Question: (Closed) Identification of SNPs
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gravatar for abdul.suboor123
8 days ago by
abdul.suboor1230 wrote:

I was trying to realign my bam files through GATK realigner target creator, so this error occurred, please anyboy tell me what is the problem?

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/020/305/20305000/_job_tmp -Xmx15g  -Xms256m
[Sun Aug 05 21:33:18 CDT 2018] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/galaxy-repl/main/jobdir/020/305/20305000/_job_tmp/tmp-gatk-uwF95H/gatk_input.fasta OUTPUT=/galaxy-repl/main/jobdir/020/305/20305000/_job_tmp/tmp-gatk-uwF95H/dict8138026083857024436.tmp    TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Aug 05 21:33:18 CDT 2018] Executing as g2main@roundup61.tacc.utexas.edu on Linux 3.10.0-693.21.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_40-b43; Picard version: 1.58(1057)
[Sun Aug 05 21:33:36 CDT 2018] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.31 minutes.
Runtime.totalMemory()=1938292736
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version exported): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: SAM/BAM file /galaxy-repl/main/jobdir/020/305/20305000/_job_tmp/tmp-gatk-uwF95H/gatk_input.bam is malformed: SAM file doesn't have any read groups defined in the header.  The GATK no longer supports SAM files without read groups
##### ERROR -------------------------------------------------------------------------------------
ADD COMMENTlink written 8 days ago by abdul.suboor1230

Hello abdul.suboor123!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: The current wrapped GATK tool are deprecated and may fail for many reasons. Please consider alternative variant analysis methods: https://galaxyproject.org/learn/
ADD REPLYlink written 8 days ago by Jennifer Hillman Jackson25k
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