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>
Cc: Holbrook J. <j.holbr...@soton.ac.uk>; 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
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.
[jh1m15@cyan01 SureSelect]$ zless Sample1b_unmasked.bam
BAM^A<EB>^C^@^@@HD VN:1.0 SO:unsorted
@PG ID:ERNE VN:2.1.1 CL: erne-bs5 --reference unmasked_htable.ebm
--query1 Trimmed/Sample_1b-1/Sample1b_catR1.fastq --query2
Trimmed/Sample_1b-1/Sample1b_catR2.fastq --output Sample1b_unmasked.bam
@CO 1481027931: ERNE version 2.1.1
@CO 1481027931: --query1 =
Trimmed/Sample_1b-1/Sample1b_catR1.fastq
@CO 1481027931: --query2 =
Trimmed/Sample_1b-1/Sample1b_catR2.fastq
@CO 1481027931: --output = Sample1b_unmasked.bam
@CO 1481027931: --sample = no_sample_specified
@CO 1481027931: --reference = unmasked_htable.ebm
@CO 1481027931: --contamination-reference =
@CO 1481027931: --auto-errors = true
@CO 1481027931: --errors-rate = 15
@CO 1481027931: --errors = 0
@CO 1481027931: --threads = 1
@CO 1481027931: --min-size = 25
@CO 1481027931: --min-phred-value-CLC = 20
@CO 1481027931: --min-mean-phread-quality = 20
@CO 1481027931: --no-quality-check = false
@RG ID:1481027931 SM:no_sample_specified
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