A GATK RUNTIME ERROR has occurred

[Mike_Brown]

I am new to GATK. Today, I run

java -jar /media/zwang10/Elements/UK10K/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T CountLoci -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -I _EGAR00001038931_36843.pe.raw.sorted.bam

But I got

INFO  14:59:39,061 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  14:59:39,064 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56 
INFO  14:59:39,064 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  14:59:39,064 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  14:59:39,068 HelpFormatter - Program Args: -T CountReads -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -I _EGAR00001038931_36843.pe.raw.sorted.bam 
INFO  14:59:39,076 HelpFormatter - Executing as zwang10@office on Linux 3.13.0-74-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b02. 
INFO  14:59:39,077 HelpFormatter - Date/Time: 2016/01/03 14:59:39 
INFO  14:59:39,077 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  14:59:39,077 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  14:59:39,138 GenomeAnalysisEngine - Strictness is SILENT 
INFO  14:59:39,342 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  14:59:39,354 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  14:59:39,416 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06 
INFO  14:59:42,897 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)_EGAR00001038931_36843.pe.raw.sorted.bam.bai
	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:319)
	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.<init>(GATKBAMIndex.java:97)
	at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.<init>(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:347)
	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)_EGAR00001038931_36843.pe.raw.sorted.bam.bai
##### ERROR ------------------------------------------------------------------------------------------
zwang10@office:/media/zwang10/Elements/UK10K$ java -jar /media/zwang10/Elements/UK10K/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T CountReads -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -I _EGAR00001038931_36843.pe.raw.sorted.bam > temp
INFO  15:08:54,928 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  15:08:54,931 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56 
INFO  15:08:54,931 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  15:08:54,931 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  15:08:54,935 HelpFormatter - Program Args: -T CountReads -R /media/zwang10/Elements/UK10K/human_g1k_v37.fasta -I _EGAR00001038931_36843.pe.raw.sorted.bam 
INFO  15:08:54,943 HelpFormatter - Executing as zwang10@office on Linux 3.13.0-74-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b02. 
INFO  15:08:54,943 HelpFormatter - Date/Time: 2016/01/03 15:08:54 
INFO  15:08:54,943 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  15:08:54,944 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  15:08:55,005 GenomeAnalysisEngine - Strictness is SILENT 
INFO  15:08:55,171 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  15:08:55,181 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  15:08:55,237 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06 
INFO  15:08:57,411 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)_EGAR00001038931_36843.pe.raw.sorted.bam.bai
	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.openIndexFile(GATKBAMIndex.java:319)
	at org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndex.<init>(GATKBAMIndex.java:97)
	at org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource.<init>(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:347)
	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)_EGAR00001038931_36843.pe.raw.sorted.bam.bai
##### ERROR ------------------------------------------------------------------------------------------

I did check _EGAR00001038931_36843.pe.raw.sorted.bam.bai is in the same folder.
What happened?

[blancha]

I have no idea, but I wouldn't start a filename with an underscore.

[Mike_Brown]

I have no idea, but I wouldn't start a filename with an underscore.

It is the original name of the file. Do I need to change it?

[GenoMax]

Certainly worth trying.

Remember to rename both bam and index files. Not sure if the file name is embedded in the index, otherwise you may need to re-index the bam after changing the name.

[Mike_Brown]

Certainly worth trying.

Remember to rename both bam and index files. Not sure if the file name is embedded in the index, otherwise you may need to re-index the bam after changing the name.

I changed name as EGAR00001038931.36843.pe.raw.sorted.bam and EGAR00001038931.36843.pe.raw.sorted.bam.bai


I still get the same problem.