GetPileupSummaries error
a) GATK version used: v4.1.8.0-4
b) Exact command used:
/home/ubuntu/gatk/gatk GetPileupSummaries -I /home/ubuntu/lab_dlbcl/hSNVFiles/I063057_RNA-Seq_gatk/I063057_cutadapt_RG_MD_SC_BQ.bam -V /home/ubuntu/common_all_biallelic.vcf.gz -O I063057_pileups.table -R /home/ubuntu/GRCh38.p13.genome.fa -L /home/ubuntu/common_all_biallelic.vcf.gz
c) Entire error log:
java.lang.ClassCastException: class java.util.ArrayList cannot be cast to class java.lang.String (java.util.ArrayList and java.lang.String are in module java.base of loader 'bootstrap')
at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsDouble(CommonInfo.java:324)
at htsjdk.variant.variantcontext.VariantContext.getAttributeAsDouble(VariantContext.java:820)
at org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries.alleleFrequencyInRange(GetPileupSummaries.java:224)
at org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries.apply(GetPileupSummaries.java:198)
at org.broadinstitute.hellbender.engine.LocusWalker.lambda$traverse$0(LocusWalker.java:162)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at org.broadinstitute.hellbender.engine.LocusWalker.traverse(LocusWalker.java:160)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
- After performing base recalibration on my RNA-Seq samples, I can't seem to run my ".bam" file through GetPileupSummaries file.
-When I tried to use ValidateSamFile, the output was:
WARNING 2021-01-31 22:58:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
INFO 2021-01-31 22:58:43 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 32s. Last read position: chr12:56,713,604
INFO 2021-01-31 22:59:15 SamFileValidator Validated Read 20,000,000 records. Elapsed time: 00:01:04s. Time for last 10,000,000: 31s. Last read position: GL000251.2:4,497,565
## HISTOGRAM java.lang.String
Error Type Count
WARNING:MISSING_TAG_NM 21233869
ÆSun Jan 31 22:59:32 UTC 2021Å picard.sam.ValidateSamFile done. Elapsed time: 1.37 minutes.
Runtime.totalMemory()=2986344448
Could you please tell me what the issue maybe? Thanks in advance.
-
Hi Aqshin Balayev,
It looks like this issue is coming from your VCF file, and the error is being thrown because the tool is not expecting the fields of your VCF to be formatted as they are.
Could you check your VCF file with ValidateVariants? Could you also provide more information on how you obtained that file? It could be malformed.
Genevieve
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Hello Genevieve Brandt,
I tried to run "ValidateVariants" on my VCF file and got:
A USER ERROR has occurred: Input common_all_biallelic.vcf.gz fails strict validation of type ALL: the AF tag has the incorrect number of records at position chr1:10177, 2 vs. 1
Could you please let me know why the function complains? Thanks in advance.
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As additional information I forgot to mention, I downloaded files "common_all_20180418.vcf.gz" and "common_all_20180418.vcf.gz.tbi" from https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/
and selected biallelic variants from it. However I think, AF field contains allelic frequencies of both reference and alternate alleles and GetPileupSummaries can't take it as an input. Thank you for help.
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It sounds like you are on the right track. Have you figured out the cause of this issue?
Best,
Genevieve
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