Hi all,

I’m having  problems when I click to visualize one BAM file from galaxy to IGV version 2.1.24. I’ve tried the local and also the web display options  but I have the same problem. I have tried also to download first the bam file from galaxy and then loading into IGV manually and it works. I also have tried to modify the .jnlp generated but it does not work.

IGV shows the next error message:

ERROR [2012-11-26 11:44:54,591]  [IGV.java:1555] [pool-1-thread-1]  net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in readmode; streamed file (filename not available)

ERROR [2012-11-26 11:44:54,592]  [IGV.java:1494] [pool-1-thread-1]  Error loading tracks

org.broad.igv.exceptions.DataLoadException: An error occurred while accessing:    http://172.21.104.21:8080/display_application/9e23127bd2c9a880/igv_bam/web_link_main/8d9bcc17f9fede63/data/galaxy_9e23127bd2c9a880.bam<br>Premature EOF; BinaryCodec in readmode; streamed file (filename not available)

Thanks for your help.

Joan Protasio,  Bioinformatician & Software Engineer
Bioinformatics Platform 

August Pi i Sunyer Biomedical Research Institute (IDIBAPS)
C/ Rosselló 153, Barcelona

http://bioinformatics.fcrb.es
+34  93 227 54 00 ext. 4522