I have realigned, recalibrated BAM files on which I am trying to run final QC metrics. I have tried running HS metrics and AlignmentSumaryMetrics and I get the following error messages.
1. CalculateHSMetrics - "Sequence dictionaries are not the same size (0, 25)"
Does this refer to the difference between my reference file and BMA file? Do I need to create a BAM Sequence dictionary for my reference file (in fasta format)?
[Wed Jan 05 11:06:13 GMT 2011] net.sf.picard.analysis.directed.CalculateHsMetrics done.
Runtime.totalMemory()=2058027008
Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (0, 25)
at net.sf.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:76)
at net.sf.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:118)
at net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:87)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:68)
2. Alignment Summary Metrics - myfile.bam has no sequence dictionary
Again, does this mean that I need to make a separate sequence dictionary associated with myfile.bam? Presumably this is the source of the error above. Is it possible to generate a sequence dictionary from a bam file with Picard? It also says "If any reads in the file are aligned then alignment summary metrics collection will fail" (which I found confusing because I thought that the file was supposed to be aligned).
WARNING 2011-01-05 11:36:59 CollectAlignmentSummaryMetrics myfile.bam has no sequence dictionary. If any reads in the file are aligned then alignment summary metrics collection will fail.
[Wed Jan 05 11:37:00 GMT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done.
Runtime.totalMemory()=2058027008
I am sorry if these are really simple questions - I am totally new to all of these programs. I have tried searching through previous help questions on samtools and here . Part of the problem is that I can't work out exactly what a "sequence dictionary" is (other than a header file - which I am sure is so obvious that it doesn't require explaining!)
If anyone can help I would be very appreciative!
Thanks.
1. CalculateHSMetrics - "Sequence dictionaries are not the same size (0, 25)"
Does this refer to the difference between my reference file and BMA file? Do I need to create a BAM Sequence dictionary for my reference file (in fasta format)?
[Wed Jan 05 11:06:13 GMT 2011] net.sf.picard.analysis.directed.CalculateHsMetrics done.
Runtime.totalMemory()=2058027008
Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (0, 25)
at net.sf.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:76)
at net.sf.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:118)
at net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:87)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:68)
2. Alignment Summary Metrics - myfile.bam has no sequence dictionary
Again, does this mean that I need to make a separate sequence dictionary associated with myfile.bam? Presumably this is the source of the error above. Is it possible to generate a sequence dictionary from a bam file with Picard? It also says "If any reads in the file are aligned then alignment summary metrics collection will fail" (which I found confusing because I thought that the file was supposed to be aligned).
WARNING 2011-01-05 11:36:59 CollectAlignmentSummaryMetrics myfile.bam has no sequence dictionary. If any reads in the file are aligned then alignment summary metrics collection will fail.
[Wed Jan 05 11:37:00 GMT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done.
Runtime.totalMemory()=2058027008
I am sorry if these are really simple questions - I am totally new to all of these programs. I have tried searching through previous help questions on samtools and here . Part of the problem is that I can't work out exactly what a "sequence dictionary" is (other than a header file - which I am sure is so obvious that it doesn't require explaining!)
If anyone can help I would be very appreciative!
Thanks.
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