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error:Unable to open index file of bam.bai

douymdouym Member Posts: 18

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 - ><.....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!

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