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Error While running Indel Realigner

mano2991mano2991 MADURAIMember

First i have created the target creator for my indel realignment
the command used for trarget creation is

java -jar Tools/GenomeAnalysisTK.jar -T RealignerTargetCreator -R Reference/BWA/Homo_sapiens_assembly38.fasta -I output/sample1/BWA_alignment_RG.bam -o output/sample1/BWA_Realignement.list

this command works fine

but while running the indel Realigner
i stuck with some errors

Comannd used for realignment

java -jar Tools/GenomeAnalysisTK.jar -T IndelRealigner -R Reference/BWA/Homo_sapiens_assembly38.fasta -targetIntervals output/sample1/BWA_Realignement.list -I output/sample1/BWA_alignment_RG.bam -o output/sample1/BWA_Realignment.bam

Error while running Realignment

INFO 13:01:24,584 HelpFormatter - ---------------------------------------------------------------------------------
INFO 13:01:24,587 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
INFO 13:01:24,587 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 13:01:24,588 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 13:01:24,593 HelpFormatter - Program Args: -T IndelRealigner -R Reference/BWA/Homo_sapiens_assembly38.fasta -targetIntervals output/sample1/BWA_Realignement.list -I output/sample1/BWA_alignment_RG.bam -o output/sample1/BWA_Realignment.bam
INFO 13:01:24,596 HelpFormatter - Executing as [email protected] on Linux 3.19.0-56-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_77-b03.
INFO 13:01:24,597 HelpFormatter - Date/Time: 2016/04/14 13:01:24
INFO 13:01:24,597 HelpFormatter - ---------------------------------------------------------------------------------
INFO 13:01:24,598 HelpFormatter - ---------------------------------------------------------------------------------
INFO 13:01:24,999 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:01:25,153 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 13:01:25,159 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 13:01:25,303 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
INFO 13:01:25,440 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 13:01:25,443 GenomeAnalysisEngine - Done preparing for traversal
INFO 13:01:25,443 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 13:01:25,444 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 13:01:25,444 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 13:01:26,051 ReadShardBalancer$1 - Loading BAM index data
INFO 13:01:26,052 ReadShardBalancer$1 - Done loading BAM index data
INFO 13:01:55,449 ProgressMeter - chr1:150513415 1200014.0 30.0 s 25.0 s 4.7% 10.7 m 10.2 m
INFO 13:02:25,452 ProgressMeter - chr2:84816103 2715517.0 60.0 s 22.0 s 10.4% 9.6 m 8.6 m
INFO 13:02:55,455 ProgressMeter - chr3:31182497 3932473.0 90.0 s 22.0 s 16.2% 9.2 m 7.7 m
INFO 13:03:25,457 ProgressMeter - chr4:75787095 5388526.0 120.0 s 22.0 s 23.8% 8.4 m 6.4 m
INFO 13:03:55,459 ProgressMeter - chr5:179729704 6861376.0 2.5 m 21.0 s 32.9% 7.6 m 5.1 m
INFO 13:04:25,460 ProgressMeter - chr7:36686822 8129203.0 3.0 m 22.0 s 39.4% 7.6 m 4.6 m
INFO 13:04:55,462 ProgressMeter - chr8:109486775 9556787.0 3.5 m 21.0 s 46.6% 7.5 m 4.0 m
INFO 13:05:25,464 ProgressMeter - chr10:69240749 1.0932107E7 4.0 m 21.0 s 54.2% 7.4 m 3.4 m
INFO 13:05:55,465 ProgressMeter - chr11:125485282 1.2536117E7 4.5 m 21.0 s 60.1% 7.5 m 3.0 m
INFO 13:06:25,467 ProgressMeter - chr13:95020893 1.4115976E7 5.0 m 21.0 s 67.5% 7.4 m 2.4 m
INFO 13:06:55,469 ProgressMeter - chr15:89155504 1.5506828E7 5.5 m 21.0 s 74.2% 7.4 m 114.0 s
INFO 13:07:25,471 ProgressMeter - chr17:50976077 1.7117276E7 6.0 m 21.0 s 79.0% 7.6 m 95.0 s
INFO 13:07:55,472 ProgressMeter - chr20:87839 1.8696835E7 6.5 m 20.0 s 84.3% 7.7 m 72.0 s
INFO 13:08:25,475 ProgressMeter - chrX:56565071 2.0179893E7 7.0 m 20.0 s 91.1% 7.7 m 40.0 s
INFO 13:08:55,486 ProgressMeter - HLA-DRB1*15:01:01:01:9686 2.1461918E7 7.5 m 20.0 s 100.0% 7.5 m 0.0 s

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.4-46-gbc02625):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: SAM/BAM/CRAM file [email protected]53070c is malformed: the BAM file has a read with no stored bases (i.e. it uses '*') which is not supported in the GATK; see the --filter_bases_not_stored argument. Offender: MI71I:00039:10107
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