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error:Unable to open index file of bam.bai

douymdouym Posts: 18Member

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!

Best Answer

Answers

  • douymdouym Posts: 18Member

    Thanks alot @Geraldine_VdAuwera, I think I have found out the problem: it seems that I shouldn't set the the value of RGID tag to be "null".

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,469Administrator, Dev admin

    Ah yes that woul indeed be a problem. I'm glad you found the solution.

    Geraldine Van der Auwera, PhD

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