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=500000 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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