[mira_talk] Undefined readgroup
- From: Yasir Suhail <yusuhail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 1 May 2013 16:16:56 -0400
I am trying to do an EST assembly. This is my manifest file:
project = ESTAccurateAgain
job = denovo,est,accurate
parameters = -GE:not=4
parameters = TEXT_SETTINGS -AS:epoq=no mrpc=1 mrl=40
readgroup = AllData
data = combined.fna
technology = text
When I run mira, it seems it tries to load 2 readgroups, of which one is
undefined. This is the relevant part of the output:
Readgroups after loading manifest:
RGI: 0 RGID: 0
RGN: UnassigneReads SN:
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 8 (UNDEFINED!!! SHOULD NEVER BE SEEN) namschem: 0 SID: 0
DQ: 212
BB: 0 Rail: 0 CER: 0
RGI: 1 RGID: 1
RGN: AllData SN: StrainX
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 5 (Text) namschem: 6 SID: 0
DQ: 10
BB: 0 Rail: 0 CER: 0
What is the RGI: 0? Also, it seems to think there are some sanger sequences:
Load reads options (-LR):
Wants quality file (wqf) : [san] yes
[txt] yes
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 4
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 2
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [san] 80
[txt] 40
Minimum reads per contig (mrpc) : [san] 2
[txt] 1
Enforce presence of qualities (epoq) : [san] yes
[txt] no
Why does it think there is some sanger input when there is none? Are there
any errors in my manifest file?
Thanks!
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