(no subject)
- From: Jac Trew <jac.trew@xxxxxxxxx>
- To: mira <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 12 Jul 2013 08:10:22 -0700 (PDT)
Hello,
I'm new to mira, and I'm just trying the tutorial on MITObim. There seems to be
a problem with the step after I run the initial mira assembly. It stops at the
1st iteration, and the log output gives an error message (top):
"All paramters seem to make sense:
startiteration: 1
enditeration: 10
strainname: testpool
refname: Salpinus_mt_genome
readpool:
/home/jahcub/tutorial1/initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq
maf:
/home/jahcub/tutorial1/initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf
quick: 0
paired: 0
denovo: 0 (mapping=0, denovo=1)
noshow: 0
proofread: 0
read trimming: 0 (off=0, on=1)
platform: SOLEXA
Starting MITObim
==============
ITERATION 1
==============
Jul 12 15:49:29
recover backbone by running convert_project on maf file
Parsing special MIRA parameters: SOLEXA_SETTINGS -CO:fnicpst=yes
========================= Parameter parsing error(s) ==========================
* Seen parameters for Solexa, but no readgroup has that sequencing technology?
===============================================================================
Fatal error (may be due to problems of the input data or parameters):
*******************************************************************************
* Error while parsing parameters, sorry. "
This is the command used "MITObim.pl -start 1 -end 10 -strain testpool -ref
Salpinus_mt_genome -readpool
initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq -maf
initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf
&> log"
I would be greatful for any help,
Thanks,
Jahcub.
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