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From: Thomas W. B. <tb...@um...> - 2014-06-04 12:49:30
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Marine - The command lines look good. Could this be a local file system problem -- "no space left on device", or something like that ? Or a typing error in one of the file names ? I'm just guessing, but that's what I would look for. Oh, just remembered: a favorite error of mine used to be making <out.prefix> the same as the name of the unsorted input .bam file. When I do that, the unsorted .bam file gets deleted from the file system before it is ever read. The two file names have to be different. - tom blackwell - On Wed, 4 Jun 2014, Marine Rohmer wrote: > Hello Samtools team, > > I try to convert some SAM files to BAM files following the FAQ method : > First indexing my reference fasta file (I have no header in my SAM file) > : > samtools faidx ref.fa > Then converting my SAM file to BAM file : > samtools view -bt ref.fa.fai aln.sam > aln.bam > > Until here, everything seems fine, but... > > When trying to sort my BAM file : > samtools sort aln.bam aln-sorted > I instantly get : > [bam_header_read] invalid BAM binary header (this is not a BAM file). > [bam_sort_core] truncated file. Continue anyway. > Seegmentation fault (core dumped) > > I really don't understand what is happening. My SAM file seems OK. > Several weeks ago I've already done that on another data and everything > went fine... Could someone tell me what is wrong ? > I'd be very grateful if someone could help me !!! :) > > Hoping I'm writing to good mailing list > > Best regards, > > Marine > > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help > |