Hi Nitin, I think I saw this error years ago when I was working with a bam that had multiple reads with the same name. How many times do you see
ST1023:220:H84P1ADXX:2:2115:7649:16177 in your starting bam file? Are there multiple fragments (read pairs) with the same ID? I think I ran in to this issue when I merged the same file multiple times ( that was a bad day :) ) Richard On 02/12/2016 08:43 AM, Nitin Bhardwaj wrote: > > Hi, > > I saw this error encountered by a few other users and I tried all that > was suggested but nothing worked for me. I am still getting the error > on Picard MarkDuplicates step: > > Exception in thread "main" htsjdk.samtools.SAMException: Value was put into > PairInfoMap more than once. 1: > GIAB:HWI-ST1023:220:H84P1ADXX:2:2115:7649:16177 > > Here is what I did: > > First sorted and converted bams to fastq as I did not have original > fastqs: > > samtools sort -n NIST-hg001-7001-b-ready.bam -o > NIST-hg001-7001-b-ready.sorted.bam > > bedtools bamtofastq -i NIST-hg001-7001-b-ready.sorted.bam -fq > NIST-hg001-7001-b-ready_R1.fastq -fq2 NIST-hg001-7001-b-ready_R2.fastq > > Then I aligned using BWA mem: > > bwa mem -t 8 -M -R '@RG\tID:GIAB\tSM:NA12878\tPL:illumina\tLB:lib\tPU:7001' > reference_genome/hg19 NIST-hg001-7001-ready_R1.fastq > NIST-hg001-7001-ready_R2.fastq > NIST-hg001-7001.sam > > Sort Sam using Picard: > > java -jar picard-tools-1.119/SortSam.jar I=NIST-hg001-7001.sam > O=NIST-hg001-7001_sorted.bam SO=coordinate CREATE_INDEX=true > > And mark duplicates: > > java -jar picard-tools-1.119/MarkDuplicates.jar I=NIST-hg001-7001_sorted.bam > O=NIST-hg001-7001_dedup.bam M=NIST-hg001-7001.metric > > When it gives the error: > > Exception in thread "main" htsjdk.samtools.SAMException: Value was put into > PairInfoMap more than once. 1: > GIAB:HWI-ST1023:220:H84P1ADXX:2:2115:7649:16177 > > I tried to clean the bam using Samtools: > > samtools view -h NIST-hg001-7001_sorted.bam | grep -v null | samtools view > -bS - > cleaned.bam > > And also used FixMateInformation using Picard: > > java -jar > /home/nitin/Bioinformatics/Toolbox/src/Misc/picard-tools-1.119/FixMateInformation.jar > I=NIST-hg001-7001_sorted.bam O=NIST-hg001-7001_fixedMate.bam > > But none of them worked. I still get the same error. > > Does anybody have a solution. I have spent a lot of time on it without > any use. Thank a lot in advance. > > ~N > > -- The contents of this electronic mail transmission are intended to be CONFIDENTIAL and for the sole use of the designated recipient. If this message has been misdirected, please contact the sender as soon as possible. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
