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Advice ERROR ----------

I am using the workflow for best practices for variant calling. I used the sam files obtained with bowtie
So far I index and create the .dict files using this commands:

java -jar CreateSequenceDictionary.jar R= file.fasta O= file.dict (picard-tools-194)
samtools faidx file.fasta ( samtools-0.1.19)

Then I ran this commands with gatk latest version

java -jar picard.jar AddOrReplaceReadGroups I=file.sam O=file_added_sorted.bam SO=coordinate RGID=id RGLB=library RGPL=platform RGPU=machine RGSM=sample

java -jar picard.jar MarkDuplicates I=file_added_sorted.bam O=file_dedupped.bam CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=output.metrics

So far so good, until i tried to ran the following commands:
java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R ref.fasta -I file_dedupped.bam -o file_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS

This error appeared and the program stop running and no output was generated :
[email protected]:~/Bandamae_vs_gom/bowtie$ java -jar /user/shinojosa/GenomeAnalysisTK.jar -T SplitNCigarReads -R Dsil.fasta -I JV4a_gom.bam -o JV4a_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
INFO 14:30:57,696 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:30:57,698 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 14:30:57,698 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 14:30:57,698 HelpFormatter - For support and documentation go to
INFO 14:30:57,698 HelpFormatter - [Tue Feb 07 14:30:57 CET 2017] Executing on Linux 3.16.0-4-amd64 amd64
INFO 14:30:57,698 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14
INFO 14:30:57,702 HelpFormatter - Program Args: -T SplitNCigarReads -R Dsil.fasta -I JV4a_gom.bam -o JV4a_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
INFO 14:30:57,705 HelpFormatter - Executing as [email protected] on Linux 3.16.0-4-amd64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14.
INFO 14:30:57,705 HelpFormatter - Date/Time: 2017/02/07 14:30:57
INFO 14:30:57,706 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:30:57,706 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:30:57,813 GenomeAnalysisEngine - Strictness is SILENT
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ERROR ------------------------------------------------------------------------------------------

I have tried using the orignal bam file not the dedupped and I have the same Error

Any advice? I am doing something wrong?

Best Answer


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