Question: (Closed) Getting error while using GATK tools, Realignment Target Creator.
gravatar for abdul.suboor123
3 months ago by
abdul.suboor1230 wrote:

Dataset Error An error occured while running the tool

Tool execution generated the following messages:

Picked up _JAVA_OPTIONS: -Xmx15g -Xms256m [Mon Aug 20 04:29:24 CDT 2018] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/galaxy-repl/main/jobdir/020/422/20422896/_job_tmp/tmp-gatk-XawHqz/gatk_input.fasta OUTPUT=/galaxy-repl/main/jobdir/020/422/20422896/_job_tmp/tmp-gatk-XawHqz/dict6958918825417136237.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 [Mon Aug 20 04:29:24 CDT 2018] Executing as 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) [Mon Aug 20 04:29:24 CDT 2018] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=756023296

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 See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our wiki for extensive documentation
ERROR Visit our forum to view answers to commonly asked questions
ERROR MESSAGE: Invalid command line: Failed to load reference dictionary
ERROR ------------------------------------------------------------------------------------------
realignment gatk • 141 views
ADD COMMENTlink written 3 months 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.


PS: The currently wrapped GATK tools are still deprecated. Please try alternatives:
ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k
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