Hello, I need a GTF file for S. purpuratus (v. 2.1) RefSeq Genes and tried to use the TableBrowser to generate it. The file is truncated after 3726 rows and has this error at the end of the file:
Scaffold34065 strPur2_refGene CDS 7387 7584 0.000000 - 0 gene_id "NM_214508"; transcript_id "NM_214508"; Scaffold34065 strPur2_refGene start_codon 7582 7584 0.000000 - . gene_id "NM_214508"; transcript_id "NM_214508"; Scaffold34065 strPur2_refGene exon 7387 7657 0.000000 - . gene_id "NM_214508"; transcript_id "NM_214508"; --------------------------------------------------------------------------- carefulAlloc: Allocated too much memory - more than 6,442,450,941 bytes (6,442,546,903) --------------------------------------------------------------------------- It seems that this problem was reported back in September (see below). Is there a work around or can the file I need be generated at UCSC? Thank you, - Ben Tue Sep 28 14:26:02 PDT 2010 Previous message: [Genome] X tropicalis gtf file is truncated Next message: [Genome] Question about repetitive regions in Drosophila Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hello Irwin, There appears to be a bug in the Table Browser. We are looking into what might be causing it. Thank you for reporting it! I will alert you when we get it fixed. -- Brooke Rhead UCSC Genome Bioinformatics Group Irwin Jungreis wrote on 9/27/10 12:28 PM: > I am trying to get the gene annotations for X. tropicalis from here: > http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=170244280&clade=vertebrate&org=X.+tropicalis&db=xenTro2&hgta_group=genes&hgta_track=ensGene&hgta_table=0&hgta_regionType=genome&position=scaffold_27%3A565941-578374&hgta_outputType=gff&hgta_outFileName=xenTro2.JGI4.1.Aug2005.Ensembl.gtf.gz > > I've tried downloading several versions of the GTF file (Ensembl > Genes, RefSeq Genes, and TransMap mRNA) and in all cases the file > appears to be truncated and ends with the lines: > > --------------------------------------------------------------------------- > Allocated too much memory - more than 6,442,450,941 bytes > (6,442,678,139) > --------------------------------------------------------------------------- > > This happens whether I download plain text or gzip, so it isn't a > problem with the decompression. > > Does anyone know where I can get the complete GTF file, and if there > is someone else who should be notified about this? > > Thanks. > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
