Error: Unable to open index file (mark/reset not supported)

erinsybouts

I have been trying to use multiple GATK tools after processing my sample bam files with multiple Picard tools (AddOrReplaceReadGroups, SortSam, MarkDuplicates, and ReorderSam in that order) and creating a new index file with each step. However, I keep getting the same error:

My input:
java -jar $GATK -T RealignerTargetCreator -R $human_wgfa -I 000ordered.bam -o 000realignertargetcreator.intervals

Output:

INFO 15:22:51,165 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:22:51,166 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 15:22:51,166 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 15:22:51,166 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 15:22:51,169 HelpFormatter - Program Args: -T RealignerTargetCreator -R /Users/sybouts/Genomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa -I 000ordered.bam -o 000realignertargetcreator.intervals
INFO 15:22:51,173 HelpFormatter - Executing as [email protected] on Mac OS X 10.11.4 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14.
INFO 15:22:51,173 HelpFormatter - Date/Time: 2016/05/13 15:22:51
INFO 15:22:51,174 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:22:51,174 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:22:51,435 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:22:51,507 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 15:22:51,511 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
WARNING: BAM index file /Users/sybouts/SA_BLM_family/000ordered.bai is older than BAM /Users/sybouts/SA_BLM_family/000ordered.bam
INFO 15:22:51,529 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 15:22:52,424 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to open index file (mark/reset not supported)000ordered.bai
at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:319)
at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.(GATKBAMIndex.java:97)
at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.(SAMDataSource.java:388)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.createReadsDataSource(GenomeAnalysisEngine.java:931)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:822)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:286)
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:106)
Caused by: java.io.IOException: mark/reset not supported
at java.io.InputStream.reset(InputStream.java:348)
at htsjdk.samtools.SamIndexes.asBaiSeekableStreamOrNull(SamIndexes.java:80)
at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:314)
... 9 more

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):

ERROR

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

ERROR MESSAGE: Unable to open index file (mark/reset not supported)000ordered.bai

ERROR ------------------------------------------------------------------------------------------

I am really frustrated and done everything I can to figure out what is going on, but the same thing keeps happening. Please let me know if there is any other information that may be helpful! Thanks!

dekling

Try ValidateSamFile. Also make sure that your Picard is the most recent version.

dekling

Try ValidateSamFile. Also make sure that your Picard is the most recent version.

erinsybouts

Thanks, figured out that the person who did the alignment used a different reference genome than I was using... facepalm
Everything works now!