[mira_talk] Re: Mapping a sequence with MIRA
- From: Federico Sanchez <federicosq@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Mar 2010 14:23:13 +0100
Hi Marina:
I had it like that from the begging:
This is the command line that I use:
/aplic/mira-3.0.0/bin/mira -fasta
-project=*454_muestra2*-job=mapping,genome,normal,454 --noclipping=all
--notraceinfo
COMMON_SETTINGS -AS:sd=yes -SK:mnr=no
-SB:lb=yes:bsn=454_muestra2_backbone_in.454.fasta:bbq=100:bft=fasta:abnc=yes:sbuip=2
And this the name of the files right now:
1) 454_muestra2_in.454.fasta
2) 454_muestra2_in.454.fasta.qual
3) 454_muestra2_backbone_in.fasta
And I have changed the backbone as it was before (backbone_in.fasta, but if
I do this I get the same message as before that it ""Could not find FASTA
quality file 454_muestra2_backbone_in.fasta.qual, using default values for
these reads"" eventhough I use used the -SK:bbq and sbuip parameters to
describe that I have a good quality on the backbone sequence.
This is the error print out:
Loading backbone from FASTA file: 454_muestra2_backbone_in.fasta (quality:
454_muestra2_backbone_in.fasta.qual)
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Found 1 sequences.
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Could not find FASTA quality file 454_muestra2_backbone_in.fasta.qual, using
default values for these reads.
Done.
Loaded 1 reads with 954 raw bases.
0 reads have quality accounted for.
Postprocessing backbone (this may take a while)
1 to process
gi|193083133:1381-2334_bb 954
Localtime: Mon Mar 15 14:08:59 2010
Seeing strain 1: "454_muestra2_backbone_in.fasta"
Generated 1 unique strain ids for 1 reads.
Strain "default" has 0 reads.
Strain "454_muestra2_backbone_in.fasta" has 1 reads.
Loading data (454) from FASTA files,
Fatal Error (may be due to problems of the input data):
"File not found: 454_muestra2_in.454.fasta"
->Thrown: size_t ReadPool::loadDataFromFASTA(const string & filename, const
uint8 loadaction, uint32 & longestread, const bool wantsqualfiletoexist,
const string & qualfilename, const bool generatefilenames, const uint8
seqtype, const bool sxa_mustconvert)
->Caught: Assembly::loadFASTA(const string & fastafile, const string &
fastaqualfile, const uint8 seqtype, const uint8 loadaction)
Program aborted, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
So I am back to square one, because this is the same error message that I
used to get before changing the files extension. Could you give any other
advice and help me out with it? Thanks again for the help
Federico
On Mon, Mar 15, 2010 at 12:39 PM, Marina Manrique <mmanrique@xxxxxxxx>wrote:
> Hi Federico,
>
> try setting up input file names as follows (replacing miraProjecName with
> your real mira project name...)
>
> miraProjectName_backbone_in.fasta
> miraProjectName_in.454.fasta.qual
> miraProjectName_in.454.fasta
> miraProjectName_traceinfo_in.454.xml
>
> Note that for the backbone file you shouldn't name it with
> ~backbone_in.454.fasta
>
> Hope this helps
>
> Marina
>
> Federico Sanchez escribió:
>
> Hi:
>
> Thanks for the quick answer. I just did what you suggeested me. and change
> the files to the _in.454.fasta format, for all of them (the quality file and
> the backbone too). However I am still getting an error with the backbone
> file --->
>
> Fatal Error (may be due to problems of the input data):
> "File not found: 454_muestra2_backbone_in.fasta"
>
> ->Thrown: size_t ReadPool::loadDataFromFASTA(const string & filename, const
> uint8 loadaction, uint32 & longestread, const bool wantsqualfiletoexist,
> const string & qualfilename, const bool generatefilenames, const uint8
> seqtype, const bool sxa_mustconvert)
>
> ->Caught: main
>
> Program aborted, probably due to error in the input data or
> parametrisation.
> Please check the output log for more information.
> For help, please write a mail to the mira talk mailing list.
>
> CWD: /home/homes/users/fsanchez/MIRA_ASSEMBLY
> Aborted
>
> My command line is the same but changing the backbone file to
> backbone_in.454.fasta instead of the 454_muestra2_backbone_in.fasta, what
> else could be going wrong? any suggestions?. At the moment I am not able to
> download the newer versions of mira but I hope mira 3.0.0 is up for the
> task.
>
> /aplic/mira-3.0.0/bin/mira -fasta -project=454_muestra2
> -job=mapping,genome,normal,454 --noclipping=all --notraceinfo
> COMMON_SETTINGS -AS:sd=yes -SK:mnr=no
> -SB:lb=yes:bsn=454_muestra2_backbone_in.454.fasta:bbq=100:bft=fasta:abnc=yes
>
>
> Thanks again for the help
>
>
> Federico
>
>
>
>
>
> On Mon, Mar 15, 2010 at 11:36 AM, Jan Paces <hpaces@xxxxxxxxxx> wrote:
>
>> On 03/15/10 04:56, Federico Sanchez wrote:
>> > 1) /aplic/mira-3.0.0/bin/mira -fasta -project=454_muestra2
>> > -job=mapping,genome,normal,454 --noclipping=all --notraceinfo
>> > COMMON_SETTINGS -AS:sd=yes -SK:mnr=no
>> > -SB:lb=yes:bsn=454_muestra2_backbone_in.fasta:bbq=100:bft=fasta:abnc=yes
>>
>> For mapping, I suggest to use mira-3.0.3, there were some problems with
>> parsing input data in version 3.0.2 a maybe lower as well, I am not sure.
>>
>> As for the error with input files, you need _in.454. in the names -
>> as pointed out by Sven befora I sent this email ;-)
>>
>> Jan
>>
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>
>
>
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