[mira_talk] Mapping a sequence with MIRA
- From: Federico Sanchez <federicosq@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Mar 2010 04:56:53 +0100
HI Bastien:
I am trying to assemble some 454 reads by mapping themto a NCBI backbone
fasta file. I have no XML files and I dont want the reads to be clipped. I
always get an error when I use the comand line; it basically tells me that
it couldnt load the the quality backbone file even thought I put in the
parameters that I dont have a backbone quality file. Moreover I think it
dosent loads the reads fasta and quality files either. I have tried loading
the files by using the same name with of the project and the fasta, quality
and backbone file but it is not able to upload them. I have tried to load
them with the -FN paramter using -FN:faii and fqui. This are the two command
lines and the error that I got when I try to run mira, I will appreaciate
your help very much and any comments on waht could possibly be going wrong,
thank you in advance for the help.
Just in case this are the names of my fies:
1) 454_muestra2_in.fasta
2) 454_muestra2_in.fasta.qual
3) 454_muestra2_backbone_in.fasta
COMAND LINES
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
ERROR ------>>
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 04:46:40 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,
Counting sequences in FASTA file:
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)
2) /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
-FN:fai=454_muestra2_in.fasta:fqui=454_muestra2_in.fasta.qual
========================= Parameter parsing error(s)
==========================
* Parameter section: '-FN'
* Parameter '454_muestra2_in.fasta' can only be set as sequencing type
specific
* parameter (SANGER_SETTINGS, 454_SETTINGS, etc.pp)
* and not for COMMON_SETTINGS.
* Parameter section: '-FN'
* Parameter '454_muestra2_in.fasta.qual' can only be set as sequencing
type specific
* parameter (SANGER_SETTINGS, 454_SETTINGS, etc.pp)
* and not for COMMON_SETTINGS.
===============================================================================
Fatal Error (may be due to problems of the input data):
"Error while parsing parameters, sorry."
->Thrown: void MIRAParameters::parse(istream & is, vector<MIRAParameters> &
Pv, MIRAParameters * singlemp)
->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
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