Unexpected error: null. See igv.log for more details

[Dezso David]

I’m trying to analyze a BAM file. After Load From File…of the BAM file I got an error message “Error encountered querying alignments: java.lang.RuntimeException: Invalid file pointer: 393847712541920” and “Unexpected error: null. See igv.log for more details “.
I’m not familiar with this software therefore, I would really appreciate if somebody could help me to “translate” this.
Thank you,
David

[Jim Robinson]

Hi, this is indicating either a corrupt bam file, or more likely a corrupt or out-of-date index file.  You could try regenerating the index.   The "Picard" suite has a "ValidateBam" program which might be helpful.

Jim

[Dezso David]

Hi, thank you for your opinion. The same files (bam and bam.bai files) are working in the service provider lab. Therefore I assume that the files are not corrupt.
Please find enclosed Java Console – IGV2.3 log file. Any further comment would be helpful!
Sincerely,
David

[Jim Robinson]

In that case I do not have any suggestions.�� The error is coming from Picard,� I suggest you post a query on the samtools-help email list.�� The relevant portion of your stack trace to post there is below.�� The Picard developers monitor that list and are quick to respond to queries.�

Error loading alignment data

java.lang.RuntimeException: Invalid file pointer: 721563114019456

����������� at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:549)

����������� at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:648)

����������� at net.sf.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:598)

����������� at net.sf.samtools.BAMFileReader.query(BAMFileReader.java:352)

����������� at net.sf.samtools.SAMFileReader.query(SAMFileReader.java:363)

Jim

Hi, thank you for your opinion. The same files (bam and bam.bai files) are working in the service provider lab. Therefore I assume that the files are not corrupt.

Please find enclosed Java Console � IGV2.3 log file. Any further comment would be helpful!

Sincerely,
David


Em quinta-feira, 9 de maio de 2013 16h01min31s UTC+1, Jim Robinson escreveu:

Hi, this is indicating either a corrupt bam file, or more likely a corrupt or out-of-date index file.� You could try regenerating the index.�� The "Picard" suite has a "ValidateBam" program which might be helpful.

Jim


On Wednesday, May 8, 2013 5:34:12 PM UTC-4, Dezso David wrote:

I�m trying to analyze a BAM file. After Load From File�of the BAM file I got an error message �Error encountered querying alignments: java.lang.RuntimeException: Invalid file pointer: 393847712541920� and �Unexpected error: null. See igv.log for more details �.
I�m not familiar with this software therefore, I would really appreciate if somebody could help me to �translate� this.
Thank you,
David

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[rchiaro...@gmail.com]

Hi,

I am having the same issues described by Dezso. I am wondering if you have had any success in resolving this issue? My BAM files are not corrupt and I have tried with a number of different BAMs and get the same error message. I noticed this sometimes happens as I am zooming in on features, rather than when loading from file- could it have anything to do with how much memory is allocated to the program?

Attached is my igv.log

Thanks in advance,

Rachel

On Wednesday, May 8, 2013 5:34:12 PM UTC-4, Dezso David wrote:

[Jim Robinson]

Hi Rachel,

The error is occuring in the code that reads the BAM file, which is part of the Picard / samtools suite of tools.�� The exact error message from your log is printed below.� I could post this on the samtools list, but they will ask that you run ValidateSamFile from the Picard suite as a first step.� This is documented at http://picard.sourceforge.net/command-line-overview.shtml.�� In particular, validate the index ( option ValidateIndex).���� The error can be caused by an invalid or out-of-date index,� by that I mean the bam file was modified or replaced but the index was not.�� Also, some versions of samtools can create invalid indeces if the file is not sorted beforehand.�� If you can reproduce this with a small Bam file and post it (and the associated index) where we can get access we will investigate further.

Other, less likely causes are firewalls and proxies in your network environment that are modifying http requests.�� Are you loading these bams over a network with http:// addresses,� or directly from a file?

The exact error is:

java.lang.RuntimeException: Invalid file pointer: 336671344530497

��� at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:549)

��� at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:648)

��� at net.sf.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:598)

��� at net.sf.samtools.BAMFileReader.query(BAMFileReader.java:352)

Jim

Hi,

I am having the same issues described by Dezso. I am wondering if you have had any success in resolving this issue? My BAM files are not corrupt and I have tried with a number of different BAMs and get the same error message. I noticed this sometimes happens as I am zooming in on features, rather than when loading from file- could it have anything to do with how much memory is allocated to the program?

Attached is my igv.log

Thanks in advance,

Rachel

On Wednesday, May 8, 2013 5:34:12 PM UTC-4, Dezso David wrote:

I�m trying to analyze a BAM file. After Load From File�of the BAM file I got an error message �Error encountered querying alignments: java.lang.RuntimeException: Invalid file pointer: 393847712541920� and �Unexpected error: null. See igv.log for more details �.
I�m not familiar with this software therefore, I would really appreciate if somebody could help me to �translate� this.
Thank you,
David

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