Problem with visualize bam file in IGV

usegalaxy.org support
1

im trying to visualize my bam data with igv
i installed it .and also run it.after that when i use “Display with IGV local” it comes up with this erorr

Error loading https://usegalaxy.org/display_application/bbd44e69cb8906b58fd5bbd6f1f1d2a3/igv_bam/local_default/f2d56f5f78d64da3/data/galaxy_bbd44e69cb8906b58fd5bbd6f1f1d2a3.bam: An error occurred while accessing: https://usegalaxy.org/display_application/bbd44e69cb8906b58fd5bbd6f1f1d2a3/igv_bam/local_default/f2d56f5f78d64da3/data/galaxy_bbd44e69cb8906b58fd5bbd6f1f1d2a3.bam Error loading BAM file: java.net.SocketTimeoutException: connect timed out

whats the problem ?

1 Like
2

Thanks for reporting the problem.

I just tested this and BAMs loaded from Galaxy Main https://usegalaxy.org into an IGV local browser successfully.

Would you try again please? It is possible that the server was under heavier load when first attempted.

3

Update: I just checked with our administrator. This error indicates that there was a problem with Galaxy connecting to your IGV. He thinks that some type of firewall is probably in place on your side. Check with your institution or ISP provider to find out if they can resolve the block.