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# base recalibration problem

Member Posts: 8

Hi,

I am working on bovine exome sequencing datasets. I have 22 animals ( the read length of 11 samples is 90 bp, others are 100 bp) . I merged all of them into a big bam file, and did Indel realignment on it. When I run BaseRecalibrator, my job was aborted on chr12. And I check the region chr12(28982297, 29984297) of my reference file with Samtools, it seems not damaged. Any suggestion?

Wanbo

##### ERROR stack trace

net.sf.picard.PicardException: Unable to load chr12(28982297, 29984297) from /data/Wanbo/genomes/bosTau6.fasta
at net.sf.picard.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:208)

##### ERROR MESSAGE: Unable to load chr12(28982297, 29984297) from /data/Wanbo/genomes/bosTau6.fasta
Tagged:

Hi there,

Try validating all your input files using the Picard validation tools, that will tell you if there is anything wrong with your files.

You can also run again using -XL argument to exclude the interval where the program choked the first time, and see if it still errors out. That may help identify whether it's a problem with the file or a problem of not enough computing resources.

Geraldine Van der Auwera, PhD