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Created 2015-12-03 06:53:58 | Updated | Tags: indelrealigner nwayout
Comments (1)

I'm using the GenomeAnalysisTK-3.4-0.jar version to co-realign paired tumor-normal BAMs. The -Input is set to a list file contains the paired tumor-normal BAMs directory. For example: /pipiline-test/Normal/rmdup-realn/Normal.rmdup.bam /pipline-test/Tumor/rmdup-realn/Tumor.rmdup.bam And the -nWayOut is set to .realn.bam. The problem is that the output files are generated in the same folder where the shell script is in. Is there a way I can get the output realn.bam to be in the same folder with the preview rmdup.bam?

Created 2014-09-18 11:58:28 | Updated | Tags: indelrealigner nwayout
Comments (5)

Hello, I'm trying to realign approximately 115 bam files. I am able to do this with the -o command, but this results in an impressively large bam file that I cannot fix in Picard (FixMateInformation and SortSam). Unfortunately these are corrections that need to happen before the downstream GATK snp discovery. So I tried the -nWayOut command, to get an individual realigned bam file for each input, but this returns a stack trace ERROR that includes something about an unavailable reader id. I've pasted it below.

INFO 14:06:32,838 ProgressMeter - scaffold_0:4430818 1.17606954E8 59.5 m 30.0 s 0.4% 9.8 d 9.7 d INFO 14:07:32,840 ProgressMeter - scaffold_0:4474066 1.18707144E8 60.5 m 30.0 s 0.4% 9.8 d 9.8 d INFO 14:08:32,841 ProgressMeter - scaffold_0:4505563 1.1980727E8 61.5 m 30.0 s 0.4% 9.9 d 9.9 d INFO 14:09:32,843 ProgressMeter - scaffold_0:4506325 1.20407434E8 62.5 m 31.0 s 0.4% 10.1 d 10.0 d INFO 14:09:55,236 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: No such reader id is available at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$SAMResourcePool.getReaderID(SAMDataSource.java:809) at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.getReaderID(SAMDataSource.java:430) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.getReaderIDForRead(GenomeAnalysisEngine.java:803) at org.broadinstitute.gatk.utils.sam.NWaySAMFileWriter.addAlignment(NWaySAMFileWriter.java:158) at org.broadinstitute.gatk.tools.walkers.indels.ConstrainedMateFixingManager.writeRead(ConstrainedMateFixingManager.java:356) at org.broadinstitute.gatk.tools.walkers.indels.ConstrainedMateFixingManager.addRead(ConstrainedMateFixingManager.java:261) at org.broadinstitute.gatk.tools.walkers.indels.ConstrainedMateFixingManager.addRead(ConstrainedMateFixingManager.java:237) at org.broadinstitute.gatk.tools.walkers.indels.IndelRealigner.emit(IndelRealigner.java:492) at org.broadinstitute.gatk.tools.walkers.indels.IndelRealigner.map(IndelRealigner.java:529) at org.broadinstitute.gatk.tools.walkers.indels.IndelRealigner.map(IndelRealigner.java:146) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:102) at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: No such reader id is available
ERROR ------------------------------------------------------------------------------------------

I'm not sure if it's the number of bam files submitted or if it is something with the specific position when the error occurs. Any help in this matter would be greatly appreciated!


Created 2014-07-04 19:05:39 | Updated | Tags: indelrealigner nwayout
Comments (7)

I'm putting together an in-house pipeline for processing of paired tumor-normal BAMs. I've set it up to make a single intervals file for each pair and then want to have separate BAMs for BQSR, so I thought I'd use IndelRealigner with -nWayOut. However, the realigned BAMs are output to whatever directory I've run the script from, rather than the same directory as the BAM files I provided to -I.

I tried to create a .map file with full pathnames to both the input and output files, but received the error:

##### ERROR MESSAGE: Bad input: Input-output bam filename map does not contain an entry for the input file 3528.dedup.bam

The corresponding entry in the .map file had the format:

/users/home/project/cocleaned/3528.dedup.bam /users/home/project/cocleaned/3528.realigned.bam

Is there a way to specify an output directory in conjunction with -nWayOut? If not, I can probably hackishly search for the realigned files, but I thought I'd check.

Created 2012-10-31 07:52:07 | Updated 2012-10-31 17:35:25 | Tags: indelrealigner nwayout
Comments (1)

Hi, I've run into what appears to be a bug in handling output in IndelRealigner. When specifying --nWayOut everything works, but when I add --disable_bam_indexing, it appears to be expecting --out instead?

##### ERROR A USER ERROR has occurred (version 2.1-13-g1706365): 
##### ERROR MESSAGE: Value for argument with name '--out' (-o) is missing.