Issues with CollectAlignmentSummaryMetrics Picard tool
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15 months ago
Elisa • 0

Hi everyone,

I was running the following comand line:

java -jar /home/Picard/picard.jar CollectAlignmentSummaryMetrics -R GRCh38.fna -I 2H.bam -O output2H.txt

but I got the following error:

Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (194, 639) at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:259) at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:342) at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:328) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:117)

I am sure that the reference genome I gave in input is the same reference genome used to align and obtain the BAM file: so, how can I solve this error?

Thanks in advance.

Picard • 509 views
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Actually I've just figured out that the sam header and the referencegenome.dict header are not the same (but I'm sure that the reference genome I gave in input is the same used to align). How can I solve this issue?

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but I'm sure that the reference genome I gave in input is the same used to align)

there is something wrong in your workflow.

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