Error encountered querying alignments: java.lang.ArrayIndexOutOfBoundsExcpetions

[Roy Blum]

While loading a sorted and indexed BAM (chip-seq) file onto IGV(2.4.4) -  per some of the chromosomes (chrX, 4,6,11,12,13,14,15,16,17) all reads would be nicely presented and matching the coordinates indicated within the BAM file itself (as evident by grep command).

However, when attempting to observe reads within other chromosomes - such as - chr1,2,3 for example - (also after zoom-in within regions that macs2 identified as peak-enriched, and that the BAM file clearly indicates that read exists in - by running grep on SAM) - we get the following error message:  Error encountered querying alignments: java.lang.ArrayIndexOutOfBoundsExcpetions. 

Our Java version is the latest for Ubuntu 16.04.3 LTS 

java version "1.8.0_92"

Java(TM) SE Runtime Environment (build 1.8.0_92-b14)

Java HotSpot(TM) 64-Bit Server VM (build 25.92-b14, mixed mode)

We loaded igv with 30GB [by executing: java -Xmx30000m -jar /home/roy/Downloads/IGV_snapshot/igv.jar ] so we don't suspect of memory issue. 

We encountered this problem with a few BAM files of ours, whereas others BAM files seem to be fine and nicely present all reads per all chromosomes. 

We couldn't find any clues as for what would cause this problem, and would appreciate your advise. 

Thanks a lot in advance,
Roy

[James Robinson]

Its hard to say based on this information,  it could be a problem with the bam file.   Are you able to query the regions you are having problems with using samtools?   

Please include your igv.log file,    this should contain the whole strack trace and should identify the problem.

Jim

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