The manifest you create looks like this:
---------
#manifest file for basic mapping assembly with illumina data using MIRA 4
project = initial-mapping-of-XXXXXXXXXX-to-Mbra-mt
job=genome,mapping,accurate
parameters = -NW:mrnl=0 -AS:nop=1 SOLEXA_SETTINGS -CO:msr=no
readgroup
is_reference
data = ...
strain = Mbra-mt-genome
readgroup = reads
-CL:pec=yes
data = XXXXXXXXXX_L001_R1_001.fastq XXXXXXXXXX_L001_R2_001.fastq
technology = solexa
strain = XXXXXXXXXX
---------
I see what you did there and if I were to rewrite MIRA, I would probably opt to
enable a thing like this, but this is not going to happen anytime soon. Anyway,
the correct answer to your problem is this manifest:
---------
#manifest file for basic mapping assembly with illumina data using MIRA 4
project = initial-mapping-of-XXXXXXXXXX-to-Mbra-mt
job=genome,mapping,accurate
parameters = -NW:mrnl=0 -AS:nop=1 SOLEXA_SETTINGS -CO:msr=no -CL:pec=yes
readgroup
is_reference
data = ...
strain = Mbra-mt-genome
readgroup = reads
data = XXXXXXXXXX_L001_R1_001.fastq XXXXXXXXXX_L001_R2_001.fastq
technology = solexa
strain = XXXXXXXXXX
---------
See where "-CL:pec" went to?
Regarding your other problem, that is described in the manual, in the section
"The manifest file: defining the data to load ":
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_manifest_readgroups
More specifically, look for the paragraph "data=" which describes which file
endings are automatically recognised and what to do when you want to force a
given file type if the ending is not recognised.
B.
On 11 May 2016 at 12:52 Kevin Sullivan <kev.am.sullivan@xxxxxxxxx> wrote:
Hi,
I am emailing you because I'm having a couple of separate issues with
running MIRA and Mitobim. First is that the genomes aren't being assembled
due to not being able to determine the filetype of my reference genome.
Second is that I later added the "CL:pec=yes" command to trim the raw
reads, but that went unrecognized as well. It might just be due to
placement within the command, but any help would be appreciated. I should
add that this is to assemble rodent mitochondrial genomes, and my script,
as well as both error files, are attached below. Any help would be greatly
appreciated and I hope to hear from you soon.
Sincerely,
--
Kevin A.M. Sullivan
Graduate Research & Teaching Assistant
Biological Sciences
Texas Tech University
Lubbock, Texas 79409
