[mira_talk] problem with miraSearchESTSNPs
- From: "Jackie" <jc807177@xxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Sat, 23 Apr 2011 12:08:51 -0300
I am having issue running ESTSNP search.
Here is my code: miraSearchESTSNPs --project=skt --job==denovo,normal,454
454_SETTINGS,esps1 >log_assembly_esps1.txt
In my working director I have a FASTA file containing all sequences from
both strains, uniquely labelled. I then have the same for the QUAL file. My
straindata_in.txt file contains a list of all the sequence names, and strain
name.
If I put in the above code, nothing happens;
jackie@ubuntu:~/Desktop/Mira$ miraSearchESTSNPs --project=skt
--job==denovo,normal,454 454_SETTINGS,esps1 >log_assembly_esps1.txt
jackie@ubuntu:~/Desktop/Mira$
If I then remove the creat log commant I get the following error:
Parsing parameters: --project=skt --job==denovo,normal,454
454_SETTINGS,esps1
Seen no assembly quality in job definition, assuming 'normal'.
Seen no assembly type in job definition, assuming 'genome'.
Seen no assembly method in job definition, assuming 'denovo'.
,,,
========================= Parameter parsing error(s)
==========================
* Parameter section: '(none)'
* unrecognised string or unexpected character: denovo
* Parameter section: '(none)'
* unrecognised string or unexpected character: normal
* (may be due to previous errors)
* Parameter section: '(none)'
* unrecognised string or unexpected character: 454
* (may be due to previous errors)
* Parameter section: '(none)'
* unrecognised string or unexpected character: esps1
* (may be due to previous errors)
============================================================================
===
Fatal error (may be due to problems of the input data or parameters):
"Error while parsing parameters, sorry."
->Thrown: void MIRAParameters::parse(istream & is, vector<MIRAParameters> &
Pv, MIRAParameters * singlemp)
->Caught: main
Aborting process, probably due to error in the input data or
parametrisation.
Please check the output log for more information.
Any help would be much appreciated!
Jack
Other related posts:
