Hi,
that seems like an GATK2 error and not wrapper or Galaxy related. Any
chance to use a more recent GATK2 version? I only tested it with GATK
2.7 and 2.8.
Also you may try to
delete /tmp/tmp-gatk-BG9Hkr/dict7357081511697052096.tmp.
Ciao,
Bjoern
P.S. Any feedback regarding the wrapper is very much appreciated.
Thanks!
> I used BWA on a local galaxy installation (Ubuntu 12.10) to generate
> an alignment of my FastQ reads. Now I am trying to use GATK Unified
> Genotyper with my own reference sequence. The first time I ran it, I
> had forgotten to edit env.sh to show the path to the GATK .jar file.
> After I fixed that, the next time I tried to run it I got the error
> shown below.
>
>
>
> If I understand this correctly, it already tried to create a tmp file
> from the first run and now is unable to continue until I delete it.
> However, I cannot locate the file.
>
>
> 1) Am I correct in my understanding of the error?
>
> 2) How do I delete the file to clear the error?
>
>
> Thanks everyone!
>
>
>
> [Thu Jan 23 22:24:59 CST 2014] net.sf.picard.sam.CreateSequenceDictionary
> REFERENCE=/tmp/tmp-gatk-BG9Hkr/gatk_input.fasta
> OUTPUT=/tmp/tmp-gatk-BG9Hkr/dict7357081511697052096.tmp
> TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO
> QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5
> MAX_RECORDS_IN_RAM=50 CREATE_INDEX=false CREATE_MD5_FILE=false
> [Thu Jan 23 22:24:59 CST 2014] Executing as
> heidi@heidi-HP-Pavilion-dv6-Notebook-PC on Linux 3.5.0-44-generic amd64;
> OpenJDK 64-Bit Server VM 1.7.0_25-b30; Picard version: null
> [Thu Jan 23 22:24:59 CST 2014] net.sf.picard.sam.CreateSequenceDictionary
> done. Elapsed time: 0.00 minutes.
> Runtime.totalMemory()=173146112
> FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
> # ERROR
> --
> # ERROR A USER ERROR has occurred (version 2.4-7-g5e89f01):
> # 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 website and forum for extensive documentation and
> answers to
> # ERROR commonly asked questions http://www.broadinstitute.org/gatk
> # ERROR
> # ERROR MESSAGE: Index file /tmp/tmp-gatk-BG9Hkr/gatk_input.dict does not
> exist but could not be created because: .
> /tmp/tmp-gatk-BG9Hkr/dict7357081511697052096.tmp already exists. Delete this
> file and try again, or specify a different output file.
> # ERROR
> --
>
>
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