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
<mailto: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
<mailto: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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