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Old 05-06-2018, 07:40 AM   #1
cursecatcher
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Location: Italy

Join Date: May 2018
Posts: 5
Default Dictionary size problem in Picard HsMetrics

Hi everyone,

I'm following a Roche pipeline for the analysis of targeted bisulfite sequencing data and I'm in trouble with Picard CalculateHsMetrics.

I create the indexed reference file with samtools faidx command and the indexed .bam with samtools index.

When I run Picard, with the following command

Code:
java -Xmx4g -Xms4g -jar ~/bioTool/picard-tools-2.2.1/picard.jar CalculateHsMetrics BAIT_INTERVALS=DESIGN_bait_intervals.txt TARGET_INTERVALS=DESIGN_target_intervals.txt INPUT=2101435_S8_L001.clipped.bam.bai OUTPUT=2101435_S8_L001_picard_hs_metrics.txt METRIC_ACCUMULATION_LEVEL=ALL_READS REFERENCE_SEQUENCE=~/Data/MethylSeq/genomes/GRCh37_latest_genomic_idx.fa  VALIDATION_STRINGENCY=LENIENT TMP_DIR=.
it terminates with the following exception:

Code:
Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (0, 297)
	at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:188)
	at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:271)
	at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:257)
	at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:114)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
It seems like there is a problem in the indexes, but I cannot figure it out.
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Old 05-06-2018, 03:49 PM   #2
cursecatcher
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Location: Italy

Join Date: May 2018
Posts: 5
Default

Solved,
I was using indexed files (.bai and .fai) instead of proper files.
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