Re: [Seqan-dev] rabema_prepare_sam "File must be sorted by query name."

[Uwe Appelt <uappelt@clcbio.com>]

Thanks for clarifying, Manuel! It works now.

Cheers,
Uwe



On 11/09/2012 16:14, Holtgrewe, Manuel wrote:
> Hi Uwe,
>
> RazerS 3 will write out the reads in the same order as in the input. This is independent of multi-threading.
>
> The problem is that rabema_prepare_sam assumes that the reads are sorted by their name with "Windows 7 Explorer File Sorting", i.e. zz100zz comes after zz10zz. Thus this sorting is not lexicographically. This is also the sorting that "samtools sort" uses when sorting by query name. In rabema_prepare_sam, this is only used as a sanity check.
>
> I have just added an option --dont-check-sorting to rabema_prepare_sam that disables this check. I hope this fixes your issues.
>
> Sorry for any inconvenience.
>
> Cheers,
> Manuel
> ________________________________________
> From: Uwe Appelt [uappelt@clcbio.com]
> Sent: Tuesday, September 11, 2012 11:10 AM
> To: SeqAn Development
> Subject: [Seqan-dev] rabema_prepare_sam "File must be sorted by query name."
>
> Hi guys,
>
> I've got a small problem in Rabema: I am preparing another gold standard
> for a Rabema benchmark and received the following error msg:
>
> ./razers3 -v -tc 32 -of sam -rr 100 -i 90 -m 1000000 -ds -o
> ./output0.sam ./hg19.fa ./input.fastq
> [load of outputs]
> ./rabema_prepare_sam ./output0.sam > ./output.sam
>
> ERROR: 16A7I:4:100 succeeds 16A7I:49:92 in SAM file.
> File must be sorted by query name.
>
> Seems like razers3 and rabema_prepare_sam are somehow out of sync with
> respect to their sorting code (maybe it's just the multi-threading in
> razers3 that sometimes results in slightly "unordered" output of mapping
> results)? The Trunk-checkout is, however, already a week old, so I might
> have to re-run everything. Before doing so, I wanted to ask for advice
> here, because re-running razers3 will take 4 days. Any ideas or suggestions?
>
> Thanks in advance,
> Uwe
>
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