Loading BAM index data for next contig
INFO 16:22:07,596 ReadShardBalancer$1 - Done loading BAM index data for next contig
INFO 16:22:37,574 ProgressMeter - 1:27547695 0.00e+00 30.0 s 49.6 w 0.9% 56.3 m 55.8 m
INFO 16:23:07,584 ProgressMeter - 1:62606707 1.00e+05 60.0 s 10.0 m 2.0% 49.5 m 48.5 m
INFO 16:23:37,594 ProgressMeter - 1:119405961 1.00e+05 90.0 s 15.0 m 3.8% 39.0 m 37.5 m
INFO 16:24:07,605 ProgressMeter - 1:203302345 2.00e+05 120.0 s 10.0 m 6.6% 30.5 m 28.5 m
INFO 16:24:37,616 ProgressMeter - 1:249191380 3.00e+05 2.5 m 8.3 m 8.0% 31.1 m 28.6 m
INFO 16:25:08,493 ProgressMeter - 2:46544672 3.63e+05 3.0 m 8.3 m 9.5% 31.5 m 28.5 m
INFO 16:25:38,503 ProgressMeter - 2:97745730 4.63e+05 3.5 m 7.6 m 11.2% 31.3 m 27.8 m
INFO 16:26:08,517 ProgressMeter - 2:141375959 5.63e+05 4.0 m 7.1 m 12.6% 31.8 m 27.8 m
INFO 16:26:38,527 ProgressMeter - 2:221046892 5.63e+05 4.5 m 8.0 m 15.2% 29.7 m 25.2 m
INFO 16:27:08,538 ProgressMeter - 3:10071132 6.99e+05 5.0 m 7.2 m 16.2% 30.9 m 25.9 m
INFO 16:27:38,548 ProgressMeter - 3:66821801 6.99e+05 5.5 m 7.9 m 18.0% 30.5 m 25.0 m
INFO 16:28:08,559 ProgressMeter - 3:134762061 7.99e+05 6.0 m 7.5 m 20.2% 29.8 m 23.7 m
INFO 16:28:38,842 ProgressMeter - 3:191481932 8.99e+05 6.5 m 7.3 m 22.0% 29.6 m 23.0 m
INFO 16:29:08,853 ProgressMeter - 4:34101052 9.64e+05 7.0 m 7.3 m 23.4% 30.0 m 23.0 m
INFO 16:29:38,863 ProgressMeter - 4:82832343 1.06e+06 7.5 m 7.1 m 24.9% 30.2 m 22.6 m
INFO 16:30:08,874 ProgressMeter - 4:151647250 1.06e+06 8.0 m 7.5 m 27.1% 29.5 m 21.5 m
INFO 16:30:38,884 ProgressMeter - 5:3806120 1.21e+06 8.5 m 7.0 m 28.5% 29.8 m 21.3 m
INFO 16:31:08,895 ProgressMeter - 5:79596315 1.21e+06 9.0 m 7.4 m 31.0% 29.1 m 20.1 m
INFO 16:31:38,905 ProgressMeter - 5:143680795 1.31e+06 9.5 m 7.3 m 33.1% 28.8 m 19.3 m
INFO 16:32:08,916 ProgressMeter - 5:180678089 1.41e+06 10.0 m 7.1 m 34.2% 29.2 m 19.2 m
INFO 16:32:38,926 ProgressMeter - 6:58717151 1.45e+06 10.5 m 7.3 m 36.1% 29.1 m 18.6 m
INFO 16:33:08,937 ProgressMeter - 6:117106171 1.55e+06 11.0 m 7.1 m 38.0% 29.0 m 18.0 m
INFO 16:33:38,947 ProgressMeter - 6:170991744 1.65e+06 11.5 m 7.0 m 39.8% 29.0 m 17.4 m
INFO 16:34:08,958 ProgressMeter - 7:50243192 1.68e+06 12.0 m 7.1 m 41.4% 29.0 m 17.0 m
INFO 16:34:38,968 ProgressMeter - 7:101200087 1.78e+06 12.5 m 7.0 m 43.0% 29.1 m 16.6 m
INFO 16:35:08,979 ProgressMeter - 7:156036181 1.88e+06 13.0 m 6.9 m 44.8% 29.1 m 16.0 m
INFO 16:35:38,988 ProgressMeter - 8:37364205 1.93e+06 13.5 m 7.0 m 46.1% 29.3 m 15.8 m
INFO 16:36:08,998 ProgressMeter - 8:97079882 2.03e+06 14.0 m 6.9 m 48.0% 29.2 m 15.2 m
INFO 16:36:39,008 ProgressMeter - 8:146292633 2.13e+06 14.5 m 6.8 m 49.6% 29.3 m 14.7 m
INFO 16:37:09,018 ProgressMeter - 9:89065984 2.13e+06 15.0 m 7.1 m 52.5% 28.6 m 13.6 m
INFO 16:37:39,028 ProgressMeter - 9:135394782 2.23e+06 15.5 m 7.0 m 54.0% 28.7 m 13.2 m
INFO 16:38:09,038 ProgressMeter - 10:30154466 2.30e+06 16.0 m 7.0 m 55.1% 29.0 m 13.0 m
INFO 16:38:39,048 ProgressMeter - 10:86113015 2.40e+06 16.5 m 6.9 m 57.0% 29.0 m 12.5 m
INFO 16:39:09,058 ProgressMeter - 11:1747804 2.51e+06 17.0 m 6.8 m 58.6% 29.0 m 12.0 m
INFO 16:39:39,069 ProgressMeter - 11:1877044 2.61e+06 17.5 m 6.7 m 58.6% 29.9 m 12.4 m
INFO 16:40:09,079 ProgressMeter - 11:2008155 2.71e+06 18.0 m 6.7 m 58.6% 30.7 m 12.7 m
INFO 16:40:39,090 ProgressMeter - 11:2124930 2.81e+06 18.5 m 6.6 m 58.6% 31.6 m 13.1 m
INFO 16:41:09,101 ProgressMeter - 11:2259894 2.91e+06 19.0 m 6.5 m 58.6% 32.4 m 13.4 m
INFO 16:41:39,112 ProgressMeter - 11:2389552 3.01e+06 19.5 m 6.5 m 58.6% 33.3 m 13.8 m
INFO 16:42:09,122 ProgressMeter - 11:2530316 3.11e+06 20.0 m 6.4 m 58.6% 34.1 m 14.1 m
INFO 16:42:39,133 ProgressMeter - 11:2647149 3.21e+06 20.5 m 6.4 m 58.6% 35.0 m 14.5 m
INFO 16:43:09,143 ProgressMeter - 11:2764819 3.31e+06 21.0 m 6.4 m 58.6% 35.8 m 14.8 m
INFO 16:43:39,154 ProgressMeter - 11:2889029 3.41e+06 21.5 m 6.3 m 58.6% 36.7 m 15.2 m
INFO 16:44:04,517 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 251
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateIsIndel(BaseRecalibrator.java:387)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:253)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:131)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:230)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:218)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:109)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-9-g532efad):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, 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: 251
ERROR ------------------------------------------------------------------------------------------

It would be most helpful if someone can tell me what might be reason causing the problem. Many thanks in advance.

Regards

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Alright folks, sorry this took a while, I was up to my ears in deadlines all converging on this week.

    @opulcy, I narrowed your bug down to a bad cigar in interval 11:2959000-2959100. If you run with -rf BadCigar the offending read will be filtered out. It looks like an isolated case (ie not many reads affected) so you can safely discard the bad reads without losing data. We'll put in a check to make sure this bad cigar configuration gets caught in future.

    @Martin1, try using the same read filter; hopefully your case is the same and this will allow you to proceed with your work.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    I think this might be due to a bug that was recently fixed. Could you please try running this again using the latest nightly build (see Downloads page)?

  • Thanks Geraldine. I will try the nightly build and let you know.

    Regards

  • Hi Geraldine,

    I have used the latest nightly build (version nightly-2013-04-25-gbc128e7) and the problem has still occurred! The error occurred again after the completion of 58.6%! I ran my previous successful bam file with the nightly build and it ran fine. I have also ran both of the bam files with PICARD ValidateSamFile and it generated same type of errors for both of the files. However, one of them ran fine and other one is failing. I should mention that I am using targeted genomic data which has reads for chromosome 11 and 20 only. I have observed that the error is occurring while BaseRecalibrator is running on chromosome 11. Let me know what I should do next. Many thanks for your time and effort.

    Regards

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    I see. Can you tell me what errors are given by ValidateSamFile, just in case they're relevant?

    Also, can you tell me what version number of BWA mem you used for alignment?

  • Hi Geraldine,

    Thanks for the reply. I am using bwa mem from "bwa-0.7.1". The errors produced by ValidateSamFile for the both successful and unsuccessful bam files are as follows:

    For the sample which produces error with BaseRecalibrator:

    ================================================================================================
    ERROR: Header version: 1.4 does not match any of the acceptable versions: 1.0, 1.3
    ERROR: Record 32145, Read name M00321:18:000000000-A36GK:1:1109:17285:22181, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 32224, Read name M00321:18:000000000-A36GK:1:1109:17285:22181, Mate alignment does not match alignment start of mate
    ERROR: Record 32224, Read name M00321:18:000000000-A36GK:1:1109:17285:22181, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 43276, Read name M00321:18:000000000-A36GK:1:2109:8951:7185, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 43279, Read name M00321:18:000000000-A36GK:1:2109:8951:7185, Mate alignment does not match alignment start of mate
    ERROR: Record 56829, Read name M00321:18:000000000-A36GK:1:2104:13064:17860, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 56830, Read name M00321:18:000000000-A36GK:1:2104:13064:17860, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 56831, Read name M00321:18:000000000-A36GK:1:2104:13064:17860, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 56832, Read name M00321:18:000000000-A36GK:1:2104:13064:17860, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 210247, Read name M00321:18:000000000-A36GK:1:2103:14708:25442, NM tag (nucleotide differences) in file [15] does not match reality [16]
    ERROR: Record 211628, Read name M00321:18:000000000-A36GK:1:2108:16850:10555, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 212916, Read name M00321:18:000000000-A36GK:1:2108:16850:10555, Mate alignment does not match alignment start of mate
    ERROR: Record 211627, Read name M00321:18:000000000-A36GK:1:1112:15501:20113, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 212938, Read name M00321:18:000000000-A36GK:1:1112:15501:20113, Mate alignment does not match alignment start of mate
    ERROR: Record 301363, Read name M00321:18:000000000-A36GK:1:2105:8409:11233, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 301364, Read name M00321:18:000000000-A36GK:1:2105:8409:11233, Mate alignment does not match alignment start of mate
    ERROR: Record 301364, Read name M00321:18:000000000-A36GK:1:2105:8409:11233, Mate reference index (MRNM) does not match reference index of mate
    ERROR: Record 301364, Read name M00321:18:000000000-A36GK:1:2105:8409:11233, Mate unmapped flag does not match read unmapped flag of mate
    ERROR: Record 380628, Read name M00321:18:000000000-A36GK:1:2103:16924:23120, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 380629, Read name M00321:18:000000000-A36GK:1:2103:16924:23120, Mate alignment does not match alignment start of mate
    ERROR: Record 380629, Read name M00321:18:000000000-A36GK:1:2103:16924:23120, Mate reference index (MRNM) does not match reference index of mate
    ERROR: Record 380629, Read name M00321:18:000000000-A36GK:1:2103:16924:23120, Mate unmapped flag does not match read unmapped flag of mate
    ERROR: Record 425011, Read name M00321:18:000000000-A36GK:1:1107:20910:5603, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 425014, Read name M00321:18:000000000-A36GK:1:1107:20910:5603, Mate alignment does not match alignment start of mate
    ERROR: Record 425014, Read name M00321:18:000000000-A36GK:1:1107:20910:5603, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 429650, Read name M00321:18:000000000-A36GK:1:2110:23220:13653, NM tag (nucleotide differences) in file [11] does not match reality [12]
    ERROR: Record 429956, Read name M00321:18:000000000-A36GK:1:2110:11705:8285, NM tag (nucleotide differences) in file [17] does not match reality [18]
    ERROR: Record 430005, Read name M00321:18:000000000-A36GK:1:1107:11581:15633, NM tag (nucleotide differences) in file [11] does not match reality [12]
    ERROR: Record 430039, Read name M00321:18:000000000-A36GK:1:1112:9250:20245, NM tag (nucleotide differences) in file [6] does not match reality [7]
    ERROR: Record 430047, Read name M00321:18:000000000-A36GK:1:1101:6044:25099, NM tag (nucleotide differences) in file [13] does not match reality [16]
    ERROR: Record 430050, Read name M00321:18:000000000-A36GK:1:2114:20084:25782, NM tag (nucleotide differences) in file [6] does not match reality [8]
    ERROR: Record 430052, Read name M00321:18:000000000-A36GK:1:1114:20430:26398, NM tag (nucleotide differences) in file [7] does not match reality [10]
    ERROR: Record 430053, Read name M00321:18:000000000-A36GK:1:1101:13408:19144, NM tag (nucleotide differences) in file [6] does not match reality [8]
    ERROR: Record 430062, Read name M00321:18:000000000-A36GK:1:2101:12028:15349, NM tag (nucleotide differences) in file [2] does not match reality [3]
    ERROR: Record 430064, Read name M00321:18:000000000-A36GK:1:1112:18737:3472, NM tag (nucleotide differences) in file [3] does not match reality [4]
    ERROR: Record 430065, Read name M00321:18:000000000-A36GK:1:2106:26754:9578, NM tag (nucleotide differences) in file [2] does not match reality [3]
    ERROR: Record 430067, Read name M00321:18:000000000-A36GK:1:1106:16310:14939, NM tag (nucleotide differences) in file [1] does not match reality [3]
    ERROR: Record 430068, Read name M00321:18:000000000-A36GK:1:1111:22129:17709, NM tag (nucleotide differences) in file [1] does not match reality [2]
    ERROR: Record 430070, Read name M00321:18:000000000-A36GK:1:1104:16062:10303, NM tag (nucleotide differences) in file [1] does not match reality [2]
    ERROR: Record 430071, Read name M00321:18:000000000-A36GK:1:1102:13193:11379, NM tag (nucleotide differences) in file [1] does not match reality [4]
    ERROR: Record 430079, Read name M00321:18:000000000-A36GK:1:2103:27600:21954, NM tag (nucleotide differences) in file [2] does not match reality [9]
    ERROR: Record 430081, Read name M00321:18:000000000-A36GK:1:1104:7948:23745, NM tag (nucleotide differences) in file [0] does not match reality [2]
    ERROR: Record 430082, Read name M00321:18:000000000-A36GK:1:1103:21187:10313, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 430083, Read name M00321:18:000000000-A36GK:1:1106:6867:14239, NM tag (nucleotide differences) in file [0] does not match reality [2]
    ERROR: Record 430085, Read name M00321:18:000000000-A36GK:1:1114:20529:9158, NM tag (nucleotide differences) in file [0] does not match reality [3]
    ERROR: Record 430086, Read name M00321:18:000000000-A36GK:1:2111:14239:12674, NM tag (nucleotide differences) in file [0] does not match reality [3]
    ERROR: Record 430087, Read name M00321:18:000000000-A36GK:1:2112:20478:20711, NM tag (nucleotide differences) in file [0] does not match reality [3]
    ERROR: Record 449214, Read name M00321:18:000000000-A36GK:1:2102:20179:24918, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 449215, Read name M00321:18:000000000-A36GK:1:2102:20179:24918, Mate alignment does not match alignment start of mate
    ERROR: Record 449215, Read name M00321:18:000000000-A36GK:1:2102:20179:24918, Mate reference index (MRNM) does not match reference index of mate
    ERROR: Record 449215, Read name M00321:18:000000000-A36GK:1:2102:20179:24918, Mate unmapped flag does not match read unmapped flag of mate
    ERROR: Record 509237, Read name M00321:18:000000000-A36GK:1:1101:15528:17645, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 509699, Read name M00321:18:000000000-A36GK:1:1101:15528:17645, Mate alignment does not match alignment start of mate
    ERROR: Record 602004, Read name M00321:18:000000000-A36GK:1:2111:26544:20489, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 602005, Read name M00321:18:000000000-A36GK:1:2111:26544:20489, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 681022, Read name M00321:18:000000000-A36GK:1:2114:18195:10242, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 681023, Read name M00321:18:000000000-A36GK:1:2114:18195:10242, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 681024, Read name M00321:18:000000000-A36GK:1:2114:18195:10242, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 681025, Read name M00321:18:000000000-A36GK:1:2114:18195:10242, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 724332, Read name M00321:18:000000000-A36GK:1:2107:18463:7683, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 724348, Read name M00321:18:000000000-A36GK:1:2107:18463:7683, Mate alignment does not match alignment start of mate
    ERROR: Record 791875, Read name M00321:18:000000000-A36GK:1:1114:16639:18007, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 791888, Read name M00321:18:000000000-A36GK:1:1114:16639:18007, Mate alignment does not match alignment start of mate
    ERROR: Record 791888, Read name M00321:18:000000000-A36GK:1:1114:16639:18007, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1000676, Read name M00321:18:000000000-A36GK:1:1104:16421:21816, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 1000678, Read name M00321:18:000000000-A36GK:1:2111:16601:23392, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 1000679, Read name M00321:18:000000000-A36GK:1:2111:27844:14263, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 1007293, Read name M00321:18:000000000-A36GK:1:2103:4927:18634, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1007360, Read name M00321:18:000000000-A36GK:1:2103:4927:18634, Mate alignment does not match alignment start of mate
    ERROR: Record 1007360, Read name M00321:18:000000000-A36GK:1:2103:4927:18634, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1020437, Read name M00321:18:000000000-A36GK:1:2101:20685:4647, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1020438, Read name M00321:18:000000000-A36GK:1:2101:20685:4647, Mate alignment does not match alignment start of mate
    ERROR: Record 1020438, Read name M00321:18:000000000-A36GK:1:2101:20685:4647, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1020438, Read name M00321:18:000000000-A36GK:1:2101:20685:4647, Mate reference index (MRNM) does not match reference index of mate
    ERROR: Record 1020438, Read name M00321:18:000000000-A36GK:1:2101:20685:4647, Mate unmapped flag does not match read unmapped flag of mate
    ERROR: Record 1076140, Read name M00321:18:000000000-A36GK:1:1105:13327:3742, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1076197, Read name M00321:18:000000000-A36GK:1:1105:13327:3742, Mate alignment does not match alignment start of mate
    ERROR: Record 1077498, Read name M00321:18:000000000-A36GK:1:2112:16864:11508, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1077751, Read name M00321:18:000000000-A36GK:1:2112:16864:11508, Mate alignment does not match alignment start of mate
    ERROR: Record 1081078, Read name M00321:18:000000000-A36GK:1:1111:16924:14456, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1081236, Read name M00321:18:000000000-A36GK:1:1111:16924:14456, Mate alignment does not match alignment start of mate
    ERROR: Record 1082117, Read name M00321:18:000000000-A36GK:1:1101:18815:5907, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1082128, Read name M00321:18:000000000-A36GK:1:1101:18815:5907, Mate alignment does not match alignment start of mate
    ERROR: Record 1082128, Read name M00321:18:000000000-A36GK:1:1101:18815:5907, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1134410, Read name M00321:18:000000000-A36GK:1:1108:23389:19355, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1134411, Read name M00321:18:000000000-A36GK:1:1108:23389:19355, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1134412, Read name M00321:18:000000000-A36GK:1:1108:23389:19355, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1134413, Read name M00321:18:000000000-A36GK:1:1108:23389:19355, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1146789, Read name M00321:18:000000000-A36GK:1:2110:24203:9898, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1146790, Read name M00321:18:000000000-A36GK:1:2110:24203:9898, Mate alignment does not match alignment start of mate
    ERROR: Record 1146790, Read name M00321:18:000000000-A36GK:1:2110:24203:9898, Mate reference index (MRNM) does not match reference index of mate
    ERROR: Record 1146790, Read name M00321:18:000000000-A36GK:1:2110:24203:9898, Mate unmapped flag does not match read unmapped flag of mate
    ERROR: Record 1185177, Read name M00321:18:000000000-A36GK:1:2110:9151:24875, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1185183, Read name M00321:18:000000000-A36GK:1:2110:9151:24875, Mate alignment does not match alignment start of mate
    ERROR: Record 1185183, Read name M00321:18:000000000-A36GK:1:2110:9151:24875, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1339515, Read name M00321:18:000000000-A36GK:1:1104:2046:16449, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1339516, Read name M00321:18:000000000-A36GK:1:1104:2046:16449, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1339517, Read name M00321:18:000000000-A36GK:1:1104:2046:16449, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 1339518, Read name M00321:18:000000000-A36GK:1:1104:2046:16449, Mate negative strand flag does not match read negative strand flag of mate

    ==================================================================================================

    For the sample which runs successfully with BaseRecalibrator:

    ==================================================================================================

    ERROR: Header version: 1.4 does not match any of the acceptable versions: 1.0, 1.3
    ERROR: Record 6465, Read name M00321:17:000000000-A394Y:1:2103:17144:16195, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 6519, Read name M00321:17:000000000-A394Y:1:2103:17144:16195, Mate alignment does not match alignment start of mate
    ERROR: Record 9082, Read name M00321:17:000000000-A394Y:1:1108:14559:20416, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 9112, Read name M00321:17:000000000-A394Y:1:1108:14559:20416, Mate alignment does not match alignment start of mate
    ERROR: Record 75712, Read name M00321:17:000000000-A394Y:1:2102:2917:18790, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 75713, Read name M00321:17:000000000-A394Y:1:2102:2917:18790, Mate alignment does not match alignment start of mate
    ERROR: Record 75713, Read name M00321:17:000000000-A394Y:1:2102:2917:18790, Mate reference index (MRNM) does not match reference index of mate
    ERROR: Record 75713, Read name M00321:17:000000000-A394Y:1:2102:2917:18790, Mate unmapped flag does not match read unmapped flag of mate
    ERROR: Record 110313, Read name M00321:17:000000000-A394Y:1:1114:23952:24803, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 110314, Read name M00321:17:000000000-A394Y:1:1114:23952:24803, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 110315, Read name M00321:17:000000000-A394Y:1:1114:23952:24803, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 110316, Read name M00321:17:000000000-A394Y:1:1114:23952:24803, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 114272, Read name M00321:17:000000000-A394Y:1:1105:23421:7188, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 114273, Read name M00321:17:000000000-A394Y:1:1105:23421:7188, Mate alignment does not match alignment start of mate
    ERROR: Record 114273, Read name M00321:17:000000000-A394Y:1:1105:23421:7188, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 114273, Read name M00321:17:000000000-A394Y:1:1105:23421:7188, Mate reference index (MRNM) does not match reference index of mate
    ERROR: Record 114273, Read name M00321:17:000000000-A394Y:1:1105:23421:7188, Mate unmapped flag does not match read unmapped flag of mate
    ERROR: Record 158020, Read name M00321:17:000000000-A394Y:1:2109:11218:18865, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 158027, Read name M00321:17:000000000-A394Y:1:2109:11218:18865, Mate alignment does not match alignment start of mate
    ERROR: Record 158028, Read name M00321:17:000000000-A394Y:1:2109:11218:18865, Mate alignment does not match alignment start of mate
    ERROR: Record 158030, Read name M00321:17:000000000-A394Y:1:2109:11218:18865, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 177048, Read name M00321:17:000000000-A394Y:1:1103:11820:7756, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 177049, Read name M00321:17:000000000-A394Y:1:1103:11820:7756, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 177050, Read name M00321:17:000000000-A394Y:1:1103:11820:7756, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 177051, Read name M00321:17:000000000-A394Y:1:1103:11820:7756, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 198063, Read name M00321:17:000000000-A394Y:1:1103:19321:9542, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 198154, Read name M00321:17:000000000-A394Y:1:1103:19321:9542, Mate alignment does not match alignment start of mate
    ERROR: Record 198154, Read name M00321:17:000000000-A394Y:1:1103:19321:9542, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 248429, Read name M00321:17:000000000-A394Y:1:1108:19750:13257, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 248434, Read name M00321:17:000000000-A394Y:1:1108:19750:13257, Mate alignment does not match alignment start of mate
    ERROR: Record 248435, Read name M00321:17:000000000-A394Y:1:1108:19750:13257, Mate alignment does not match alignment start of mate
    ERROR: Record 248436, Read name M00321:17:000000000-A394Y:1:1108:19750:13257, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 262788, Read name M00321:17:000000000-A394Y:1:2103:16477:15688, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 262789, Read name M00321:17:000000000-A394Y:1:2103:16477:15688, Mate alignment does not match alignment start of mate
    ERROR: Record 262790, Read name M00321:17:000000000-A394Y:1:2103:16477:15688, Mate alignment does not match alignment start of mate
    ERROR: Record 262791, Read name M00321:17:000000000-A394Y:1:2103:16477:15688, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 264285, Read name M00321:17:000000000-A394Y:1:1102:13353:10224, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 264286, Read name M00321:17:000000000-A394Y:1:1102:13353:10224, Mate alignment does not match alignment start of mate
    ERROR: Record 264286, Read name M00321:17:000000000-A394Y:1:1102:13353:10224, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 264287, Read name M00321:17:000000000-A394Y:1:1102:13353:10224, Mate alignment does not match alignment start of mate
    ERROR: Record 264287, Read name M00321:17:000000000-A394Y:1:1102:13353:10224, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 264288, Read name M00321:17:000000000-A394Y:1:1102:13353:10224, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 360508, Read name M00321:17:000000000-A394Y:1:2113:11902:16141, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 360509, Read name M00321:17:000000000-A394Y:1:2113:11902:16141, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 361941, Read name M00321:17:000000000-A394Y:1:2114:19791:26348, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 361943, Read name M00321:17:000000000-A394Y:1:2114:19791:26348, Mate alignment does not match alignment start of mate
    ERROR: Record 361943, Read name M00321:17:000000000-A394Y:1:2114:19791:26348, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 362350, Read name M00321:17:000000000-A394Y:1:2107:27352:12747, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 362351, Read name M00321:17:000000000-A394Y:1:2107:27352:12747, Mate alignment does not match alignment start of mate
    ERROR: Record 362351, Read name M00321:17:000000000-A394Y:1:2107:27352:12747, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 362351, Read name M00321:17:000000000-A394Y:1:2107:27352:12747, Mate reference index (MRNM) does not match reference index of mate
    ERROR: Record 362351, Read name M00321:17:000000000-A394Y:1:2107:27352:12747, Mate unmapped flag does not match read unmapped flag of mate
    ERROR: Record 366471, Read name M00321:17:000000000-A394Y:1:2103:4332:16007, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 366472, Read name M00321:17:000000000-A394Y:1:2103:4332:16007, Mate alignment does not match alignment start of mate
    ERROR: Record 366472, Read name M00321:17:000000000-A394Y:1:2103:4332:16007, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 366473, Read name M00321:17:000000000-A394Y:1:2103:4332:16007, Mate alignment does not match alignment start of mate
    ERROR: Record 366473, Read name M00321:17:000000000-A394Y:1:2103:4332:16007, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 366474, Read name M00321:17:000000000-A394Y:1:2103:4332:16007, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 378863, Read name M00321:17:000000000-A394Y:1:1110:12372:11360, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 378864, Read name M00321:17:000000000-A394Y:1:1110:12372:11360, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 403457, Read name M00321:17:000000000-A394Y:1:1113:24407:12790, NM tag (nucleotide differences) in file [9] does not match reality [11]
    ERROR: Record 403572, Read name M00321:17:000000000-A394Y:1:1106:16718:19296, NM tag (nucleotide differences) in file [6] does not match reality [7]
    ERROR: Record 403677, Read name M00321:17:000000000-A394Y:1:2108:16051:17339, NM tag (nucleotide differences) in file [12] does not match reality [13]
    ERROR: Record 403717, Read name M00321:17:000000000-A394Y:1:1112:25878:21933, NM tag (nucleotide differences) in file [11] does not match reality [13]
    ERROR: Record 403732, Read name M00321:17:000000000-A394Y:1:2108:14210:18551, NM tag (nucleotide differences) in file [17] does not match reality [18]
    ERROR: Record 403740, Read name M00321:17:000000000-A394Y:1:2114:8912:7089, NM tag (nucleotide differences) in file [16] does not match reality [17]
    ERROR: Record 403761, Read name M00321:17:000000000-A394Y:1:1102:16716:26876, NM tag (nucleotide differences) in file [15] does not match reality [16]
    ERROR: Record 403774, Read name M00321:17:000000000-A394Y:1:2108:10567:16333, NM tag (nucleotide differences) in file [9] does not match reality [10]
    ERROR: Record 403776, Read name M00321:17:000000000-A394Y:1:2113:7427:8633, NM tag (nucleotide differences) in file [11] does not match reality [13]
    ERROR: Record 403787, Read name M00321:17:000000000-A394Y:1:1104:23756:5595, NM tag (nucleotide differences) in file [7] does not match reality [10]
    ERROR: Record 403794, Read name M00321:17:000000000-A394Y:1:1103:21014:22952, NM tag (nucleotide differences) in file [5] does not match reality [8]
    ERROR: Record 403798, Read name M00321:17:000000000-A394Y:1:2106:22412:4997, NM tag (nucleotide differences) in file [7] does not match reality [9]
    ERROR: Record 403801, Read name M00321:17:000000000-A394Y:1:2108:22262:16673, NM tag (nucleotide differences) in file [4] does not match reality [7]
    ERROR: Record 403806, Read name M00321:17:000000000-A394Y:1:2108:10101:12125, NM tag (nucleotide differences) in file [8] does not match reality [11]
    ERROR: Record 403807, Read name M00321:17:000000000-A394Y:1:2104:14542:4836, NM tag (nucleotide differences) in file [8] does not match reality [11]
    ERROR: Record 403811, Read name M00321:17:000000000-A394Y:1:2106:7972:22101, NM tag (nucleotide differences) in file [3] does not match reality [4]
    ERROR: Record 403812, Read name M00321:17:000000000-A394Y:1:1114:23230:6694, NM tag (nucleotide differences) in file [2] does not match reality [3]
    ERROR: Record 403815, Read name M00321:17:000000000-A394Y:1:1105:20239:22275, NM tag (nucleotide differences) in file [4] does not match reality [5]
    ERROR: Record 403820, Read name M00321:17:000000000-A394Y:1:2102:13728:4047, NM tag (nucleotide differences) in file [2] does not match reality [3]
    ERROR: Record 403822, Read name M00321:17:000000000-A394Y:1:1110:21883:16570, NM tag (nucleotide differences) in file [2] does not match reality [5]
    ERROR: Record 403826, Read name M00321:17:000000000-A394Y:1:1105:13832:6337, NM tag (nucleotide differences) in file [1] does not match reality [2]
    ERROR: Record 403831, Read name M00321:17:000000000-A394Y:1:2102:10091:18541, NM tag (nucleotide differences) in file [2] does not match reality [4]
    ERROR: Record 403832, Read name M00321:17:000000000-A394Y:1:1106:10864:20788, NM tag (nucleotide differences) in file [2] does not match reality [6]
    ERROR: Record 403833, Read name M00321:17:000000000-A394Y:1:2110:3972:18073, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 403836, Read name M00321:17:000000000-A394Y:1:2111:19241:17618, NM tag (nucleotide differences) in file [1] does not match reality [4]
    ERROR: Record 403838, Read name M00321:17:000000000-A394Y:1:2102:10780:15451, NM tag (nucleotide differences) in file [0] does not match reality [2]
    ERROR: Record 403842, Read name M00321:17:000000000-A394Y:1:1109:9393:11510, NM tag (nucleotide differences) in file [0] does not match reality [3]
    ERROR: Record 403843, Read name M00321:17:000000000-A394Y:1:2107:20515:10458, NM tag (nucleotide differences) in file [0] does not match reality [2]
    ERROR: Record 403844, Read name M00321:17:000000000-A394Y:1:1102:20988:6713, NM tag (nucleotide differences) in file [1] does not match reality [5]
    ERROR: Record 403845, Read name M00321:17:000000000-A394Y:1:1103:10758:15616, NM tag (nucleotide differences) in file [0] does not match reality [3]
    ERROR: Record 403846, Read name M00321:17:000000000-A394Y:1:1108:10208:16114, NM tag (nucleotide differences) in file [0] does not match reality [3]
    ERROR: Record 403847, Read name M00321:17:000000000-A394Y:1:1111:18268:27118, NM tag (nucleotide differences) in file [0] does not match reality [3]
    ERROR: Record 403848, Read name M00321:17:000000000-A394Y:1:2111:2955:12788, NM tag (nucleotide differences) in file [0] does not match reality [5]
    ERROR: Record 403849, Read name M00321:17:000000000-A394Y:1:2106:22224:26146, NM tag (nucleotide differences) in file [0] does not match reality [3]
    ERROR: Record 403850, Read name M00321:17:000000000-A394Y:1:2109:7440:6425, NM tag (nucleotide differences) in file [0] does not match reality [4]
    ERROR: Record 403851, Read name M00321:17:000000000-A394Y:1:2105:12126:14375, NM tag (nucleotide differences) in file [0] does not match reality [6]
    ERROR: Record 456549, Read name M00321:17:000000000-A394Y:1:2109:13004:27078, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 456550, Read name M00321:17:000000000-A394Y:1:2109:13004:27078, Mate negative strand flag does not match read negative strand flag of mate
    ERROR: Record 456551, Read name M00321:17:000000000-A394Y:1:2109:13004:27078, Mate negative strand flag does not match read negative strand flag of mate

    =================================================================================================

    Many thanks for your time and effort.

    Regards.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    OK, nothing in there would be causing your error. Could you please upload a snippet of BAM file so that we can reproduce your error locally? Instructions here: http://www.broadinstitute.org/gatk/guide/article?id=1894

    By the way, you should upgrade to a more recent version of BWA, the program has been considerably improved since the version you're using.

  • Hi Geraldine,

    I found that the problem is occuring in the following regions of my bam file:
    11:1751172 - 2886857

    I used the following command to produce the snippet of the bamfile:
    java -jar $gatkPath/GenomeAnalysisTK.jar -R $humanRefSequence -T PrintReads -I sample.GATK.realigned.bam -o sample.snippet.GATK.realigned.bam -L 11:1750672-2887357

    Here I have used "human_g1k_v37.fasta" from the GATK bundle as the reference sequence.

    You can download the snippet file from the following source:
    https://dl.dropboxusercontent.com/u/82223730/sample.snippet.GATK.realigned.bam

    However, I ran the snippet with GATK BaseCalibrator and it ran fine!

    I have also updated BWA to 0.7.4.

    Thanks once again for all your support.

    Regards

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @opulcy,

    Unfortunately if the snippet runs fine then we cannot use it to reproduce your bug locally. Are you able to reproduce the bug if you run on the full file with that interval?

  • Hi Geraldine,

    Yes. The error is still occurs if I use the full bam file. I tried with another sample and it ran fine. If you want I can send you the full bam file with all the auxiliary files needed for that part of the code to run. Let me know if that suits you. Thanks a lot

    Regards.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    OK - there is just data for two chromosomes in your bam, correct?

  • Yes. For chromosome 11 and 20 and the bam file is about 1GB in size. Should I send you the bam files with other auxiliary files?

    Regards

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Yes please. You can upload to our FTP server if it's too large for your Dropbox account, by the way.

  • Hi Geraldine,

    I have uploaded the file to a folder called "OPULCY" to your ftp site. There will be two files: sample.GATK.realigned.bam and sample.GATK.realigned.bai.

    My command was as follows:

    $javaPath/java -Xmx4g \
    -jar $gatkPath/GenomeAnalysisTK.jar \
    -T BaseRecalibrator \
    -I "$sampleID".GATK.realigned.bam \
    -R $humanRefSequence \
    -knownSites $humanDbsnpFile \
    -o "$sampleID".recal_data.grp

    Here, I have used $humanDbsnpFile = "dbsnp_137.b37.vcf" from the GATK bundle.

    Let me know if you need anything else. Thank you once again for your help.

    Regards

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Thanks, I'll try to have a look at your files later today. I'll let you know what I find out.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    OK, I finally got around to looking at your files and I can reproduce your bug, so hopefully we should be able to fix this soon. Sorry for the delay, had some deadlines to deal with in priority.

  • opulcyopulcy Member

    Hi Geraldine,

    Thanks a lot for your efforts. Please take your time. Thanks once again.

    Regards

  • Martin1Martin1 Member

    Hello,

    I have the same problem and I also did (full)validation of my bam file using picard tools.

    That gave me a few of these:

    ERROR: Record 101395, Read name D5N3XBQ1:209:C1NN9ACXX:8:2107:15007:47976, NM tag (nucleotide differences) in file [1] does not match reality [2]
    ERROR: Record 101396, Read name D5N3XBQ1:209:C1NN9ACXX:8:2215:11390:2946, NM tag (nucleotide differences) in file [3] does not match reality [4]
    ERROR: Record 101397, Read name D5N3XBQ1:209:C1NN9ACXX:8:2312:11494:56906, NM tag (nucleotide differences) in file [0] does not match reality [1]
    ERROR: Record 101398, Read name D5N3XBQ1:209:C1NN9ACXX:8:1303:17816:84612, NM tag (nucleotide differences) in file [2] does not match reality [3]
    ERROR: Record 168243, Read name D5N3XBQ1:209:C1NN9ACXX:8:1312:13641:59653, NM tag (nucleotide differences) in file [2] does not match reality [11]
    ERROR: Record 204094, Read name D5N3XBQ1:209:C1NN9ACXX:8:1110:3950:45994, NM tag (nucleotide differences) in file [0] does not match reality [20]
    

    And a lot of these: (380000 for a 10gig sorted deduped bam)

    ERROR: Read name D5N3XBQ1:209:C1NN9ACXX:8:1311:4928:69978, Mate not found for paired read
    ERROR: Read name D5N3XBQ1:209:C1NN9ACXX:8:2204:8180:76770, Mate not found for paired read
    ERROR: Read name D5N3XBQ1:209:C1NN9ACXX:8:2215:17866:3141, Mate not found for paired read
    ERROR: Read name D5N3XBQ1:200:C1J3FACXX:8:2209:8918:61051, Mate not found for paired read
    ERROR: Read name D5N3XBQ1:209:C1NN9ACXX:8:1101:4856:2106, Mate not found for paired read
    ERROR: Read name D5N3XBQ1:200:C1J3FACXX:8:2202:14206:87600, Mate not found for paired read
    ERROR: Read name D5N3XBQ1:209:C1NN9ACXX:8:2116:16343:5258, Mate not found for paired read
    ERROR: Read name D5N3XBQ1:200:C1J3FACXX:8:2315:11351:60460, Mate not found for paired read
    

    I'm mapping using BWA mem v0.7.3a

    I have no problems with other samples which run trough the same pipeline.

    Regards

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @Martin1, we're looking into this and will post here once we find the cause of the problem.

  • Martin1Martin1 Member

    Thank you Geraldine :)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Alright folks, sorry this took a while, I was up to my ears in deadlines all converging on this week.

    @opulcy, I narrowed your bug down to a bad cigar in interval 11:2959000-2959100. If you run with -rf BadCigar the offending read will be filtered out. It looks like an isolated case (ie not many reads affected) so you can safely discard the bad reads without losing data. We'll put in a check to make sure this bad cigar configuration gets caught in future.

    @Martin1, try using the same read filter; hopefully your case is the same and this will allow you to proceed with your work.

  • opulcyopulcy Member

    Hi Geraldine,

    Thanks a lot. I will run the BaseRecalibrator with -rf BadCigar and then let you know the result.

    Regards.

  • opulcyopulcy Member

    Hi Geraldine,

    BaseCalibrator worked smoothly after using -rf BadCigar. Thanks a lot for all you help.

    Regards.

  • Martin1Martin1 Member

    Hi Geraldine,

    Problem is solved with -rf BadCigar but haplotypecaller also failed for the same reason, bad cigar strings. I'm now trying with bwa mem 0.7.4 to see if that also resolves the problem.

    Regards

  • CarneiroCarneiro Charlestown, MAMember

    you can use -rf BadCigar with all GATK tools.

  • NehaNeha AustraliaMember

    Hello I have run the BQSR on one WES sample. The following error came up after running BQSR
    This is my script
    java -jar GenomeAnalysisTK.jar \
    -T BaseRecalibrator \
    -nct 1 \
    -R /data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta \
    -knownSites /data/ref_GATK/dbsnp_138.hg19.sorted.vcf \
    -L /data/ref_GATK/TruSeq_exome_targeted_regions_noX.hg19.bed \
    -I /data/filename.rmdup.bam \
    -o /data/filename.recal_report.grp
    and then I ran PrintReads

    java -jar GenomeAnalysisTK.jar \
    -T PrintReads \
    -nct 1 \
    -R /data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta \
    -BQSR /data/filename.recal_report.grp \
    -o /data/filename.recal.bam \
    -I /data/filename.rmdup.bam

    INFO 17:04:14,407 HelpFormatter - Executing as dgokhaleagashe@MDHS-NIX-028 on Linux 3.13.0-55-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_79-b14.
    INFO 17:04:14,407 HelpFormatter - Date/Time: 2016/05/10 17:04:14
    INFO 17:04:14,407 HelpFormatter - --------------------------------------------------------------------------------
    INFO 17:04:14,407 HelpFormatter - --------------------------------------------------------------------------------
    INFO 17:04:14,488 GenomeAnalysisEngine - Strictness is SILENT
    INFO 17:04:15,035 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
    INFO 17:04:15,075 GenomeAnalysisEngine - Downsampling Settings: No downsampling
    INFO 17:04:15,082 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 17:04:15,108 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
    INFO 17:04:15,176 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
    INFO 17:04:15,180 GenomeAnalysisEngine - Done preparing for traversal
    INFO 17:04:15,180 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 17:04:15,180 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 17:04:15,180 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
    INFO 17:04:15,190 ReadShardBalancer$1 - Loading BAM index data
    INFO 17:04:15,191 ReadShardBalancer$1 - Done loading BAM index data
    INFO 17:04:45,183 ProgressMeter - chr1:7737762 200019.0 30.0 s 2.5 m 0.3% 3.1 h 3.1 h
    INFO 17:05:15,183 ProgressMeter - chr1:12907102 500025.0 60.0 s 120.0 s 0.4% 3.7 h 3.7 h
    INFO 17:05:45,184 ProgressMeter - chr1:16945584 800028.0 90.0 s 112.0 s 0.6% 4.3 h 4.2 h
    INFO 17:06:15,185 ProgressMeter - chr1:24766926 1100033.0 120.0 s 109.0 s 0.9% 3.9 h 3.8 h
    INFO 17:06:45,186 ProgressMeter - chr1:33161454 1400037.0 2.5 m 107.0 s 1.2% 3.6 h 3.6 h
    INFO 17:07:25,187 ProgressMeter - chr1:44438295 1800041.0 3.2 m 105.0 s 1.5% 3.4 h 3.4 h
    INFO 17:08:05,188 ProgressMeter - chr1:61818340 2300046.0 3.8 m 100.0 s 2.1% 3.0 h 2.9 h
    INFO 17:08:35,189 ProgressMeter - chr1:78430081 2600049.0 4.3 m 100.0 s 2.7% 2.7 h 2.6 h
    INFO 17:09:05,190 ProgressMeter - chr1:93995479 2900053.0 4.8 m 100.0 s 3.3% 2.5 h 2.4 h
    INFO 17:09:35,625 ProgressMeter - chr1:109840953 3300058.0 5.3 m 97.0 s 3.8% 2.3 h 2.2 h
    INFO 17:10:05,626 ProgressMeter - chr1:118424507 3600062.0 5.8 m 97.0 s 4.1% 2.4 h 2.3 h
    INFO 17:10:45,627 ProgressMeter - chr1:145318851 4000068.0 6.5 m 97.0 s 5.0% 2.1 h 2.0 h
    INFO 17:11:25,628 ProgressMeter - chr1:148579735 4500078.0 7.2 m 95.0 s 5.2% 2.3 h 2.2 h
    INFO 17:11:55,628 ProgressMeter - chr1:152186907 4800086.0 7.7 m 95.0 s 5.3% 2.4 h 2.3 h
    INFO 17:12:25,629 ProgressMeter - chr1:155185403 5100092.0 8.2 m 96.0 s 5.4% 2.5 h 2.4 h
    INFO 17:12:55,630 ProgressMeter - chr1:160281817 5500097.0 8.7 m 94.0 s 5.6% 2.6 h 2.5 h
    INFO 17:13:25,631 ProgressMeter - chr1:170707377 5800101.0 9.2 m 94.0 s 5.9% 2.6 h 2.4 h
    INFO 17:13:55,632 ProgressMeter - chr1:182783993 6100105.0 9.7 m 95.0 s 6.3% 2.5 h 2.4 h
    INFO 17:14:25,633 ProgressMeter - chr1:200959669 6500110.0 10.2 m 93.0 s 7.0% 2.4 h 2.3 h
    INFO 17:14:55,653 ProgressMeter - chr1:207131812 6800114.0 10.7 m 94.0 s 7.2% 2.5 h 2.3 h
    INFO 17:15:25,655 ProgressMeter - chr1:220487923 7100119.0 11.2 m 94.0 s 7.7% 2.4 h 2.2 h
    INFO 17:15:55,655 ProgressMeter - chr1:230503911 7500125.0 11.7 m 93.0 s 8.0% 2.4 h 2.2 h
    INFO 17:16:25,656 ProgressMeter - chr1:245010226 7800128.0 12.2 m 93.0 s 8.5% 2.4 h 2.2 h
    INFO 17:16:55,657 ProgressMeter - chr2:11242449 8106221.0 12.7 m 93.0 s 9.0% 2.3 h 2.1 h
    INFO 17:17:27,013 ProgressMeter - chr2:27599433 8406226.0 13.2 m 94.0 s 9.6% 2.3 h 2.1 h
    INFO 17:17:57,013 ProgressMeter - chr2:40392233 8806235.0 13.7 m 93.0 s 10.1% 2.3 h 2.0 h
    INFO 17:18:27,014 ProgressMeter - chr2:61510412 9106239.0 14.2 m 93.0 s 10.8% 2.2 h 117.3 m
    INFO 17:18:57,015 ProgressMeter - chr2:74327764 9506245.0 14.7 m 92.0 s 11.2% 2.2 h 116.1 m
    INFO 17:19:27,016 ProgressMeter - chr2:89084266 9806251.0 15.2 m 92.0 s 11.7% 2.2 h 114.1 m
    INFO 17:19:57,017 ProgressMeter - chr2:99720602 1.0106255E7 15.7 m 93.0 s 12.1% 2.2 h 113.8 m
    INFO 17:20:37,018 ProgressMeter - chr2:113513945 1.0606265E7 16.4 m 92.0 s 12.6% 2.2 h 113.5 m
    INFO 17:21:07,019 ProgressMeter - chr2:131176885 1.0906271E7 16.9 m 92.0 s 13.2% 2.1 h 110.8 m
    INFO 17:21:47,020 ProgressMeter - chr2:152692668 1.1306275E7 17.5 m 93.0 s 14.0% 2.1 h 108.0 m
    INFO 17:22:17,021 ProgressMeter - chr2:169018306 1.1706281E7 18.0 m 92.0 s 14.5% 2.1 h 106.1 m
    INFO 17:22:47,021 ProgressMeter - chr2:179414192 1.2006287E7 18.5 m 92.0 s 14.9% 2.1 h 105.9 m
    INFO 17:23:17,577 ProgressMeter - chr2:192551416 1.2306292E7 19.0 m 92.0 s 15.3% 2.1 h 105.1 m
    INFO 17:23:47,577 ProgressMeter - chr2:206661864 1.2706296E7 19.5 m 92.0 s 15.8% 2.1 h 103.9 m
    INFO 17:24:17,578 ProgressMeter - chr2:219617710 1.3006301E7 20.0 m 92.0 s 16.3% 2.1 h 103.1 m
    INFO 17:24:47,579 ProgressMeter - chr2:233899167 1.3306307E7 20.5 m 92.0 s 16.8% 2.0 h 101.9 m
    INFO 17:25:17,580 ProgressMeter - chr3:9023755 1.3609323E7 21.0 m 92.0 s 17.4% 2.0 h 99.8 m
    INFO 17:25:47,581 ProgressMeter - chr3:23848570 1.400933E7 21.5 m 92.0 s 17.9% 2.0 h 98.6 m
    INFO 17:26:17,582 ProgressMeter - chr3:39162516 1.4309334E7 22.0 m 92.0 s 18.5% 119.4 m 97.4 m
    INFO 17:26:47,583 ProgressMeter - chr3:48302459 1.4609344E7 22.5 m 92.0 s 18.8% 2.0 h 97.5 m
    INFO 17:27:27,584 ProgressMeter - chr3:57304801 1.510935E7 23.2 m 92.0 s 19.1% 2.0 h 98.4 m
    INFO 17:28:07,585 ProgressMeter - chr3:97783763 1.5509357E7 23.9 m 92.0 s 20.5% 116.5 m 92.6 m
    INFO 17:28:37,586 ProgressMeter - chr3:113376406 1.5909363E7 24.4 m 91.0 s 21.0% 115.9 m 91.5 m
    INFO 17:29:17,587 ProgressMeter - chr3:128814135 1.6309369E7 25.0 m 92.0 s 21.6% 116.1 m 91.1 m
    INFO 17:29:47,588 ProgressMeter - chr3:139302444 1.6609372E7 25.5 m 92.0 s 21.9% 116.4 m 90.9 m
    INFO 17:30:17,588 ProgressMeter - chr3:156528005 1.6909377E7 26.0 m 92.0 s 22.5% 115.6 m 89.5 m
    INFO 17:30:47,589 ProgressMeter - chr3:180043786 1.7309388E7 26.5 m 91.0 s 23.3% 113.7 m 87.1 m
    INFO 17:31:17,590 ProgressMeter - chr3:193335232 1.7609394E7 27.0 m 92.0 s 23.8% 113.6 m 86.5 m
    INFO 17:31:47,591 ProgressMeter - chr4:1222010 1.7950979E7 27.5 m 92.0 s 24.0% 114.7 m 87.1 m
    INFO 17:32:17,592 ProgressMeter - chr4:9361263 1.8250985E7 28.0 m 92.0 s 24.3% 115.4 m 87.4 m
    INFO 17:32:47,593 ProgressMeter - chr4:37962743 1.8650992E7 28.5 m 91.0 s 25.3% 112.9 m 84.3 m
    INFO 17:33:17,594 ProgressMeter - chr4:55565773 1.8950995E7 29.0 m 91.0 s 25.9% 112.1 m 83.1 m
    INFO 17:33:47,595 ProgressMeter - chr4:74864246 1.9251003E7 29.5 m 92.0 s 26.6% 111.2 m 81.6 m
    INFO 17:34:27,596 ProgressMeter - chr4:95173723 1.9751008E7 30.2 m 91.0 s 27.3% 110.7 m 80.5 m
    INFO 17:34:57,596 ProgressMeter - chr4:114095793 2.0051011E7 30.7 m 91.0 s 27.9% 109.9 m 79.2 m
    INFO 17:35:27,597 ProgressMeter - chr4:137836520 2.0451018E7 31.2 m 91.0 s 28.8% 108.5 m 77.3 m
    INFO 17:35:57,598 ProgressMeter - chr4:156763618 2.0751022E7 31.7 m 91.0 s 29.4% 107.8 m 76.1 m
    INFO 17:36:27,599 ProgressMeter - chr4:184938761 2.1051027E7 32.2 m 91.0 s 30.4% 106.0 m 73.8 m
    INFO 17:36:57,600 ProgressMeter - chr5:13817808 2.1337812E7 32.7 m 91.0 s 31.1% 105.2 m 72.5 m
    INFO 17:37:27,601 ProgressMeter - chr5:34192877 2.1737827E7 33.2 m 91.0 s 31.8% 104.4 m 71.2 m
    INFO 17:37:57,602 ProgressMeter - chr5:52360984 2.2037832E7 33.7 m 91.0 s 32.4% 104.0 m 70.3 m
    INFO 17:38:27,603 ProgressMeter - chr5:68930916 2.2437838E7 34.2 m 91.0 s 33.0% 103.7 m 69.5 m
    INFO 17:39:07,712 ProgressMeter - chr5:78981344 2.2837848E7 34.9 m 91.0 s 33.3% 104.6 m 69.7 m
    INFO 17:39:37,713 ProgressMeter - chr5:98858489 2.3137852E7 35.4 m 91.0 s 34.0% 103.9 m 68.6 m
    INFO 17:40:07,714 ProgressMeter - chr5:122734846 2.3537858E7 35.9 m 91.0 s 34.9% 102.9 m 67.0 m
    INFO 17:40:47,715 ProgressMeter - chr5:140208723 2.3937863E7 36.5 m 91.0 s 35.5% 103.0 m 66.5 m
    INFO 17:41:17,716 ProgressMeter - chr5:148720830 2.4237867E7 37.0 m 91.0 s 35.8% 103.6 m 66.5 m
    INFO 17:41:47,716 ProgressMeter - chr5:160975105 2.4637874E7 37.5 m 91.0 s 36.2% 103.7 m 66.2 m
    INFO 17:42:17,717 ProgressMeter - chr5:177613937 2.493788E7 38.0 m 91.0 s 36.8% 103.4 m 65.4 m
    INFO 17:42:47,823 ProgressMeter - chr6:10397659 2.5242546E7 38.5 m 91.0 s 37.2% 103.5 m 64.9 m
    INFO 17:43:17,823 ProgressMeter - chr6:26523189 2.5642553E7 39.0 m 91.0 s 37.8% 103.3 m 64.2 m
    INFO 17:43:47,824 ProgressMeter - chr6:36169360 2.5942556E7 39.5 m 91.0 s 38.1% 103.7 m 64.1 m
    INFO 17:44:17,825 ProgressMeter - chr6:44394496 2.6242562E7 40.0 m 91.0 s 38.4% 104.2 m 64.2 m
    INFO 17:44:47,826 ProgressMeter - chr6:63242308 2.6542566E7 40.5 m 91.0 s 39.1% 103.7 m 63.2 m
    INFO 17:45:17,827 ProgressMeter - chr6:83921038 2.6842569E7 41.0 m 91.0 s 39.8% 103.1 m 62.1 m
    INFO 17:45:47,828 ProgressMeter - chr6:105281094 2.7242574E7 41.5 m 91.0 s 40.5% 102.5 m 60.9 m
    INFO 17:46:17,829 ProgressMeter - chr6:119345931 2.7542577E7 42.0 m 91.0 s 41.0% 102.5 m 60.4 m
    INFO 17:46:47,830 ProgressMeter - chr6:138412594 2.784258E7 42.5 m 91.0 s 41.7% 102.0 m 59.5 m
    INFO 17:47:17,831 ProgressMeter - chr6:153296440 2.8242586E7 43.0 m 91.0 s 42.2% 102.0 m 58.9 m
    INFO 17:47:47,832 ProgressMeter - chr6:169067746 2.8542589E7 43.5 m 91.0 s 42.7% 101.8 m 58.3 m
    INFO 17:48:17,968 ProgressMeter - chr7:12273264 2.8847707E7 44.0 m 91.0 s 43.2% 101.8 m 57.8 m
    INFO 17:48:47,969 ProgressMeter - chr7:29591492 2.914771E7 44.5 m 91.0 s 43.8% 101.6 m 57.0 m
    INFO 17:49:17,970 ProgressMeter - chr7:44803978 2.9547714E7 45.0 m 91.0 s 44.4% 101.5 m 56.5 m
    INFO 17:49:47,971 ProgressMeter - chr7:56441273 2.9847718E7 45.5 m 91.0 s 44.8% 101.7 m 56.2 m
    INFO 17:50:17,972 ProgressMeter - chr7:66453212 3.0247726E7 46.0 m 91.0 s 45.1% 102.0 m 56.0 m
    INFO 17:50:57,973 ProgressMeter - chr7:76688721 3.0647731E7 46.7 m 91.0 s 45.5% 102.7 m 56.0 m
    INFO 17:51:27,974 ProgressMeter - chr7:94034078 3.0947734E7 47.2 m 91.0 s 46.1% 102.4 m 55.2 m
    INFO 17:51:57,975 ProgressMeter - chr7:100642879 3.1247737E7 47.7 m 91.0 s 46.3% 103.0 m 55.3 m
    INFO 17:52:27,996 ProgressMeter - chr7:107052925 3.1647744E7 48.2 m 91.0 s 46.5% 103.6 m 55.4 m
    INFO 17:53:07,997 ProgressMeter - chr7:130500797 3.204775E7 48.9 m 91.0 s 47.3% 103.2 m 54.3 m
    INFO 17:53:47,998 ProgressMeter - chr7:143964239 3.2547758E7 49.5 m 91.0 s 47.8% 103.6 m 54.1 m
    INFO 17:54:27,999 ProgressMeter - chr8:7119390 3.2979279E7 50.2 m 91.0 s 48.6% 103.3 m 53.1 m
    INFO 17:54:57,999 ProgressMeter - chr8:10755619 3.3279285E7 50.7 m 91.0 s 48.7% 104.1 m 53.4 m
    INFO 17:55:28,000 ProgressMeter - chr8:22478881 3.3579288E7 51.2 m 91.0 s 49.1% 104.2 m 53.0 m
    INFO 17:55:58,001 ProgressMeter - chr8:38126566 3.3979294E7 51.7 m 91.0 s 49.7% 104.1 m 52.4 m
    INFO 17:56:28,002 ProgressMeter - chr8:57389771 3.4279299E7 52.2 m 91.0 s 50.3% 103.7 m 51.5 m
    INFO 17:57:08,003 ProgressMeter - chr8:86556568 3.4679306E7 52.9 m 91.0 s 51.3% 103.0 m 50.1 m
    INFO 17:57:38,004 ProgressMeter - chr8:86748694 3.5079331E7 53.4 m 91.0 s 51.4% 103.9 m 50.6 m
    INFO 17:58:18,005 ProgressMeter - chr8:86819648 3.5579374E7 54.0 m 91.0 s 51.4% 105.2 m 51.2 m
    INFO 17:58:48,006 ProgressMeter - chr8:99956791 3.5879382E7 54.5 m 91.0 s 51.8% 105.3 m 50.7 m
    INFO 17:59:18,007 ProgressMeter - chr8:123966391 3.6179385E7 55.0 m 91.0 s 52.6% 104.5 m 49.5 m
    INFO 17:59:48,008 ProgressMeter - chr8:145067613 3.6579389E7 55.5 m 91.0 s 53.4% 104.0 m 48.5 m
    INFO 18:00:28,009 ProgressMeter - chr9:20948907 3.6980759E7 56.2 m 91.0 s 54.2% 103.8 m 47.6 m
    INFO 18:00:58,963 ProgressMeter - chr9:35440476 3.7280767E7 56.7 m 91.0 s 54.7% 103.8 m 47.1 m
    INFO 18:01:28,964 ProgressMeter - chr9:43098484 3.7680771E7 57.2 m 91.0 s 54.9% 104.2 m 47.0 m
    INFO 18:02:08,965 ProgressMeter - chr9:71396884 3.8080777E7 57.9 m 91.0 s 55.9% 103.5 m 45.7 m
    INFO 18:02:48,966 ProgressMeter - chr9:92220732 3.8580784E7 58.6 m 91.0 s 56.6% 103.4 m 44.8 m
    INFO 18:03:28,967 ProgressMeter - chr9:108289018 3.8980789E7 59.2 m 91.0 s 57.2% 103.6 m 44.3 m
    INFO 18:04:08,968 ProgressMeter - chr9:125681962 3.9380795E7 59.9 m 91.0 s 57.8% 103.6 m 43.7 m
    INFO 18:04:48,969 ProgressMeter - chr9:137715160 3.9880803E7 60.6 m 91.0 s 58.2% 104.0 m 43.5 m
    INFO 18:05:19,657 ProgressMeter - chr10:11984738 4.015449E7 61.1 m 91.0 s 58.7% 104.0 m 42.9 m
    INFO 18:05:49,658 ProgressMeter - chr10:27447577 4.0554494E7 61.6 m 91.0 s 59.3% 103.9 m 42.3 m
    INFO 18:06:19,659 ProgressMeter - chr10:43556787 4.0854501E7 62.1 m 91.0 s 59.8% 103.7 m 41.7 m
    INFO 18:06:49,660 ProgressMeter - chr10:51633323 4.1154504E7 62.6 m 91.0 s 60.1% 104.1 m 41.5 m
    INFO 18:07:19,661 ProgressMeter - chr10:70946206 4.1454507E7 63.1 m 91.0 s 60.8% 103.7 m 40.7 m
    INFO 18:07:49,662 ProgressMeter - chr10:81756120 4.1854514E7 63.6 m 91.0 s 61.2% 103.9 m 40.4 m
    INFO 18:08:19,663 ProgressMeter - chr10:95263037 4.2154519E7 64.1 m 91.0 s 61.6% 104.0 m 39.9 m
    INFO 18:08:49,664 ProgressMeter - chr10:103546510 4.2454526E7 64.6 m 91.0 s 61.9% 104.3 m 39.7 m
    INFO 18:09:29,665 ProgressMeter - chr10:121582639 4.2954532E7 65.2 m 91.0 s 62.5% 104.3 m 39.1 m
    INFO 18:10:09,666 ProgressMeter - chr11:2017402 4.3384977E7 65.9 m 91.0 s 63.1% 104.4 m 38.5 m
    INFO 18:10:39,667 ProgressMeter - chr11:8969367 4.3684981E7 66.4 m 91.0 s 63.3% 104.8 m 38.4 m
    INFO 18:11:09,667 ProgressMeter - chr11:20530061 4.3984985E7 66.9 m 91.0 s 63.7% 105.0 m 38.1 m
    INFO 18:11:39,668 ProgressMeter - chr11:44956353 4.4384991E7 67.4 m 91.0 s 64.6% 104.4 m 37.0 m
    INFO 18:12:09,669 ProgressMeter - chr11:57243639 4.4684994E7 67.9 m 91.0 s 65.0% 104.4 m 36.5 m
    INFO 18:12:39,670 ProgressMeter - chr11:63012416 4.4984998E7 68.4 m 91.0 s 65.2% 104.9 m 36.5 m
    INFO 18:13:19,671 ProgressMeter - chr11:71726367 4.5485008E7 69.1 m 91.0 s 65.5% 105.4 m 36.3 m
    INFO 18:13:59,672 ProgressMeter - chr11:89665931 4.5885015E7 69.7 m 91.0 s 66.1% 105.4 m 35.7 m
    INFO 18:14:29,672 ProgressMeter - chr11:107048195 4.6185019E7 70.2 m 91.0 s 66.7% 105.2 m 35.0 m
    INFO 18:14:59,673 ProgressMeter - chr11:118373812 4.6585024E7 70.7 m 91.0 s 67.1% 105.4 m 34.6 m
    INFO 18:15:29,674 ProgressMeter - chr11:128330764 4.6885028E7 71.2 m 91.0 s 67.5% 105.6 m 34.3 m
    INFO 18:15:59,675 ProgressMeter - chr12:6121467 4.7276589E7 71.7 m 91.0 s 67.9% 105.6 m 33.9 m
    INFO 18:16:29,676 ProgressMeter - chr12:10599106 4.7576594E7 72.2 m 91.0 s 68.1% 106.1 m 33.9 m
    INFO 18:16:59,677 ProgressMeter - chr12:24968354 4.7876598E7 72.7 m 91.0 s 68.6% 106.1 m 33.3 m
    INFO 18:17:29,678 ProgressMeter - chr12:43963932 4.8176601E7 73.2 m 91.0 s 69.2% 105.8 m 32.5 m
    INFO 18:17:59,679 ProgressMeter - chr12:51518321 4.8576606E7 73.7 m 91.0 s 69.5% 106.1 m 32.4 m
    INFO 18:18:39,680 ProgressMeter - chr12:57110104 4.8976614E7 74.4 m 91.0 s 69.7% 106.7 m 32.3 m
    INFO 18:19:09,680 ProgressMeter - chr12:69348508 4.9276619E7 74.9 m 91.0 s 70.1% 106.8 m 31.9 m
    INFO 18:19:39,681 ProgressMeter - chr12:91505094 4.9576622E7 75.4 m 91.0 s 70.9% 106.4 m 31.0 m
    INFO 18:20:09,682 ProgressMeter - chr12:104425490 4.9976627E7 75.9 m 91.0 s 71.3% 106.4 m 30.5 m
    INFO 18:20:39,683 ProgressMeter - chr12:113728816 5.0276631E7 76.4 m 91.0 s 71.7% 106.6 m 30.2 m
    INFO 18:21:09,684 ProgressMeter - chr12:124350409 5.0576634E7 76.9 m 91.0 s 72.0% 106.8 m 29.9 m
    INFO 18:21:39,685 ProgressMeter - chr13:21979964 5.0932951E7 77.4 m 91.0 s 73.1% 105.8 m 28.4 m
    INFO 18:22:09,686 ProgressMeter - chr13:33923611 5.1232957E7 77.9 m 91.0 s 73.5% 105.9 m 28.0 m
    INFO 18:22:39,687 ProgressMeter - chr13:49746120 5.1632961E7 78.4 m 91.0 s 74.1% 105.8 m 27.4 m
    INFO 18:23:09,710 ProgressMeter - chr13:77672151 5.1932966E7 78.9 m 91.0 s 75.1% 105.1 m 26.2 m
    INFO 18:23:39,711 ProgressMeter - chr13:109672345 5.2232969E7 79.4 m 91.0 s 76.2% 104.2 m 24.8 m
    INFO 18:24:09,711 ProgressMeter - chr14:21492379 5.2641226E7 79.9 m 91.0 s 77.1% 103.6 m 23.7 m
    INFO 18:24:39,817 ProgressMeter - chr14:33293487 5.2941231E7 80.4 m 91.0 s 77.5% 103.7 m 23.3 m
    INFO 18:25:09,818 ProgressMeter - chr14:52471652 5.3241234E7 80.9 m 91.0 s 78.2% 103.5 m 22.6 m
    INFO 18:25:39,819 ProgressMeter - chr14:65064054 5.3541238E7 81.4 m 91.0 s 78.6% 103.5 m 22.1 m
    INFO 18:26:09,820 ProgressMeter - chr14:75388187 5.3941242E7 81.9 m 91.0 s 79.0% 103.7 m 21.8 m
    INFO 18:26:39,821 ProgressMeter - chr14:93406665 5.4241247E7 82.4 m 91.0 s 79.6% 103.5 m 21.1 m
    INFO 18:27:09,822 ProgressMeter - chr14:105408577 5.4541254E7 82.9 m 91.0 s 80.0% 103.6 m 20.7 m
    INFO 18:27:39,894 ProgressMeter - chr15:23257887 5.4867446E7 83.4 m 91.0 s 80.9% 103.1 m 19.7 m
    INFO 18:28:09,895 ProgressMeter - chr15:30381882 5.5267454E7 83.9 m 91.0 s 81.1% 103.4 m 19.5 m
    INFO 18:28:49,896 ProgressMeter - chr15:41191183 5.5667459E7 84.6 m 91.0 s 81.5% 103.7 m 19.2 m
    INFO 18:29:29,897 ProgressMeter - chr15:49319709 5.6067465E7 85.2 m 91.0 s 81.8% 104.2 m 19.0 m
    INFO 18:29:59,898 ProgressMeter - chr15:59955172 5.6467474E7 85.7 m 91.0 s 82.2% 104.3 m 18.6 m
    INFO 18:30:29,899 ProgressMeter - chr15:72040875 5.6767477E7 86.2 m 91.0 s 82.6% 104.4 m 18.2 m
    INFO 18:31:09,900 ProgressMeter - chr15:79851872 5.7167484E7 86.9 m 91.0 s 82.9% 104.9 m 18.0 m
    INFO 18:31:49,901 ProgressMeter - chr15:90444010 5.7667492E7 87.6 m 91.0 s 83.2% 105.2 m 17.7 m
    INFO 18:32:29,902 ProgressMeter - chr16:2633515 5.8100996E7 88.2 m 91.0 s 83.7% 105.4 m 17.1 m
    INFO 18:32:59,903 ProgressMeter - chr16:14858231 5.8401003E7 88.7 m 91.0 s 84.2% 105.4 m 16.7 m
    INFO 18:33:29,903 ProgressMeter - chr16:20871425 5.8801007E7 89.2 m 91.0 s 84.4% 105.8 m 16.5 m
    INFO 18:33:59,904 ProgressMeter - chr16:27689240 5.9101011E7 89.7 m 91.0 s 84.6% 106.1 m 16.3 m
    INFO 18:34:29,905 ProgressMeter - chr16:31497245 5.9401019E7 90.2 m 91.0 s 84.7% 106.5 m 16.3 m
    INFO 18:34:59,906 ProgressMeter - chr16:53348971 5.9801024E7 90.7 m 91.0 s 85.5% 106.1 m 15.4 m
    INFO 18:35:29,907 ProgressMeter - chr16:67984099 6.0101027E7 91.2 m 91.0 s 86.0% 106.1 m 14.8 m
    INFO 18:36:09,908 ProgressMeter - chr16:81181700 6.0601035E7 91.9 m 91.0 s 86.5% 106.3 m 14.4 m
    INFO 18:36:39,909 ProgressMeter - chr17:1686408 6.0875845E7 92.4 m 91.0 s 86.8% 106.4 m 14.0 m
    INFO 18:37:19,910 ProgressMeter - chr17:8352014 6.1375853E7 93.1 m 90.0 s 87.1% 106.9 m 13.8 m
    INFO 18:37:49,911 ProgressMeter - chr17:18045556 6.1675857E7 93.6 m 91.0 s 87.4% 107.0 m 13.5 m
    INFO 18:38:19,911 ProgressMeter - chr17:26030807 6.1975865E7 94.1 m 91.0 s 87.7% 107.3 m 13.2 m
    INFO 18:38:49,912 ProgressMeter - chr17:32964298 6.2375871E7 94.6 m 90.0 s 87.9% 107.6 m 13.0 m
    INFO 18:39:19,913 ProgressMeter - chr17:38191999 6.2675874E7 95.1 m 91.0 s 88.1% 107.9 m 12.8 m
    INFO 18:39:49,914 ProgressMeter - chr17:42157958 6.2975882E7 95.6 m 91.0 s 88.2% 108.3 m 12.7 m
    INFO 18:40:29,915 ProgressMeter - chr17:49280108 6.347589E7 96.2 m 90.0 s 88.5% 108.7 m 12.5 m
    INFO 18:40:59,916 ProgressMeter - chr17:61432216 6.3775894E7 96.7 m 91.0 s 88.9% 108.8 m 12.1 m
    INFO 18:41:29,917 ProgressMeter - chr17:72200352 6.4175899E7 97.2 m 90.0 s 89.3% 108.9 m 11.7 m
    INFO 18:41:59,918 ProgressMeter - chr17:80012878 6.4475902E7 97.7 m 90.0 s 89.6% 109.1 m 11.4 m
    INFO 18:42:39,919 ProgressMeter - chr18:15305794 6.4868178E7 98.4 m 91.0 s 90.1% 109.2 m 10.8 m
    INFO 18:43:19,920 ProgressMeter - chr18:44556137 6.5368185E7 99.1 m 90.0 s 91.1% 108.7 m 9.6 m
    INFO 18:43:59,921 ProgressMeter - chr18:74680754 6.5768192E7 99.7 m 90.0 s 92.2% 108.2 m 8.4 m
    INFO 18:44:30,548 ProgressMeter - chr19:6590003 6.6104201E7 100.3 m 90.0 s 92.5% 108.3 m 8.1 m
    INFO 18:45:00,549 ProgressMeter - chr19:11322768 6.6504206E7 100.8 m 90.0 s 92.7% 108.7 m 7.9 m
    INFO 18:45:30,549 ProgressMeter - chr19:16131317 6.6804213E7 101.3 m 90.0 s 92.9% 109.0 m 7.8 m
    INFO 18:46:00,550 ProgressMeter - chr19:22362021 6.7104217E7 101.8 m 90.0 s 93.1% 109.3 m 7.6 m
    INFO 18:46:30,551 ProgressMeter - chr19:36673873 6.7504221E7 102.3 m 90.0 s 93.6% 109.3 m 7.0 m
    INFO 18:47:00,552 ProgressMeter - chr19:42012491 6.7804226E7 102.8 m 90.0 s 93.8% 109.6 m 6.8 m
    INFO 18:47:30,553 ProgressMeter - chr19:48533834 6.8104229E7 103.3 m 90.0 s 94.0% 109.8 m 6.6 m
    INFO 18:48:00,554 ProgressMeter - chr19:53086212 6.8504234E7 103.8 m 90.0 s 94.2% 110.2 m 6.4 m
    INFO 18:48:30,555 ProgressMeter - chr19:56466730 6.880424E7 104.3 m 90.0 s 94.3% 110.6 m 6.3 m
    INFO 18:49:00,556 ProgressMeter - chr20:2443843 6.9115317E7 104.8 m 90.0 s 94.4% 110.9 m 6.2 m
    INFO 18:49:30,557 ProgressMeter - chr20:19804554 6.9515326E7 105.3 m 90.0 s 95.0% 110.7 m 5.5 m
    INFO 18:50:10,558 ProgressMeter - chr20:34844473 6.9915333E7 105.9 m 90.0 s 95.6% 110.8 m 4.9 m
    INFO 18:50:50,559 ProgressMeter - chr20:52774773 7.0315338E7 106.6 m 90.0 s 96.2% 110.8 m 4.2 m
    INFO 18:51:30,560 ProgressMeter - chr21:19642168 7.0859456E7 107.3 m 90.0 s 97.2% 110.3 m 3.1 m
    INFO 18:52:00,561 ProgressMeter - chr21:39673591 7.1159459E7 107.8 m 90.0 s 97.9% 110.0 m 2.3 m
    INFO 18:52:30,561 ProgressMeter - chr22:16653016 7.1478393E7 108.3 m 90.0 s 98.8% 109.6 m 79.0 s
    INFO 18:53:00,563 ProgressMeter - chr22:22890900 7.1778398E7 108.8 m 90.0 s 99.0% 109.8 m 64.0 s
    INFO 18:53:30,564 ProgressMeter - chr22:30899651 7.2178404E7 109.3 m 90.0 s 99.3% 110.0 m 46.0 s
    INFO 18:54:00,564 ProgressMeter - chr22:40722931 7.2478408E7 109.8 m 90.0 s 99.6% 110.2 m 24.0 s
    INFO 18:54:30,565 ProgressMeter - chr22:51193574 7.2778414E7 110.3 m 90.0 s 100.0% 110.3 m 0.0 s
    INFO 18:54:34,417 GATKRunReport - Uploaded run statistics report to AWS S3

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: BUG: requested unknown contig=chrX index=-1
    at org.broadinstitute.gatk.utils.MRUCachingSAMSequenceDictionary.updateCache(MRUCachingSAMSequenceDictionary.java:178)
    at org.broadinstitute.gatk.utils.MRUCachingSAMSequenceDictionary.getSequence(MRUCachingSAMSequenceDictionary.java:109)
    at org.broadinstitute.gatk.utils.GenomeLocParser.validateGenomeLoc(GenomeLocParser.java:284)
    at org.broadinstitute.gatk.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:239)
    at org.broadinstitute.gatk.utils.GenomeLocParser.createGenomeLoc(GenomeLocParser.java:449)
    at org.broadinstitute.gatk.engine.datasources.providers.ReadReferenceView.getReferenceContext(ReadReferenceView.java:98)
    at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$2.next(TraverseReadsNano.java:139)
    at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$2.next(TraverseReadsNano.java:128)
    at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.aggregateMapData(TraverseReadsNano.java:119)
    at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:101)
    at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.4-0-g7e26428):
    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: BUG: requested unknown contig=chrX index=-1

    Is this a known bug?
    I am using GATK version 3.4.

    Thanks,
    Neha

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @Neha
    Hi Neha,

    Do you get the error message only with PrintReads? Can you please post the FASTA .dict file contents and BAM file header here? It looks like there is a mismatch between the two.

    Thanks,
    Sheila

  • NehaNeha AustraliaMember

    Hi Sheila,
    The first part of BQSR worked fine with no errors.
    It was only the PrintReads part that gave this error.

    This is how my fasta.dict file looks.We removed out chrM, chrX and chrY.
    dgokhaleagashe@MDHS-NIX-028[autosome_ref] head -200 hg19_gatk_autosome.dict [11:46PM]
    @HD VN:1.0 SO:unsorted
    @SQ SN:chr1 LN:249250621 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:1b22b98cdeb4a9304cb5d48026a85128
    @SQ SN:chr2 LN:243199373 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:a0d9851da00400dec1098a9255ac712e
    @SQ SN:chr3 LN:198022430 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:641e4338fa8d52a5b781bd2a2c08d3c3
    @SQ SN:chr4 LN:191154276 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:23dccd106897542ad87d2765d28a19a1
    @SQ SN:chr5 LN:180915260 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:0740173db9ffd264d728f32784845cd7
    @SQ SN:chr6 LN:171115067 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:1d3a93a248d92a729ee764823acbbc6b
    @SQ SN:chr7 LN:159138663 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:618366e953d6aaad97dbe4777c29375e
    @SQ SN:chr8 LN:146364022 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:96f514a9929e410c6651697bded59aec
    @SQ SN:chr9 LN:141213431 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:3e273117f15e0a400f01055d9f393768
    @SQ SN:chr10 LN:135534747 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:988c28e000e84c26d552359af1ea2e1d
    @SQ SN:chr11 LN:135006516 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:98c59049a2df285c76ffb1c6db8f8b96
    @SQ SN:chr12 LN:133851895 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:51851ac0e1a115847ad36449b0015864
    @SQ SN:chr13 LN:115169878 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:283f8d7892baa81b510a015719ca7b0b
    @SQ SN:chr14 LN:107349540 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:98f3cae32b2a2e9524bc19813927542e
    @SQ SN:chr15 LN:102531392 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:e5645a794a8238215b2cd77acb95a078
    @SQ SN:chr16 LN:90354753 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:fc9b1a7b42b97a864f56b348b06095e6
    @SQ SN:chr17 LN:81195210 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:351f64d4f4f9ddd45b35336ad97aa6de
    @SQ SN:chr18 LN:78077248 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c
    @SQ SN:chr19 LN:59128983 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:1aacd71f30db8e561810913e0b72636d
    @SQ SN:chr20 LN:63025520 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:0dec9660ec1efaaf33281c0d5ea2560f
    @SQ SN:chr21 LN:48129895 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:2979a6085bfe28e3ad6f552f361ed74d
    @SQ SN:chr22 LN:51304566 UR:file:/data/software/NGS/callers/GATK/resources/reference/hg19_gatk_autosome.fasta M5:a718acaa6135fdca8357d5bfe94211dd

    This it the header for my bam file that I am trying to run BQSR on.
    dgokhaleagashe@MDHS-NIX-028[BU_fam] samtools view -H BU572.rmdup.bam [11:49PM]
    @HD VN:1.0 GO:none SO:coordinate
    @SQ SN:chr1 LN:249250621
    @SQ SN:chr2 LN:243199373
    @SQ SN:chr3 LN:198022430
    @SQ SN:chr4 LN:191154276
    @SQ SN:chr5 LN:180915260
    @SQ SN:chr6 LN:171115067
    @SQ SN:chr7 LN:159138663
    @SQ SN:chr8 LN:146364022
    @SQ SN:chr9 LN:141213431
    @SQ SN:chr10 LN:135534747
    @SQ SN:chr11 LN:135006516
    @SQ SN:chr12 LN:133851895
    @SQ SN:chr13 LN:115169878
    @SQ SN:chr14 LN:107349540
    @SQ SN:chr15 LN:102531392
    @SQ SN:chr16 LN:90354753
    @SQ SN:chr17 LN:81195210
    @SQ SN:chr18 LN:78077248
    @SQ SN:chr19 LN:59128983
    @SQ SN:chr20 LN:63025520
    @SQ SN:chr21 LN:48129895
    @SQ SN:chr22 LN:51304566
    @SQ SN:chrX LN:155270560
    @SQ SN:chrY LN:59373566
    @SQ SN:chrM LN:16571
    @SQ SN:chr1_gl000191_random LN:106433
    @SQ SN:chr1_gl000192_random LN:547496
    @SQ SN:chr4_ctg9_hap1 LN:590426
    @SQ SN:chr4_gl000193_random LN:189789
    @SQ SN:chr4_gl000194_random LN:191469
    @SQ SN:chr6_apd_hap1 LN:4622290
    @SQ SN:chr6_cox_hap2 LN:4795371
    @SQ SN:chr6_dbb_hap3 LN:4610396
    @SQ SN:chr6_mann_hap4 LN:4683263
    @SQ SN:chr6_mcf_hap5 LN:4833398
    @SQ SN:chr6_qbl_hap6 LN:4611984
    @SQ SN:chr6_ssto_hap7 LN:4928567
    @SQ SN:chr7_gl000195_random LN:182896
    @SQ SN:chr8_gl000196_random LN:38914
    @SQ SN:chr8_gl000197_random LN:37175
    @SQ SN:chr9_gl000198_random LN:90085
    @SQ SN:chr9_gl000199_random LN:169874
    @SQ SN:chr9_gl000200_random LN:187035
    @SQ SN:chr9_gl000201_random LN:36148
    @SQ SN:chr11_gl000202_random LN:40103
    @SQ SN:chr17_ctg5_hap1 LN:1680828
    @SQ SN:chr17_gl000203_random LN:37498
    @SQ SN:chr17_gl000204_random LN:81310
    @SQ SN:chr17_gl000205_random LN:174588
    @SQ SN:chr17_gl000206_random LN:41001
    @SQ SN:chr18_gl000207_random LN:4262
    @SQ SN:chr19_gl000208_random LN:92689
    @SQ SN:chr19_gl000209_random LN:159169
    @SQ SN:chr21_gl000210_random LN:27682
    @SQ SN:chrUn_gl000211 LN:166566
    @SQ SN:chrUn_gl000212 LN:186858
    @SQ SN:chrUn_gl000213 LN:164239
    @SQ SN:chrUn_gl000214 LN:137718
    @SQ SN:chrUn_gl000215 LN:172545
    @SQ SN:chrUn_gl000216 LN:172294
    @SQ SN:chrUn_gl000217 LN:172149
    @SQ SN:chrUn_gl000218 LN:161147
    @SQ SN:chrUn_gl000219 LN:179198
    @SQ SN:chrUn_gl000220 LN:161802
    @SQ SN:chrUn_gl000221 LN:155397
    @SQ SN:chrUn_gl000222 LN:186861
    @SQ SN:chrUn_gl000223 LN:180455
    @SQ SN:chrUn_gl000224 LN:179693
    @SQ SN:chrUn_gl000225 LN:211173
    @SQ SN:chrUn_gl000226 LN:15008
    @SQ SN:chrUn_gl000227 LN:128374
    @SQ SN:chrUn_gl000228 LN:129120
    @SQ SN:chrUn_gl000229 LN:19913
    @SQ SN:chrUn_gl000230 LN:43691
    @SQ SN:chrUn_gl000231 LN:27386
    @SQ SN:chrUn_gl000232 LN:40652
    @SQ SN:chrUn_gl000233 LN:45941
    @SQ SN:chrUn_gl000234 LN:40531
    @SQ SN:chrUn_gl000235 LN:34474
    @SQ SN:chrUn_gl000236 LN:41934
    @SQ SN:chrUn_gl000237 LN:45867
    @SQ SN:chrUn_gl000238 LN:39939
    @SQ SN:chrUn_gl000239 LN:33824
    @SQ SN:chrUn_gl000240 LN:41933
    @SQ SN:chrUn_gl000241 LN:42152
    @SQ SN:chrUn_gl000242 LN:43523
    @SQ SN:chrUn_gl000243 LN:43341
    @SQ SN:chrUn_gl000244 LN:39929
    @SQ SN:chrUn_gl000245 LN:36651
    @SQ SN:chrUn_gl000246 LN:38154
    @SQ SN:chrUn_gl000247 LN:36422
    @SQ SN:chrUn_gl000248 LN:39786
    @SQ SN:chrUn_gl000249 LN:38502
    @RG ID:BU572-1_1 PL:Solexa PU:B817G4ABXX LB:TxBiomedSolexaPipeline SM:BU572 CN:TxBiomed
    @RG ID:BU572-1_2 PL:Solexa PU:B817G4ABXX LB:TxBiomedSolexaPipeline SM:BU572 CN:TxBiomed
    @RG ID:BU572-1_3 PL:Solexa PU:B817G4ABXX LB:TxBiomedSolexaPipeline SM:BU572 CN:TxBiomed
    @PG ID:GATK IndelRealigner VN:1.4-37-g0b29d54 CL:knownAlleles=[(RodBinding name=knownAlleles source=/data/NGSEQ/Resources/Internal/Human/Genome/Variation/dbSNP135.hg19-sorted.vcf)] targetIntervals=/master/jperalta/Projects/Preeclamsia/BU572.intervals LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null
    @PG ID:GATK TableRecalibration VN:1.4-37-g0b29d54 CL:default_read_group=null default_platform=null force_read_group=null force_platform=null window_size_nqs=5 homopolymer_nback=7 exception_if_no_tile=false solid_recal_mode=SET_Q_ZERO solid_nocall_strategy=THROW_EXCEPTION recal_file=/master/jperalta/Projects/Preeclamsia/BU572.pre_recal.csv preserve_qscores_less_than=5 smoothing=1 max_quality_score=50 doNotWriteOriginalQuals=false no_pg_tag=false fail_with_no_eof_marker=false skipUQUpdate=false Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate]
    @PG ID:bwa PN:bwa VN:0.6.1-r104

    my bam file has sequence data for chrX and Y and chrM too...
    I have specified intervals using a bed file. My bed file does not contain chrX, Y and M.

    So did it give an error because my bam file contains sequence data for chrX, Y and M whereas my reference file comprises of the 22 autosomes and no sex or mitochondrial chromosomes there?

    Thanks
    Neha

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