Problem when running the example

[jana.a...@gmail.com]

Hi,

I am novice using not only Bis-SNP but also GATK. So, when I try to run the example: 

java -Xmx4g -jar BisSNP-0.71.jar -T BisulfiteGenotyper -R hg18_unmasked.plusContam.fa -D dbsnp_135.hg18.sort.vcf -I normalMerge_chr11-7M-9M.nodups.withhead.bam -vfn1 cpg.raw.vcf -vfn2 snp.raw.vcf -stand_call_conf 30 -stand_emit_conf 0 -L Interval_list-test.bed

I get the following error in my terminal:

INFO  15:19:07,477 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 

##### ERROR ------------------------------------------------------------------------------------------

##### ERROR stack trace 

java.lang.RuntimeException: Cannot use index file with textual SAM file

at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:525)

at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:167)

at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$ReaderInitializer.call(SAMDataSource.java:933)

at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMReaders.<init>(SAMDataSource.java:794)

at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMResourcePool.createNewResource(SAMDataSource.java:753)

at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource$SAMResourcePool.getAvailableReaders(SAMDataSource.java:724)

at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.<init>(SAMDataSource.java:269)

at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.createReadsDataSource(GenomeAnalysisEngine.java:757)

at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:668)

at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:225)

at edu.usc.epigenome.uecgatk.bissnp.BisSNP.execute(BisSNP.java:170)

at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)

at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)

at edu.usc.epigenome.uecgatk.bissnp.BisSNP.main(BisSNP.java:107)

##### ERROR ------------------------------------------------------------------------------------------

##### ERROR A GATK RUNTIME ERROR has occurred (version 1.5-3-gbb2c10b):

##### ERROR

##### ERROR Please visit the wiki to see if this is a known problem

##### ERROR If not, please post the error, with stack trace, to the GATK forum

##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki

##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa

##### ERROR

##### ERROR MESSAGE: Cannot use index file with textual SAM file

##### ERROR ------------------------------------------------------------------------------------------

When I tried to google this error "Cannot use index file with textual SAM file", other people using GATK mainly solved this problem by modifying their input files. However, given the fact that this is an example. I am assuming the issue is not with the input files. Any help would be much appreciated.

Thanks,

Jana

[ping]

Hi Jana,

Could you please check the bam file md5 (search md5sum ) with the number at website. I guess they might be different which indicate some part of the file may be missing during download. Just try to re-download the bam file~ If md5 is the same as website showed, please let me know. 

Thanks,

Yaping 

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Yaping Liu, Ph.D.

Postdoctoral Associate

Manolis Kellis Lab

Computer Science and Artificial Intelligence Lab (CSAIL)
Massachusetts Institute of Technology

Broad Institute of MIT and Harvard

Office Phone: +1 617 324 8436 
Email: 

lypin...@gmail.com

yap...@mit.edu

lyp...@broadinstitute.org

[jana.a...@gmail.com]

Hi Yaping,

thank you for the quick reply. That is indeed the problem. But I cannot seem to download a correct file. Safari keeps downloading a partial file of 65kb while firefox just states that the file cannot be downloaded because of a server error. Is there any other place I may download these example files from? 

Thanks

Jana

[ping]

Hi Jana,

Please open your terminal, and try it with wget -c or curl

wget -c http://epigenome.usc.edu/publicationdata/bissnp2011/normalMerge_chr11-7M-9M.nodups.withhead.bam

or 

curl http://epigenome.usc.edu/publicationdata/bissnp2011/normalMerge_chr11-7M-9M.nodups.withhead.bam -o normalMerge_chr11-7M-9M.nodups.withhead.bam

[jana asselman]

Thank you, that worked perfectly. I was able to execute all the example code in the manual.

-Jana

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Jana Asselman