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PrintReads error on Readgroup Platform nct errror, Consider having a look at it.

mmterpstrammterpstra NetherlandsMember
edited September 2015 in Ask the GATK team

Hi there GATK team,

Below is a error rapport from the PrintReads unit of the gatk platform. In short a nct error because the reproducibility is not good. But when planned this might get some clues about the wrong threads because this happens at the end of the run (==>> gatk magic) and breaks my workflow. But this one is more peculiar than haplotypecaller nct bugs and might give clues about debugging.

java -Xmx4g -Djava.io.tmpdir=/path/to/baseQualityScoreRecalibration/ -jar /path/to/GenomeAnalysisTK.jar -T PrintReads -R /path/to/human_g1k_v37.fasta -I /path/to/S1.bam -o /path/to/baseQualityScoreRecalibration/S1.bam -BQSR /path/to/baseQualityScoreRecalibration/S1.before.grp -nct 8
INFO  14:40:22,898 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  14:40:22,901 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22 
INFO  14:40:22,901 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  14:40:22,902 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  14:40:22,908 HelpFormatter - Program Args: -T PrintReads -R /path/to/human_g1k_v37.fasta -I /path/to/S1.bam -o /path/to/baseQualityScoreRecalibration/S1.bam -BQSR /path/to/baseQualityScoreRecalibration/S1.before.grp -nct 8 
INFO  14:40:22,912 HelpFormatter - Executing as [email protected] on Linux 3.0.101-0.7.17-default amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. 
INFO  14:40:22,913 HelpFormatter - Date/Time: 2015/09/10 14:40:22 
INFO  14:40:22,913 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  14:40:22,913 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  14:40:23,135 GenomeAnalysisEngine - Strictness is SILENT 
INFO  14:40:24,249 ContextCovariate -       Context sizes: base substitution model 2, indel substitution model 3 
INFO  14:40:24,354 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  14:40:24,366 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  14:40:24,973 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.61 
INFO  14:40:25,151 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 8 CPU thread(s) for each of 1 data thread(s), of 48 processors available on this machine 
INFO  14:40:25,239 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  14:40:25,247 GenomeAnalysisEngine - Done preparing for traversal 
INFO  14:40:25,247 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  14:40:25,248 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  14:40:25,248 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime 
INFO  14:40:25,802 ReadShardBalancer$1 - Loading BAM index data 
INFO  14:40:25,803 ReadShardBalancer$1 - Done loading BAM index data 
INFO  14:40:53,559 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.3-0-g37228af): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: The platform (illumina) associated with read group GATKSAMReadGroupRecord @RG:4039 is not a recognized platform. Allowable options are ILLUMINA,SLX,SOLEXA,SOLID,454,COMPLETE,PACBIO,IONTORRENT,CAPILLARY,HELICOS,UNKNOWN

This is an shortend version of the readgroup lines (generated with addorreplace), selection:

@RG ID:4038 PL:illumina PU:miseq_1  LB:S1_GCACAC    DT:2015-09-10T04:00:00+0200 SM:S1
@RG ID:4039 PL:illumina PU:miseq_1  LB:S1_TGAACC    DT:2015-09-10T04:00:00+0200 SM:S1
@RG ID:404  PL:illumina PU:miseq_1  LB:S1_TCATAG    DT:2015-09-10T04:00:00+0200 SM:S1
@RG ID:4040 PL:illumina PU:miseq_1  LB:S1_CGCAGC    DT:2015-09-10T04:00:00+0200 SM:S1
@RG ID:4041 PL:illumina PU:miseq_1  LB:S1_CGAAAC    DT:2015-09-10T04:00:00+0200 SM:S1
@RG ID:4042 PL:illumina PU:miseq_1  LB:S1_TCATAC    DT:2015-09-10T04:00:00+0200 SM:S1
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