[mira_talk] Re: miraconvert problem
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 23 Mar 2015 16:21:48 +0000
Hi Lenis,
I think you've found a known bug in MIRA 4.0rc5, see:
http://seqanswers.com/forums/showthread.php?p=126915
https://www.freelists.org/post/mira_talk/Bug-maf2sam-conversion
You ought to be able to use mira_convert from the latest MIRA 4
on any Linux machine (e.g. your desktop), rather than having to
use the very old version of MIRA on the cluster.
Peter
On Mon, Mar 23, 2015 at 4:13 PM, lenis vasilis <val1@xxxxxxxxxx> wrote:
> Hello,
>
> I'm trying to convert the maf output from Mira into sam with the miraconvert.
> The conversion seems to went well, but when I tried to make the sam into bam
> I have the following error:
>
> SAM header is present: 1 sequences.
> Line 21, sequence length 101 vs 102 from CIGAR
> Parse error at line 21: CIGAR and sequence length are inconsistent
> Aborted
>
> With previous samples everything was ok. This is the first time that I'm
> facing this error.
>
> I'm really sorry for my ignorance, but I don't know how to fix it
> The Mira version that I'm using is 4.0rc5.
> I know that there is newer version but this is the only one that is being
> installed in the cluster that I'm working.
>
> Thank you very much in advance,
> Vasilis.
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