Dear Robert, John and Sam I just wanted to say thanks. The new jobs finished successfully. I will contact the erne authors about outputting some @SQ headers.
Jo From: "Holbrook J." <j.holbr...@soton.ac.uk<mailto:j.holbr...@soton.ac.uk>> Date: Wednesday, 4 January 2017 at 10:58 To: Robert Davies <r...@sanger.ac.uk<mailto:r...@sanger.ac.uk>>, John Marshall <j...@sanger.ac.uk<mailto:j...@sanger.ac.uk>> Cc: "samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>" <samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>> Subject: RE: [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header Dear Rob and John You are right! When I use zless I don’t think I have any @SQ headers (attached). The headers that I saw using samtools view header or the grep command only had SN: and LN: fields. So... Erne is not outputting @SQ headers. It just looks that way when I use samtools view because samtools automatically generates basic ones. No @SQ headers causes samtools sort to fail, but only when the alignments a big enough to need to merge (hence the singletons worked but the paired did not) Samtools 1.3.1 will not have this problem but I must be somehow running the biobuild samtools 1.3 on my HPC. I have just set off samtools sort jobs specifying the direct path to samtools 1.3.1 - they should finish by the end of today. If they work I will contact the erne authors to ask them to output @SQ headers in future. If they don’t work I will be back in touch. Thank-you so much for this help. You can tell I am a newbie but I will try to use this mailing list wisely and sparingly. Jo -----Original Message----- From: Robert Davies [mailto:r...@sanger.ac.uk] Sent: 04 January 2017 10:24 To: John Marshall <j...@sanger.ac.uk<mailto:j...@sanger.ac.uk>> Cc: Holbrook J. <j.holbr...@soton.ac.uk<mailto:j.holbr...@soton.ac.uk>>; samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net> Subject: Re: [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header On Wed, 4 Jan 2017, John Marshall wrote: TL;DR i.e. what Rob said. But note that when you output SAM with samtools view, samtools appends basic @SQ headers if there aren't already any. So Rob's `samtools view -H ... | grep '^@SQ'` will display some headers whether the file contains textual headers or not. Removing the grep will allow some educated guesses to be made about whether @SQ headers seen with samtools view are synthetic or really in the input file: if there are any other (e.g. @RG) headers *after* the block of @SQ headers, or if the @SQ headers have any fields beyond SN and LN, then they are definitely real. Yes, I've just spotted this - samtools view fixes the problem too. Looking at the bam file with 'zless' might be the quickest way of checking for @SQ lines. The text header is fairly readable at the start. Rob Davies r...@sanger.ac.uk<mailto:r...@sanger.ac.uk> The Sanger Institute http://www.sanger.ac.uk/ Hinxton, Cambs., Tel. +44 (1223) 834244 CB10 1SA, U.K. Fax. +44 (1223) 494919 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
