Yes I have tried to perform the samtools conversion command on other sample
files resulting in the same problem. The version I'm using is 1.2. Moreover, I
was able to run samtools view with the example file and it also worked out to
see the original file contents again using the other command.
Regards, Marcel
-----Ursprüngliche Nachricht-----
Von: "Joshua Bradley" [[email protected]]
Gesendet: Mo. 06.07.2015 18:24
An: [email protected]
Kopie: [email protected]
Betreff: Re: Re: [Samtools-help] Header
Have you tried running your samtools conversion command on another sample file
first to make sure the problem isn't samtools? Also what version of samtools do
you have? Try this small file and runsamtools view -b ex1.sam > ex1.bamAssuming
it works correctly, you should be able to dosamtools view -h ex1.bam | moreand
see the original file contents again.If you're using the latest version of
samtools, you don't need the -S flag. I believe that's been left in for
backwards compatibility reasons. Samtools will automatically detect SAM/BAM
format of an input file. As a point of reference, the ex1.sam file is 559523
bytes in size. Afterwards, ex1.bam should be 126661 bytes.
Josh Bradley
On Mon, Jul 6, 2015 at 7:04 AM, <[email protected]> wrote:
Hi Josh,
here is the header information I get:
samtools view -H ./output/KMT/9557-FGS-R.sam
@SQ SN:B.FR.1983.HXB2-LAI-IIIB-BRU.K03455 LN:9719
@PG ID:bwa PN:bwa VN:0.7.12-r1044 CL:bwa mem -aCHMpP
./ref/HXB2.fasta ./KMT/9557-FGS-R-R1.fastq.gz ./KMT/9557-FGS-R-R2.fastq.gz
I read something about the -C parameter and retried with
bwa mem -aHMpP instead of bwa mem -aCHMpP, but the header looks the same:
samtools view -H ./output/KMT/9557-FGS-R.sam
@SQ SN:B.FR.1983.HXB2-LAI-IIIB-BRU.K03455 LN:9719
@PG ID:bwa PN:bwa VN:0.7.12-r1044 CL:bwa mem -aHMpP
./ref/HXB2.fasta ./KMT/9557-FGS-R-R1.fastq.gz ./KMT/9557-FGS-R-R2.fastq.gz
At least I am then able to create the bam file for whatever reason. Do you know
why? Thanks for helping,
Marcel
-----Ursprüngliche Nachricht-----
Von: "Joshua Bradley" [[email protected]]
Gesendet: Do. 02.07.2015 16:28
An: [email protected]
Betreff: Re: [Samtools-help] Header
Can you post the header information from the files? You can get it bysamtools
view -H sample_file.sam
Josh Bradley
On Thu, Jul 2, 2015 at 8:01 AM, <[email protected]>
wrote:
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Message: 1
Date: Thu, 02 Jul 2015 12:48:06 +0200
From: [email protected]
Subject: [Samtools-help] Header
To: [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset="utf-8"
Dear all,
?
I used
?? bwa mem -aCHMpP ...
?
in order to create .sam files for my pair-end reads data
When I try to perform the command
?? samtools? view -bS ...
in order to convert the .sam to .bam files, I get the following error message:
?
?? [E::sam_parse1] unrecognized type
?? [W::sam_read1] parse error at line 3
?? [main_samview] truncated file.
?
During my web search I could only find information about custom read
annotations leading to this error which I don't provide.
Could anybody tell me what I am missing?
?
Kind regards,
Marcel
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