Empty file with VariantsToVCF
Posted in Ask the GATK team | Last updated on 2013-04-25 10:43:30


Comments (13)

Hi,

I am trying to convert a dbSNP text file into a vcf file with the following command: java -jar GenomeAnalysisTK.jar -R canFam2_dog_genome.fa -T VariantsToVCF --variant:OLDDBSNP snp131.txt -o canFam2.vcf

Below is the message:

INFO 13:27:28,085 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:27:28,088 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.4-9-g532efad, Compiled 2013/03/19 07:35:36 INFO 13:27:28,088 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:27:28,088 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 13:27:28,095 HelpFormatter - Program Args: -R canFam2_dog_genome.fa -T VariantsToVCF --variant:OLDDBSNP snp131.txt -o canFam2.vcf INFO 13:27:28,095 HelpFormatter - Date/Time: 2013/04/25 13:27:28 INFO 13:27:28,095 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:27:28,095 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:27:29,123 GenomeAnalysisEngine - Strictness is SILENT INFO 13:27:29,292 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 13:27:29,315 RMDTrackBuilder - Creating Tribble index in memory for file snp131.txt INFO 13:28:05,113 IndexDictionaryUtils - Track /csc/lohi/dog_tools/GenomeAnalysisTK-2.4-9-g532efad/../../canFam3_ref_dogData/snp131.txt doesn't have a sequence dictionary built in, skipping dictionary validation INFO 13:28:05,125 RMDTrackBuilder - Writing Tribble index to disk for file GenomeAnalysisTK-2.4-9-g532efadsnp131.txt.idx INFO 13:28:05,348 GenomeAnalysisEngine - Creating shard strategy for 0 BAM files INFO 13:28:05,365 GenomeAnalysisEngine - Done creating shard strategy INFO 13:28:05,365 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 13:28:05,367 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 13:28:05,875 ProgressMeter - done 0.00e+00 0.0 s 5.9 d 100.0% 0.0 s 0.0 s INFO 13:28:05,876 ProgressMeter - Total runtime 0.51 secs, 0.01 min, 0.00 hours INFO 13:28:07,459 GATKRunReport - Uploaded run statistics report to AWS S3

Everything looks normal and no error message shown. Could anyone help to fix this?

Thanks


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