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Created 2014-01-15 12:46:24 | Updated 2014-01-15 12:47:55 | Tags: bug
Comments (1)

When GATK finds a read for which a corresponding @RG tag is missing in the header, the error message given implies that the read itself is lacking an RG tag rather than the header. Could this be fixed please so that the two error conditions are differentiated? It will save people time when debugging their pipelines if they don't have to go looking at the wrong thing.

ERROR MESSAGE: SAM/BAM file SAMFileReader{/lustre/blah/DDD_MAIN5247030.bam} is malformed: Read HS7_7515:4:2101:12189:66438#2 is missing the read group (RG) tag, which is required by the GATK. Please use to fix this problem

The reads have the RG tag but an @RG tag matching their ID does not exist in the header.

901282:HS7_7515:4:2101:12189:66438#2 99 1 37000590 60 75M = 37000629 114 * * X0:i:1 X1:i:0 BC:Z:CGATGTAT BD:Z:* MD:Z:75 PG:Z:MarkDuplicates RG:Z:1#2 BI:Z:* AM:i:37 NM:i:0 SM:i:37 MQ:i:60 QT:Z:BCAADFFE XT:A:U BQ:Z:* 901283:HS7_7515:4:2101:12189:66438#2 147 1 37000629 60 75M = 37000590 -114 * * X0:i:1 X1:i:0 BD:Z:* MD:Z:75 PG:Z:MarkDuplicates RG:Z:1#2 BI:Z:* AM:i:37 NM:i:0 SM:i:37 MQ:i:60 XT:A:U BQ:Z:*

P.S. your spam filter is stopping me posting discussions with URLs in, could you whitelist any gatkforums dot broad institute dot org urls?


Created 2013-08-30 15:34:58 | Updated | Tags:
Comments (3)

Hi, this is my logfile: (1) [pipeline] SC_run1 THREAD_NUM=3 PROJECT_NAME=shu_family (1) starts at 2013-08-30 22:48:57 (2) [eval] {1..5} (3) [shell] run_picard_1.87.sh MarkDuplicates I=shu_family.61.chr4.bam O=shu_family.61.masked.bam METRICS_FILE=shu_family.61.chr4.metrics REMOVE_DUPLICATES=TRUE ASSUME_SORTED=TRUE VALIDATION_STRINGENCY=SILENT (3) starts at 2013-08-30 22:48:57 (3) ends at 2013-08-30 22:52:21 (elapsed: 3m 24s) (4) [shell] run_picard_1.87.sh AddOrReplaceReadGroups I=shu_family.61.masked.bam O=shu_family.61.masked.rg.bam SORT_ORDER=coordinate RGID=null RGLB=bar RGPL=illumina RGSM=shu_family RGPU=barcode (4) starts at 2013-08-30 22:52:21 (4) ends at 2013-08-30 22:53:46 (elapsed: 1m 25s) (5) [shell] /rd/build/samtools-0.1.18/samtools view -f 2 -h shu_family.61.masked.rg.bam | grep -E "^@|XT:A:U" | perl -ne 'print if (/^@/||(/XM:i:(\d+)/&&$1<=3))' | samtools view -Sb - > shu_family.61.all_masked.rg.bam (5) starts at 2013-08-30 22:53:46 (5) ends at 2013-08-30 22:54:46 (elapsed: 1m) (6) [shell] /rd/build/samtools-0.1.18/samtools index shu_family.61.all_masked.rg.bam (6) starts at 2013-08-30 22:54:46 (6) ends at 2013-08-30 22:54:50 (elapsed: 4s) (7) [shell] run_gatk_1.6.sh -T RealignerTargetCreator -R /rd/user/douym/huangy/reference/human_g1k_v37.fasta -nt 3 -I shu_family.61.all_masked.rg.bam -o shu_family.61.chr4.intervals (7) starts at 2013-08-30 22:54:50 (7) ends at 2013-08-30 22:55:01 (elapsed: 11s) (7) returns 1 (1) ends at 2013-08-30 22:55:01 (elapsed: 6m 4s) Pipeline finished abnormally with exit value: 1!

the erros lines: org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to open index file shu_family.61.all_masked.rg.bam.bai ... 21 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.6-9-g47df7bb):
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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Unable to open index file shu_family.61.all_masked.rg.bam.bai
ERROR ------------------------------------------------------------------------------------------

the index file seems quite normal to me: 00000000 42 41 49 01 54 00 00 00 00 00 00 00 00 00 00 00 |BAI.T...........| 00000010 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |................| 00000020 cc 30 00 00 03 00 00 00 01 00 00 00 4e b3 4a b0 |.0..........N.J.| 00000030 5d 0d 00 00 69 b4 4a b0 5d 0d 00 00 09 00 00 00 |]...i.J.].......| 00000040 04 00 00 00 28 fa 63 06 b9 00 00 00 5f fc 63 06 |....(.c......c.| 00000050 b9 00 00 00 ef 9f a3 fb 5d 01 00 00 28 a2 a3 fb |........]...(...| 00000060 5d 01 00 00 ef a1 99 74 a4 01 00 00 92 a8 99 74 |]......t.......t| 00000070 a4 01 00 00 c5 64 ea dc de 01 00 00 fa 66 ea dc |.....d.......f..| 00000080 de 01 00 00 0a 00 00 00 01 00 00 00 db f8 f5 d5 |................| 00000090 e1 02 00 00 15 fb f5 d5 e1 02 00 00 0c 00 00 00 |................| 000000a0 01 00 00 00 c5 98 da d5 a1 03 00 00 19 9c da d5 |................| 000000b0 a1 03 00 00 0e 00 00 00 01 00 00 00 b3 c1 a5 d3 |................| 000000c0 8e 04 00 00 eb c3 a5 d3 8e 04 00 00 0f 00 00 00 |................| 000000d0 02 00 00 00 2f 74 f0 8a 15 05 00 00 4b 75 f0 8a |..../t......Ku..| 000000e0 15 05 00 00 00 00 7d 93 31 05 00 00 36 02 7d 93 |......}.1...6.}.| 000000f0 31 05 00 00 11 00 00 00 01 00 00 00 65 3f e9 da |1...........e?..| 00000100 10 06 00 00 a8 41 e9 da 10 06 00 00 13 00 00 00 |.....A..........| 00000110 02 00 00 00 2f 40 3c 9e a8 07 00 00 65 42 3c 9e |..../@<.....eB<.| 00000120 a8 07 00 00 63 42 b4 e8 2a 08 00 00 97 44 b4 e8 |....cB......D..| 00000130 2a 08 00 00 15 00 00 00 01 00 00 00 28 f5 94 14 |...........(...| 00000140 14 09 00 00 5f f7 94 14 14 09 00 00 16 00 00 00 |...............| 00000150 02 00 00 00 88 1a 56 42 36 09 00 00 4e 22 56 42 |......VB6...N"VB| 00000160 36 09 00 00 28 5f 9b f6 a8 09 00 00 a2 d6 41 2f |6...(_........A/| 00000170 a9 09 00 00 17 00 00 00 01 00 00 00 cb 93 19 a2 |................| 00000180 14 0a 00 00 e6 94 19 a2 14 0a 00 00 19 00 00 00 |................| 00000190 01 00 00 00 66 4c 40 b9 ba 0a 00 00 9e 4e 40 b9 |....fL@......N@.| 000001a0 ba 0a 00 00 1a 00 00 00 01 00 00 00 78 d4 1a 13 |............x...| 000001b0 6c 0b 00 00 b0 d6 1a 13 6c 0b 00 00 1b 00 00 00 |l.......l.......| 000001c0 02 00 00 00 18 b2 44 c3 a4 0b 00 00 6b b5 44 c3 |......D.....k.D.| 000001d0 a4 0b 00 00 37 e5 1d 6c cf 0b 00 00 52 e6 1d 6c |....7..l....R..l|

why should that be happen? How can I correct it ? Thanks alot!


Created 2013-02-06 19:48:38 | Updated 2013-02-06 19:49:03 | Tags: arrayindexoutofboundsexception
Comments (1)

Hi there, I have a set of data I'm trying to process through GATK for SNP and Indel calling. When these files get to the BaseRecalibrator I get an error as follows.

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

java.lang.ArrayIndexOutOfBoundsException: -1 at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158) at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530) at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:248) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-6-gebbba25):
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: -1
ERROR ------------------------------------------------------------------------------------------

Each file has a different error number with -1, -2, -4, -5, or -15. The only other thing different in the outputs is line 4, at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246) , in which the 246 is occasionally 225.

The same scripts I am using for these runs have successfully completed about 40+ other runs to date, so I'm at a bit of a loss here. I am running Java version 1.7.0_13 on Ubuntu 12.04. Any help resolving this would be appreciated.