The current GATK version is 3.2-2

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Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

# How do I filter the reads that result in this type of error in some of my intervals?

Posts: 5Member
edited December 2012
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Only one of refStart or refStop must be < 0, not both (-1, -8)


Here is some information

INFO  20:22:19,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-16-g9f648cb, Compiled 2012/12/04 03:48:10
INFO  20:22:19,452 HelpFormatter - Program Args: -T HaplotypeCaller


Thanks

Post edited by Geraldine_VdAuwera on
Tagged:

Hi Severin, can you please post the entire stack trace including your commandline?

Geraldine Van der Auwera, PhD

• Posts: 5Member
edited December 2012

Here is everything I have from the output and Error file. I know it occurs in the first interval of the first chromosome.

Here is my command java -Xmx3072m -XX:+UseParallelOldGC -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Djava.io.tmpdir=/scratch/rcsshoe -cp /data004/software/GIF/GIF/programs/Queue-2.2-16-g9f648cb/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T HaplotypeCaller -I /data006/GIF_2/Client/GATK-64/3.realign.bam -L /data006/GIF_2/Client/GATK-64/.queue/scatterGather/script-1-sg/temp_01_of_64/scatter.intervals -R /data006/GIF_2/Client/GATK-64/Species.fasta -o /data006/GIF_2/Client/GATK-64/.queue/scatterGather/script-1-sg/temp_01_of_64/3.realign.queue.vcf -stand_emit_conf 10.0

In case you are wondering I couldn't get Queue to finish but it did create the split commands and the intervals and output the commands it was trying to run. 63/64 of those commands ran without a problem this one I believe is complaining about some of the reads in the BAM file but I don't know which as I don't understand the error. I saw there was another post on this but its resolution was not clear.

##### ERROR If not, please post the error, with stack trace, to the GATK forum
INFO 20:24:17,911 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 20:24:17,978 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07 INFO 20:24:18,149 GenomeAnalysisEngine - Processing 15208505 bp from intervals INFO 20:24:18,159 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 20:24:18,159 ProgressMeter - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining INFO 20:24:32,692 GATKRunReport - Uploaded run statistics report to AWS S3