Hi Alban, We can offer some help to troubleshoot -
Are you running this at the main server http://genome.ucsc.edu ? Or your own mirror? If not the main server, perhaps test there and if it works, then that would help to isolate the problem to your browser mirror. You also may want to run a validator on the BAM file. Good sources are: http://picard.sourceforge.net/ http://samtools.sourceforge.net/ And finally, regenerating the index file would be something to try. If the validated BAM file and regenerated index file still have a problem loading as a custom track, please let us know. In your reply please state if the problem is at the UCSC server or your own mirror (and note when the mirror was last updated). Best regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] -------- bounced & re-posted -------- Subject: Troubleshooting with big bam datafile and UCSC genome browser From: Alban Lermine <[email protected]> Date: Tue, 06 Jul 2010 12:33:42 +0200 To: [email protected] CC: Séverine Lair <[email protected]> Good morning, I'm having some troubles using the UCSC genome browser trough a custom track file. It's seems that it's due to the size of my bam file (which is up to 3Gb), because it works with little date file. Here is the called line in my custom track file: track type=bam name="Example" bigDataUrl=http://user:p...@myserver/partage/NCRNA_RNAI/C3R1/hg19/maToBam/C3_C3R1_F3.csfasta.ma.bam Here is the returning error: Error : Invalid argument lseek(6, -8268, SEEK_CUR (1)) failed I've searched for explanations on lseek and lseek errors, an I find this webpage which is reporting a bug with lseek, multiprocessor and files up to 1Gb. In addition, my bam files are generated by Bioscope v1.2 (an ABI tools). Let me know if you have a solution to my problem. Great thanks by advance. Best regards, Alban Lermine -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 81 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
