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Running MuTect Failed to load reference dictionary

I ran MuTect as following:

PATIENT_ID=$1
java -Xmx2g -jar /common/opt/bioinformatics/mutect/muTect-1.1.4.jar \
--analysis_type MuTect \
--reference_sequence hg19/genome.fa \
--cosmic mutectdbs/b37_cosmic_v54_120711.vcf \
--dbsnp mutectdbs/dbsnp_132_b37.leftAligned.vcf \
--input_file:normal GATK_output/p_DS_bkm_$PATIENT_ID-N/p_DS_bkm_$PATIENT_ID-N.sorted.MarkDup.realn.fixed.bam \
--input_file:tumor GATK_output/p_DS_bkm_$PATIENT_ID-T/p_DS_bkm_$PATIENT_ID-T.sorted.MarkDup.realn.fixed.bam \
--out MuTect_output/$PATIENT_ID.call_stats.txt \
--coverage_file MuTect_output/$PATIENT_ID.coverage.wig.txt

However, I get the following in the output file:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.2-25-g2a68eab):
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: Invalid command line: Failed to load reference dictionary
ERROR ------------------------------------------------------------------------------------------

and I get this traceback in the error file:

INFO 23:26:16,390 HelpFormatter - ---------------------------------------------------------------------------------
INFO 23:26:16,394 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-25-g2a68eab, Compiled 2012/11/08 10:30:02
INFO 23:26:16,394 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 23:26:16,394 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 23:26:16,400 HelpFormatter - Program Args: --analysis_type MuTect --reference_sequence hg19/genome.fa --cosmic mutectdbs/b37_cosmic_v54_120711.vcf --dbsnp mutectdbs/dbsnp_132_b37.leftAligned.vcf --input_file:normal GATK_output/p_DS_bkm_085-N/p_DS_bkm_085-N.sorted.MarkDup.realn.fixed.bam --input_file:tumor GATK_output/p_DS_bkm_085-T/p_DS_bkm_085-T.sorted.MarkDup.realn.fixed.bam --out MuTect_output/085.call_stats.txt --coverage_file MuTect_output/085.coverage.wig.txt
INFO 23:26:16,401 HelpFormatter - Date/Time: 2016/05/26 23:26:16
INFO 23:26:16,401 HelpFormatter - ---------------------------------------------------------------------------------
INFO 23:26:16,401 HelpFormatter - ---------------------------------------------------------------------------------
INFO 23:26:16,434 ArgumentTypeDescriptor - Dynamically determined type of mutectdbs/dbsnp_132_b37.leftAligned.vcf to be VCF
INFO 23:26:16,448 ArgumentTypeDescriptor - Dynamically determined type of mutectdbs/b37_cosmic_v54_120711.vcf to be VCF
INFO 23:26:16,458 GenomeAnalysisEngine - Strictness is SILENT
INFO 23:26:16,474 ReferenceDataSource - Index file /archive/NabaviLab/TNBC_Project/fastq_raw_data/Project_5065_F/Patients/hg19/genome.fa.fai does not exist. Trying to create it now.
WARN 23:26:25,424 FSLockWithShared - WARNING: Unable to lock file /archive/NabaviLab/TNBC_Project/fastq_raw_data/Project_5065_F/Patients/hg19/genome.fa.fai: No locks available.
INFO 23:26:25,424 ReferenceDataSource - Unable to create write lock: No locks available
INFO 23:26:25,425 ReferenceDataSource - Skipping index creation.
INFO 23:26:25,431 ReferenceDataSource - Dict file /archive/NabaviLab/TNBC_Project/fastq_raw_data/Project_5065_F/Patients/hg19/genome.dict does not exist. Trying to create it now.
WARN 23:26:32,379 FSLockWithShared - WARNING: Unable to lock file /archive/NabaviLab/TNBC_Project/fastq_raw_data/Project_5065_F/Patients/hg19/genome.dict: No locks available.
INFO 23:26:32,379 ReferenceDataSource - Unable to create write lock: No locks available
INFO 23:26:32,379 ReferenceDataSource - Skipping dictionary creation.
WARN 23:26:32,386 FSLockWithShared - WARNING: Unable to lock file /archive/NabaviLab/TNBC_Project/fastq_raw_data/Project_5065_F/Patients/hg19/genome.dict: No locks available.
INFO 23:26:32,386 ReferenceDataSource - Unable to create a lock on dictionary file: No locks available
INFO 23:26:32,387 ReferenceDataSource - Treating existing dictionary file as complete.
WARN 23:26:32,394 FSLockWithShared - WARNING: Unable to lock file /archive/NabaviLab/TNBC_Project/fastq_raw_data/Project_5065_F/Patients/hg19/genome.fa.fai: No locks available.
INFO 23:26:32,394 ReferenceDataSource - Unable to create a lock on index file: No locks available
INFO 23:26:32,394 ReferenceDataSource - Treating existing index file as complete.
WARN 23:26:33,272 RestStorageService - Error Response: PUT '/GATK_Run_Reports/Hemq4QGv4CfIlPwQDo4203PPMejvZFK6.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 753, Content-MD5: i40rdIfTys0nEQMDffU5hg==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 8b8d2b7487d3cacd271103037df53986, Date: Fri, 27 May 2016 03:26:32 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:dh1N72j7s8YsIu0hnvtdWHS0agA=, User-Agent: JetS3t/0.8.1 (Linux/2.6.32-279.14.1.el6.x86_64; amd64; en; JVM 1.7.0_03), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 403E337AEAC9C0C9, x-amz-id-2: feG2MNzRvf9y/MTZ5NK9D8oH0KAlOn1vy4hU/Y1Ld3zZ2JsSb2lZBHQ2gP/8mAX/9aph4iMEsJM=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Fri, 27 May 2016 03:26:32 GMT, Connection: close, Server: AmazonS3]

What am I missing?

Answers

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