trouble opening downloaded bam files

[herschko]

I have not been able to load from file, bam files that I have downloaded locally to my computer.  I saved both bam and bai files in the same folder.  I can open these directly from the URL but this isnt ideal for me.  When I try load them from file locally I get the following message:

Could not load index file for C:\....\BT-20_sorted_genome_alignments.bam.

An index file is required for SAM & BAM files.

Any help would be appreciated.  Thanks.  

-Jason

[Jim Robinson]

Hi,

Could you send us your "igv.log" file, which should be in an "igv" folder in your home directory.  You can send it to igv-...@broadinstitute.org.   Is the bam file in a folder with spaces somewhere in the path?  This should work, but if it is please try saving it in a folder with no spaces.   Either way let us know,  it just changes the nature of the bug we need to fix.   

Thanks

jim

[herschko]

Hi,

I have sent the log file.  Changing the name of the folder to remove the spaces did not alleviate the issue.  I think it is something with downloading the files since I have had the same problem occur on this PC and on a friends Mac.  Thanks.

-Jason

[mcare]

I'm having exactly the same problem.  BAM files that worked locally only a few months ago (last time I checked) now aren't working unless hosted on a server.  I've tried various versions of IGV, i've moved the .bam/.bai files into paths that have no spaces, all to no avail.

An example log file from a recent attempt at loading a BAM file:

INFO [2012-09-14 19:49:46,546] [Main.java:77]  Startup  IGV Version 2.1.24 (2563)09/13/2012 09:23 AM

INFO [2012-09-14 19:49:46,546] [Main.java:78]  Default User Directory: C:\Users\Matt\Documents

INFO [2012-09-14 19:49:47,435] [GenomeManager.java:101]  Loading genome: http://igvdata.broadinstitute.org/genomes/hg19.genome

INFO [2012-09-14 19:49:47,759] [GenomeManager.java:125]  Genome loaded.  id= hg19

INFO [2012-09-14 19:49:49,096] [CommandListener.java:78]  Listening on port 60151

INFO [2012-09-14 19:50:11,475] [IGV.java:1455]  Loading1 resources.

Thanks

Matt

[James Robinson]

Hi,

Could you be more specific on what you mean by  "now aren't working"?   Are there error messages or dialogs?  Have you change java versions in that time?

Also,  could you try one of the archived 2.0 versions available here

http://www.broadinstitute.org/software/igv/download_1.5

These have not been touched for a very long time,  so testing against those will help narrow the possibilities down.

Jim

[mcare]

Hi,

The error is:

"Could not load index file for: E:\NEW\alnReads.sorted.bam

An index file is required for SAM & BAM files."

I've tried old versions of IGV (including 2), and both Java 6 update 35 and Java 7 update 7 versions of JRE (both 64bit).  Both of which display exactly the same message.  The same bam files didn't have this issue in the past but since my computer updates Java automatically it is very likely that I was using a different version of Java when everything was working.

What's strange is that the same bam files work fine if they are hosted on a webserver and I load them via a URL.  However, as these are files from very deep sequencing runs I really need to have them work locally to have any chance at analysing the data.

Thanks

Matt

[Jim Robinson]

Hi,

I've created a version of IGV that uses a different method to test for file existence,  there's a possibility it will work and if not it will at least produce a little diagnostic output.   If you could try it and give us feedback it would be helpful,  this problem is apparently rare and we haven't yet found the magic settings to reproduce it here.

The IGV version can be launched from

http://www.broadinstitute.org/igv/projects/snapshot/igv_mm_snapshot.jnlp

If it works let us know,  in the more likely case it doesn't could you send your igv.log,  or just the last 50 lines or so?

Thanks

Jim 

[hrizos]

I am having the same problems with two separate NextGen data. The first gives this log of errors...
ERROR [2012-11-27 17:25:45,581]  [IGV.java:1493] [pool-1-thread-6]  Error loading tracks
net.sf.samtools.SAMException: No index is available for this BAM file.
    at net.sf.samtools.BAMFileReader.getIndex(BAMFileReader.java:199)
    at net.sf.samtools.SAMFileReader.getIndex(SAMFileReader.java:268)
    at org.broad.igv.sam.reader.BAMFileReader.hasIndex(BAMFileReader.java:96)
    at org.broad.igv.sam.AlignmentTileLoader.hasIndex(AlignmentTileLoader.java:87)
    at org.broad.igv.sam.AlignmentDataManager.hasIndex(AlignmentDataManager.java:126)
    at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:921)
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:202)
    at org.broad.igv.track.TrackLoader.load(TrackLoader.java:101)
    at org.broad.igv.ui.IGV.load(IGV.java:1531)
    at org.broad.igv.ui.IGV$10.run(IGV.java:1475)
    at org.broad.igv.ui.IGV.loadResources(IGV.java:1502)
    at org.broad.igv.ui.IGV$4.run(IGV.java:620)
    at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:54)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:680)
INFO [2012-11-27 17:25:45,583]  [MessageUtils.java:60] [pool-1-thread-6]  Error loading /Volumes/HR_Passport/Work/Current Projects/AXEQ_sequence/Raw data/AXEQ_110729/MR85M100B_401.remdup.uniqMap.TS(1).bam: No index is available for this BAM file.

Not sure if this is helpful.

Thanks
Helen

[Jim Robinson]

Hi Helen,

I assume from the log you are trying to load the following BAM

  /Volumes/HR_Passport/Work/Current Projects/AXEQ_sequence/Raw data/AXEQ_110729/MR85M100B_401.remdup.uniqMap.TS(1).bam

Does the index exist?  It would be named either

  /Volumes/HR_Passport/Work/Current Projects/AXEQ_sequence/Raw data/AXEQ_110729/MR85M100B_401.remdup.uniqMap.TS(1).bam.bai

or

  /Volumes/HR_Passport/Work/Current Projects/AXEQ_sequence/Raw data/AXEQ_110729/MR85M100B_401.remdup.uniqMap.TS(1).bai

Jim

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