Hello Yueming, I can duplicate the submission error. This is an access problem.
The .bam file is accessible, but the file .bam.bai is not. The error if using a browser is: Safari can’t open the page “ftp://aretha.jax.org/pub/jax-churchill/C3H_chr1_175335000-175400000.bam.bmi” because Safari can’t load any data from this location. Double check that the .bmi file is named correctly and in the same location as the .bam file and that permission are readable for "world". The files must be named exactly the same with the index file having an added .bmi in the name. Please double check and let us know if you continue to have problems, Jen --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/15/10 12:05 PM, Yueming Ding wrote: > Hi Angie, > > I am trying to add the following custom BAM track but it didn't work. I paste > the following line into the text box of "Add Custom Tracks" web page: > > track type=bam name="My BAM" > bigDataUrl=ftp://aretha.jax.org/pub/jax-churchill/C3H_chr1_175335000-175400000.bam > > I got the following error: > Error Can't access My BAM's bigDataUrl > ftp://aretha.jax.org/pub/jax-churchill/C3H_chr1_175335000-175400000.bam > and/or the associated index file > ftp://aretha.jax.org/pub/jax-churchill/C3H_chr1_175335000-175400000.bam.bai > > Could you help me? Thanks, > > Yueming > > -----Original Message----- > From: Angie Hinrichs [mailto:[email protected]] > Sent: Monday, February 08, 2010 6:00 PM > To: Yueming Ding > Cc: [email protected] > Subject: Re: [Genome] custom BAM track > > Hi Yueming, > > Sorry to hear about the trouble. I think our servers are not able to connect > to new-cartman. I'm trying this command line from UCSC: > > wget --spider > http://new-cartman.jax.org/Yueming/C3H_chr1_175335000-175400000.sorted.bam > > I get this much output and then it just hangs: > > --14:52:30-- > http://new-cartman.jax.org/Yueming/C3H_chr1_175335000-175400000.sorted.bam > Resolving new-cartman.jax.org... 209.222.204.76 > Connecting to new-cartman.jax.org|209.222.204.76|:80... > > Then after 3 minutes wget says > > ... failed: Connection timed out. > Retrying. > > --14:55:40-- (try: 2) > http://new-cartman.jax.org/Yueming/C3H_chr1_175335000-175400000.sorted.bam > Connecting to new-cartman.jax.org|209.222.204.76|:80... > > and it's hanging again. > > Are you able to access http://new-cartman.jax.org/ from a non-jax site? > Perhaps your local sysadmins can help. (firewall?) > > Please let us know if there are any more issues after resolving the external > http connection. > > Angie > > > ----- "Yueming Ding"<[email protected]> wrote: > >> From: "Yueming Ding"<[email protected]> >> To: [email protected] >> Sent: Monday, February 8, 2010 1:15:11 PM GMT -08:00 US/Canada Pacific >> Subject: [Genome] custom BAM track >> >> Hi I am trying to add a custom BAM track but it didn't work. At the >> "Add Custom Tracks" web page, I pasted the following line to "Paste >> URLs or data" panel: >> >> track type=bam name="My BAM" >> bigDataUrl=http://new-cartman.jax.org/Yueming/C3H_chr1_175335000-175400000.sorted.bam >> >> Then I clicked "Submit". After ~3 minute, it shows "The website cannot >> display the page". >> >> Could you please help me out? Thanks, >> >> Yueming Ding >> The Jackson Laboratory >> Bar Harbor, Maine >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
