[mira_talk] Convert manifest from 4.0.x to 4.9.x
- From: Marcelo Brandão <brandao.marcelo@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 13 Nov 2014 17:04:24 -0200
Hello there
I just migrate from mira 4.0.3 to 4.9x
But I got this warning:
========================= Parameter parsing error(s)
==========================
* Parameter section: '-SK'
* Parameter: hss
* Parameters with a name 'bph' (bases_per_hash) in MIRA 4.0.x and
before were renamed to use 'kms' (kmer_size) as this term is what the world
now uses. Sorry about that.
* Parameter section: '-SK'
* unrecognised string or unexpected character: 2
* (may be due to previous errors)
* Parameter section: '-CL'
* Parameter: -HS
* Section -HASHSTATISTICS was renamed to section '-KMERSTATISTICS'.
Furthermore, parameters with the term 'hash' were renamed with the term
'kmer'. Please look up the new name in the documentation, sorry about that.
* (may be due to previous errors)
* Parameter section: '-CL'
* unrecognised string or unexpected character: mnr
* (may be due to previous errors)
* Parameter section: '-CL'
* unrecognised string or unexpected character: yes
* (may be due to previous errors)
===============================================================================
My original manifest is written in this format:
parameters = -GE:not=8:kpmf=5 -SK:mmhr=1:pr=70:hss=2 -CL:ascdc=no
-HS:mnr=yes
parameters = COMMON_SETTINGS -AS:sd=y:nop=2 -DI:trt=$TMPDIR
parameters = SOLEXA_SETTINGS -CL:qc=yes:qcmq=5:qcwl=5 -AS:mrpc=3
parameters = TEXT_SETTINGS --noqualities
I am quite lost trying to solve what do I need to change.
Thanks for any help.
Cheers
Marcelo
--
Marcelo Mendes Brandão
Laboratório de Biologia Integrativa e Sistêmica - CBMEG / UNICAMP
Website: http://www.bioinfoguy.net/ <http://www.bioinfoguy.net/BBCA/>labis/
AtPIN: http://atpin.bioinfoguy.net/ <http://bioinfo.esalq.usp.br/atpin>
SKYPE: mmbrand
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