[mira_talk] Re: miraconvert problem
- From: lenis vasilis <val1@xxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 23 Mar 2015 18:44:14 +0000
Hi Peter,
Thank you very much,
It worked!
I run miraconvert in my laptop and its ok
Vasilis.
On Mar 23, 2015, at 4:21 PM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
wrote:
> 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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