Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.


edwardhustedwardhust ChinaPosts: 2Member

Hi: i met errors in my recalibration process. every time errors occur, the messages put "don't post the errors",and then i can find solution in FAQ or furom. however, this time, it tells me to post the errors. i tried to find sulotion, but failed. i am new to GATK, and know little about java.

here is the command:

nohup java -Xmx50g -Djava.io.tmpdir=/tmp\ -jar $GATKdir/GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -R ~/data/ReferAll/sortedIndex/ucsc.hg19.sorted.fasta \ -I ~/projects/TWINS/WGC007813/WGC007813.sai.sam.dedup.realigned.bam \ -knownSites ~/data/ReferAll/bundle/dbsnp_137.hg19.sorted.vcf \ -knownSites ~/data/ReferAll/bundle/1000G_phase1.indels.hg19.sorted.vcf \ -knownSites ~/data/ReferAll/bundle/Mills_and_1000G_gold_standard.indels.hg19.sorted.vcf \ -o ~/projects/TWINS/WGC007813/WGC007813.sai.sam.dedup.realigned.bam.recal.grp \

~/projects/TWINS/WGC007813/no.BaseRecalibrator.out &

and this is the errors message!

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,046 admin
    Answer ✓

    Okay, the good news is that you don't need to know any java to run GATK :)

    So, it looks like some of your reads have a CIGAR string that is causing errors. You may be able to bypass this issue by adding -rf BadCigar to your command. Let me know if that doesn't work.

    Also, in future, can you please just copy and paste the text of the errors, rather than give a screenshot? It is better for several reasons which I won't go into.


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