Unified Genotyper index file error
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 ------------------------------------------------------------------------------------------
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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participants (2)
-
Björn Grüning -
Heidi Pagán