Re: [svtoolkit-help] SVAltAlign: PicardException

[Bob H. <han...@br...>]

My first suspicion would be that there are variants in the input vcf 
that do not have IDs (i.e. field 3 is ".") - I suspect (unique) IDs are 
required on variants to run through this workflow.

If this isn't it, then I would grep through

/v4scratch/mmc256/ChargeS/GenomeStrip/chr22/record2/altalign/Chr22.pindel024s.x5.50.Strand.NoGenotypes.alt.fasta

to see what the sequence names look like, e.g.

grep '^>' /v4scratch/mmc256/ChargeS/GenomeStrip/chr22/record2/altalign/Chr22.pindel024s.x5.50.Strand.NoGenotypes.alt.fasta

In particular noting whether there are multiple entries of ">._1" and 
trying to determine which input vcf records they correspond to (by 
position in the file and sequence).

-Bob

On 8/21/12 3:06 PM, Margarida Cardoso Moreira wrote:
> Hi,
>
> I am trying to use SVAltAlign to generate alternate allele alignments for a set of deletion calls originally made by Pindel. However, I am getting the following error:
>
> ERROR 14:51:59,841 FunctionEdge - Error: java -Xmx4g -Djava.io.tmpdir=/tmp/1324184.scheduler.v4linux -cp /v4scratch/mmc256/svtoolkit_1.04.939//lib/SVToolkit.jar:/v4scratch/mmc256/svtoolkit_1.04.939//lib/gatk/GenomeAnalysisTK.jar:/v4scratch/mmc256/svtoolkit_1.04.939//lib/gatk/Queue.jar -cp "/v4scratch/mmc256/svtoolkit_1.04.939/lib/SVToolkit.jar:/v4scratch/mmc256/svtoolkit_1.04.939/lib/gatk/GenomeAnalysisTK.jar:/v4scratch/mmc256/svtoolkit_1.04.939/lib/gatk/Queue.jar" net.sf.picard.sam.CreateSequenceDictionary O=/v4scratch/mmc256/ChargeS/GenomeStrip/chr22/record2/altalign/Chr22.pindel024s.x5.50.Strand.NoGenotypes.alt.dict R=/v4scratch/mmc256/ChargeS/GenomeStrip/chr22/record2/altalign/Chr22.pindel024s.x5.50.Strand.NoGenotypes.alt.fasta TRUNCATE_NAMES_AT_WHITESPACE=TRUE
> org.broadinstitute.sting.queue.util.JobExitException: Failed to run job.
> Command line:
> sh /tmp/1324184.scheduler.v4linux/.exec12328
> Exit code: 1
> Standard error contained:
> [Tue Aug 21 14:51:59 EDT 2012] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/v4scratch/mmc256/ChargeS/GenomeStrip/chr22/record2/altalign/Chr22.pindel024s.x5.50.Strand.NoGenotypes.alt.fasta OUTPUT=/v4scratch/mmc256/ChargeS/GenomeStrip/chr22/record2/altalign/Chr22.pindel024s.x5.50.Strand.NoGenotypes.alt.dict TRUNCATE_NAMES_AT_WHITESPACE=true    NUM_SEQUENCES=2147483647 TMP_DIR=/tmp/1324184.scheduler.v4linux/mmc256 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
> [Tue Aug 21 14:51:59 EDT 2012] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
> Runtime.totalMemory()=9109504
> Exception in thread "main" net.sf.picard.PicardException: Contig '._1' already exists in fasta index.
> 	at net.sf.picard.reference.FastaSequenceIndex.add(FastaSequenceIndex.java:70)
> 	at net.sf.picard.reference.FastaSequenceIndex.parseIndexFile(FastaSequenceIndex.java:142)
> 	at net.sf.picard.reference.FastaSequenceIndex.<init>(FastaSequenceIndex.java:55)
> 	at net.sf.picard.reference.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:95)
> 	at net.sf.picard.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:75)
> 	at net.sf.picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:128)
> 	at net.sf.picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:113)
> 	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
> 	at net.sf.picard.sam.CreateSequenceDictionary.main(CreateSequenceDictionary.java:93)
>
> 	at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24)
> 	at org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54)
> 	at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56)
> 	at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383)
> 	at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123)
> 	at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111)
> 	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
> 	at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57)
> 	at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
>
>
> Here is a bit of the vcf file:
>
> ##fileformat=VCFv4.0
> ##fileDate=Aug251981
> ##source=pindel
> ##reference=HG19
> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
> ##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
> ##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
> ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
> ##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
> ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele depth, how many reads support this allele">
> #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
> 22	16849477	DEL_1	AATCGAATGGAATCATCATCGAATGGAATCGAATTGAATCATCGAATGGAATCGAATGCAATCATCTCAAACAGAATCAAATAGAACCATCCAATGAAATCAAATGGAATCATCATCGAATAGAATCAAATGGAACCATAGAATGGT	A	.	PASS	END=16849624;HOMLEN=19;HOMSEQ=ATCGAATGGAATCATCATC;SVLEN=-146;SVTYPE=DEL
> 22	16851058	DEL_2	TAATCATGGAATGGAATCGAAGGTAATCATGGAATGGAATCAAATGGAATTATCATCGAATGGGATGGAATGGAATCATCATCGAAAGGAATCGAAGAG	T	.	PASS	END=16851157;HOMLEN=19;HOMSEQ=AATCATGGAATGGAATCGA;SVLEN=-98;SVTYPE=DEL
>
> Any help would be much appreciated. I really cannot figure this one out.
>
> Thanks!
>
> Margarida
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