Hello, David. I am able to browse to http://usda02.vetmed.wsu.edu/public_bam/ and view both files in the index. I can successfully download C2R3.sorted.bam.bai, but when I attempt to download C2R3.sorted.bam, I receive errors in both Internet Explorer and Firefox. In Internet Explorer, I receive the error "Internet Explorer cannot display the webpage" and in Firefox, I receive the error "C:\Users\steve\AppData\Local\Temp\qoUCFfVW.bam.part could not be saved, because the source file could not be read. Try again later, or contact the server administrator."
This suggests to me that there is a physical problem with the bam file itself. I would first verify that the original file from which the bam file was made is properly formatted. Next, try recreating the bam file and then verifying that you can actually download the file to your local workstation from http://usda02.vetmed.wsu.edu/public_bam/. Once you can do that, try loading your custom track again. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Herndon, David Sent: Thursday, April 12, 2012 3:29 PM To: [email protected] Cc: Tibbals, David Subject: [Genome] trouble with track line connection Hello UCSC Genome Browser Staff - We are experiencing difficulties with a custom track line for a .bam and indexed .bam file constructed from the training set described in the recent TopHat publication (RNA-seq with Drosophila). We have the sorted and indexed files available at: http://usda02.vetmed.wsu.edu/public_bam/ However when we type the following into the custom track page: track type=bam name="My Bam" bigDataUrl=http://usda02.vetmed.wsu.edu/public_bam/accepted_hits.sorted.bam we get the following error: Can't access My Bam's bigDataUrl http://usda02.vetmed.wsu.edu/public_bam/accepted_hits.sorted.bam and/or the associated index file http://usda02.vetmed.wsu.edu/public_bam/accepted_hits.sorted.bam.bai: Error in TCP non-blocking connect() 111 - Connection refused bamFileExists: failed to read index corresponding to http://usda02.vetmed.wsu.edu/public_bam/accepted_hits.sorted.bam Is there something obvious that we're missing? Do we need to open a port (different than port 80)? Regards, David Herndon Molecular Biologist USDA-ARS Pullman, WA 99164-6630 509-335-6004 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
