Hey Sivakumar,
we are tracking your issue here:
https://github.com/broadinstitute/picard/issues/138
N
On Thu, Dec 18, 2014 at 2:49 PM, Sivakumar Gowrisankar <siv...@gmail.com>
wrote:
>
> Hi All
>
> We are currently sequencing some bacterial genomes and I have been using
> Picard to obtain some metrics. One module that is consistently failing is
> the CollectGcBiasMetrics. The error looks something like this:
>
> Exception in thread "main" net.sf.samtools.SAMException: Exception
> counting mismatches for read
> MAC1-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 2/2 0b aligned read.
> at
> net.sf.samtools.util.SequenceUtil.countMismatches(SequenceUtil.java:296)
> at
> net.sf.samtools.util.SequenceUtil.countMismatches(SequenceUtil.java:310)
> at
> net.sf.picard.analysis.CollectGcBiasMetrics.doWork(CollectGcBiasMetrics.java:157)
> at
> net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
> at
> net.sf.picard.analysis.CollectGcBiasMetrics.main(CollectGcBiasMetrics.java:95)
> Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
> at
> net.sf.samtools.util.SequenceUtil.countMismatches(SequenceUtil.java:282)
> ... 4 more
>
> I have the following reads corresponding to that
> --------------------------------------------------------------------------
> NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 417
> gi|557682930|ref|NC_022785.1| 14029 0 232H58M10H =
> 14225 393 * * MD:Z:48C9 RG:Z:Unknown_id NM:i:1
> AS:i:53
> NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 417
> gi|557682930|ref|NC_022785.1| 14225 60 188H112M =
> 14225 197
> CTTGACCTGTGCCGGGTACGGCGGCGGACCGGCGACTACCCGGAGGCTGGCGAGCTGGCCCAGCGGGCCTACGACCTCTACCACAGCCTCGAAAACCGCCTCCGCCAGGCCC
>
>
> DBFFDFFB>>):BFFBBBFFBFFF>B>>FB;F;36>B;??FFFFFF?<B(16>(-122:?<??((4>0>6:BB<>FFF<ABFFFF###########################
> SA:Z:gi|557682930|ref|NC_022785.1|,4137903,-,108S192M,60,0;
> MD:Z:92C9G8A0 RG:Z:Unknown_id NM:i:3 AS:i:101 XS:i:53
> NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 113
> gi|557682930|ref|NC_022785.1| 14225 60 103S197M =
> 4137903 4123674
> CCCTGTTCTCCTTCGGAGAGCAGGGGATTTTGGCTTCCGCCGTCGGCCTCGGCTAGCGCAGCCGGGCCATCAGCGCGTGCTCGACCAGGGTGATCAGCGCGCTCTTGACCTGTGCCGGGTACGGCGGCGGACCGGCGACTACCCGGAGGCTGGCGAGCTGGCCCAGCGGGCCTACGACCTCTACCACAGCCTCGACAACCGCCTCGGCCAGGCCAACGCCCGGCTTGACCTGGGCTGGGTACGGCGGCTGACAGGCGACTATCCGGAGGCGGGAGGGCTGGCCCAGCAGGCCTACGACCT
>
>
> ?FFFFBFFFFFFBBB>BFB??FFF?FB??7F?FFFFBFFFFEFFFBFFFFFFFB>FEB;FFFFFFFFFFGFFEDFFGGFGFGFGGGFGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC
> SA:Z:gi|557682930|ref|NC_022785.1|,4137903,+,193S107M,60,0; MD:Z:197
> RG:Z:Unknown_id NM:i:0 AS:i:197 XS:i:0
> NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 353
> gi|557682930|ref|NC_022785.1| 4137903 60 193H107M =
> 4137903 192
> CAAGAGCGCGCTGATCACCCTGGTCGAGCACGCGCTGATGGCCCGGCTGCGCTAGCCGAGGCCGACGGCGGAAGCCAAAATCCCCTGCTCTCCGAAGGAGAACAGGG
>
> GGGGGGGGGGGGGGGGGGGGFGGGFGFGFGGFFDEFFGFFFFFFFFFF;BEF>BFFFFFFFBFFFEFFFFBFFFF?F7??BF?FFF??BFB>BBBFFFFFFBFFFF?
> SA:Z:gi|557682930|ref|NC_022785.1|,14225,-,103S197M,60,0;
> MD:Z:107 RG:Z:Unknown_id NM:i:0 AS:i:107 XS:i:0
> NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 177
> gi|557682930|ref|NC_022785.1| 4137903 60 108S192M =
> 14225 -4123674
>
> GGGCCTGGCGGAGGCGGTTTTCGAGGCTGTGGTAGAGGTCGTAGGCCCGCTGGGCCAGCTCGCCAGCCTCCGGGTAGTCGCCGGTCCGCCGCCGTACCCGGCACAGGTCAAGAGCGCGCTGATCACCCTGGTCGAGCACGCGCTGATGGCCCGGCTGCGCTAGCCGAGGCCGACGGCGGAAGCCAAAATCCCCTGCTCTCCGAAGGAGAACAGGGGATTTGTGCGTTTCAGTGGGCCTTCTCGGGCGTCCGGGCGGTGTGCGGCCGTCCGGGCACGGCGGCGCCTGTGGGCGGTCAGCCC
>
>
> ###########################FFFFBA<FFF><BB:6>0>4((??<?:221-(>61(B<?FFFFFF??;B>63;F;BF>>B>FFFBFFBBBFFB:)>>BFFDFFBD>EFFFFFFFFFDGEFFGFGFFGFFGBDFGGGGGGECGGDGGGGGGGGGGGDGGGGGGECGGGGEDGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC
> SA:Z:gi|557682930|ref|NC_022785.1|,14225,+,188S112M,60,3; MD:Z:192
> RG:Z:Unknown_id NM:i:0 AS:i:192 XS:i:0
> --------------------------------------------------------------
>
> Of these, only two are primary alignments (since paired end data). There
> is one other thread with the same question, but the solution does not seem
> to apply to me (
> http://sourceforge.net/p/samtools/mailman/samtools-help/thread/c90b022b-e8b1-4d87-90f7-8a544a5cf...@mail.ubc.ca/).
> This is because I have only one chromosome and the length of that
> chromosome is 12 M and this alignment is at 4M bases. Also the coordinates
> in the BAM are sorted.
>
> Any pointers would be very useful!
>
> Thanks
> Siva
>
>
>
>
>
>
>
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