Issues with CollectAlignmentSummaryMetrics Picard tool

Question

[Elisa]

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.

[Pierre Lindenbaum]

the sequence defined in the sam header are not the same than in the fasta reference. Use the same reference that was used to map the reads.

Dictionary size problem in Picard CalculateHsMetrics

Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (84, 195)

CollectRnaSeqMetrics shows "Sequence dictionaries differ" error

....

[Elisa]

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?

[Pierre Lindenbaum]

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.