Hi Volkhard, It is likely that this is issue "Unrecognized format line 1" is the result of line breaks in the track line. Please take a look at step 7 on the page below:
http://genome.ucsc.edu/goldenPath/help/bigBed.html All of the information has to be on a single line. Please make sure that you have it in the proper format. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Dr. rer. nat. Volkhard Seitz <[email protected]> Date: Thu, Nov 3, 2011 at 12:46 AM Subject: [Genome] Problems to up-load large bed files (Internal Server Error E 500)] To: [email protected] Dear UCSC team Two days agou I tried today for hours to up-load ChIP-Seq bed-files. I can upload files up to 200.000 KB Since I could not up-load a file with 812.136 KB I used now a compression method you recomended an created a .gz file with 189.216 KB (The filename was: C_Hodg_Ip_Kmh2_.gz) The upload of this compressed .gz file caused the internal server error 500. After writing to your team From I got the recommendation to convert my file into the Bigbed format. http://genome.ucsc.edu/goldenPath/help/bigBed.html The next day I converted a bed file into a bigbed file employing galaxy. The original file had a size of 856.831 KB and the converted bigbedfile 245.056 kb respectively. The conversion report from Galaxy sounded fine: > 13: BED-to-bigBed on data 12 239.3 Mb > format: bigbed, database: hg19 > Info: pass1 - making usageList (25 chroms): 55588 millis > pass2 - checking and writing primary data (14673975 records, 6 fields): > 141460 millis > index write: 28 millis > pass3 - writeReducedOnceReturnReducedTwice: 66343 millis > further reductions: 9811 millis > However I still have the up-load problems for the UCSC Browser I got the following error measages employing different file formats or file names (compressed and non-compressed): 1) File 'KMH2MYCIP.bigbed.bz2' - Unrecognized format line 1 of somefile.bz2: ëò?? (note: chrom names are case sensitive) 2) File 'KMH2MYCIP.bz2' - Unrecognized format line 1 of somefile.bz2: ëò?? (note: chrom names are case sensitive) 3) Can't read file: KMH2MYCIP.bigbed Could you five me other suggestions how I can up-load files. Would be really great. Thank you and best wishes from Volkhard _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
