[mira_talk] Re: Mapping a sequence with MIRA
- From: Federico Sanchez <federicosq@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Mar 2010 16:39:59 +0100
Thanks for all the help, I got it at the end it was the
backbone_in.fasta.qual that needed to be in the exact same format as the
quality files for the regular quality files of the fasta sequences.
Cheers
On Mon, Mar 15, 2010 at 3:35 PM, Marina Manrique <mmanrique@xxxxxxxx> wrote:
> Hi Federico,
>
> it seems that the errror turns out when trying to access to the input FASTA
> file, not the backbone quality file since it says
>
>
> " Could not find FASTA quality file 454_muestra2_backbone_in.fasta.qual,
> using default values for these reads.
>
> Done."
>
> And
>
>
> "Fatal Error (may be due to problems of the input data):
> "File not found: 454_muestra2_in.454.fasta""
>
>
> Are the input files in the same folder where you're running MIRA? Are you
> sure input file names are right?
>
> Please let me know if you get it
>
> Marina
>
> Federico Sanchez escribió:
>
> 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
>
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> 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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