[mira_talk] Re: MIRA - Baccardi - ace file
- From: Shankar Manoharan <shankarmanostar@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 8 Mar 2012 01:05:59 +0530
*Sure will, I'll run the tests suggested, and get back asap :) Thanks again
*
*
*
*Shankar Manoharan
Graduate Student
Department of Genetics
Madurai Kamaraj University*
*Ph. +919790167534*
*
*
*I strongly believe in doing my best and leaving the rest to God*
*
*
On Thu, Mar 8, 2012 at 1:00 AM, Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>wrote:
> OK, *"Segmentation fault"* is the main problem you have ..
> Have you ever used Baccardi with MIRA ACE files?
>
> Can you open this ACE file with another viewer like 'tablet' just for
> checking ACE file integrity.
>
> Last but not least, it is a "ELF 32-bit LSB executable", Qt3, maybe there
> are some incompatibilities with Ubuntu 64bit?
>
> If your ace file is correct and is read by another viewer you should
> contact the developers for support.
> (And report the result back here to the list).
>
> cheers, Sven
>
> 2012/3/7 Shankar Manoharan <shankarmanostar@xxxxxxxxx>
>
>> *lol, I'm sorry :D
>>
>> Firstly, I see the error message "Segmentation fault" on the terminal
>> after the error message on Baccardi
>>
>> Secondly, the output of
>>
>> root@ubuntu:/gom/GS1_assembly/GS1_d_results# grep ^CO GS1_out.ace | head
>> -n 10
>>
>> CO GS1_c1 155103 10125 4013 U
>> COMMENT{
>> COMMENT{
>> COMMENT{
>> COMMENT{
>> COMMENT{
>> COMMENT{
>> COMMENT{
>> COMMENT{
>> COMMENT{
>>
>> *
>> *Thirdly, I see from a PhD thesis that MIRA 3 ace files can be read by
>> Baccardi. However, I use MIRA 3.4 64 bit on a UBUNTU system for assembly.
>>
>> I'm really thankful to you for trying to sort out this issue :)
>>
>> *
>> *Shankar Manoharan
>> Graduate Student
>> Department of Genetics
>> Madurai Kamaraj University*
>> *Ph. +919790167534*
>> *
>> *
>> *I strongly believe in doing my best and leaving the rest to God*
>> *
>> *
>>
>>
>>
>> On Thu, Mar 8, 2012 at 12:19 AM, Sven Klages <
>> sir.svencelot@xxxxxxxxxxxxxx> wrote:
>>
>>> OK, not what I expected to be an error message ;-)
>>>
>>> Did you get any output in the terminal after you have started " *sh
>>> baccardi.sh* "?
>>>
>>> Can you post the output of:
>>>
>>> grep ^CO YOUR_ACE_FILE | head -n 10
>>>
>>> Maybe we see something weird (I don't expect to see something weird as
>>> MIRA has written the ACE file).
>>>
>>> Have you ever successfully used Baccardi with MIRA ACE files in the past?
>>>
>>> cheers,
>>> Sven
>>>
>>>
>>> 2012/3/7 Shankar Manoharan <shankarmanostar@xxxxxxxxx>
>>>
>>>> *Thankyou for replying, and yes Baccardi is still alive among those
>>>> who aren't really convenient with linux, C, and C++ programming :D
>>>>
>>>> 1. MIRA generates an ACE file as a part of the output
>>>> 2. I start baccardi by typing 'sh baccardi.sh' >> The baccardi gui
>>>> opens up
>>>> 3. I make a new project via project>new
>>>> 4. In the following dialog box, Project name: ECGS1; sequencing
>>>> project: GS1; organism: Enterobacter cloacae GS1; working directory:
>>>> GS1_d_results (generated by MIRA)
>>>> 5. I am asked to select the ACE file.
>>>> 6. When I browse for the file, I have to select 'all files' from the
>>>> 'filetype' field to make it visible
>>>> 7. In the following dialog, selected 'naming convention: Bielefield'
>>>> 'sequences types: BACS+fosmids'; > clicked on finish
>>>> 7. Baccardi attempts to parse the file
>>>> 8. [image: Inline image 1]
>>>> :'(
>>>> *
>>>> *
>>>> *
>>>> *Shankar Manoharan
>>>> Graduate Student
>>>> Department of Genetics
>>>> Madurai Kamaraj University*
>>>> *Ph. +919790167534*
>>>> *
>>>> *
>>>> *I strongly believe in doing my best and leaving the rest to God*
>>>> *
>>>> *
>>>>
>>>>
>>>>
>>>> On Wed, Mar 7, 2012 at 5:29 PM, Sven Klages <
>>>> sir.svencelot@xxxxxxxxxxxxxx> wrote:
>>>>
>>>>> 2012/3/7 Shankar Manoharan <shankarmanostar@xxxxxxxxx>
>>>>>
>>>>>> *Hi*
>>>>>> * I'm attempting to validate a MIRA assembly using the Baccardi
>>>>>> tool. Baccardi produces an error saying that there are NO CONTIGS in the
>>>>>> ace file after parsing it. Any help in this regard will be greatly
>>>>>> appreciated :) *
>>>>>> *
>>>>>> *
>>>>>>
>>>>>>
>>>>> What exact error message do you get?
>>>>> I didn't know Baccardi is still alive out there ;-)
>>>>>
>>>>> Sven
>>>>>
>>>>>
>>>>
>>>
>>
>
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