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Old 05-10-2013, 01:35 PM   #8
carolW
Senior Member
 
Location: US

Join Date: Apr 2013
Posts: 103
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I get 2 different error messages when I run gatk

If I use the output of picard markedduplicate, I get error message on unindexed bam file whereas the bam file is already indexed as it is already generated by picard samsort before invoking picard markedduplicate. bai file exist too.

And if I use the output of picard sortsam directly, I get
ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '10'

What would you advise?

Thanks,

Carol
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java -jar SortSam.jar SO=coordinate INPUT=~/NGS/data/SRR062641.filt.sam OUTPUT=~/NGS/data/SRR062641.filt.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true

- no error is generated

~/NGS/pgm/GenomeAnalysisTK-2.4-9-g532efad$ java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R /home/carolw/NGS/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -o ~/NGS/data/SRR062641.filt.bam.list -I ~/NGS/data/SRR062641.filt.bam

ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '10'

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java -jar MarkDuplicates.jar INPUT=~/NGS/data/SRR062641.filt.bam OUTPUT=~/NGS/data/SRR062641.filt.marked.bam METRICS_FILE=metrics VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true

- no error is generated

java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R /home/carolw/NGS/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -o ~/NGS/data/SRR062641.filt.bam.list -I ~/NGS/data/SRR062641.filt.marked.bam

ERROR MESSAGE: Invalid command line: Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.
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