[mira_talk] Re: FW: 454 assembly
- From: "Shabhonam Caim (TGAC)" <Shabhonam.Caim@xxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 22 Jul 2010 11:28:24 +0100
Thanks a lot Thomas ...I am able to run the MIRA
Cheers
Shab
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On
Behalf Of Thomas Müller
Sent: 22 July 2010 11:26
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: FW: 454 assembly
Hey Shab,
The error message tells you what to do:
Either use '<technology>_SETTINGS -LR:mxti=no' (e.g. SANGER_SETTING
-LR:mxti=no),
or use the '-notraceinfo' quickswitch to kill loading traceinfo files for all
types of sequencing technologies. (place it after -fasta and -job quickswitches)
That means you can add to the section with the 454_SETTINGS -LR:mxti=no or you
can use the -notraceinfo switch. And it also tells you
However, if you are really sure that you do not want to load ancillary data
in TRACEINFO files, you can switch it off.
BUT: if you have the sff it is highly recommended to use it! Like Veljo wrote
you can use sff_ectract.
I (until now) never used the traceinfo-file because I had to do some "special"
preprocessing and there wouldn't be any new information in the xml (at least in
the ones I have and the sequences are already cut correctly).
Cheers,
Thomas
On Jul 22, 2010, at 12:04 PM, Shabhonam Caim (TGAC) wrote:
Thanks Thomas
by using your second suggestion it loaded the files without any problem but I
guess this one is the last error, which is as follows:
Command : mira --project=test --job=denovo,genome,draft,454 454_SETTINGS
-FN:fai=2.GAC.454Reads.fna -FN:fqui=2.GAC.454Reads.qual
Error: Done.
Loaded 784833 reads with 211718637 raw bases.
784833 reads have quality accounted for.
Loaded 784833 454 reads.
Total reads loaded: 784833
Localtime: Thu Jul 22 10:57:50 2010
Merging data from XML trace info file test_traceinfo_in.454.xml ...
MIRA tried to load a XML TRACEINFO file containing ancillary data, but failed.
Loading ancillary data when using FASTA files as input is
really,
really,
REALLY encouraged, and therefore MIRA sets this as default.
However, if you are really sure that you do not want to load ancillary data
in TRACEINFO files, you can switch it off.
Either use '<technology>_SETTINGS -LR:mxti=no' (e.g. SANGER_SETTING
-LR:mxti=no),
or use the '-notraceinfo' quickswitch to kill loading traceinfo files for all
types of sequencing technologies. (place it after -fasta and -job quickswitches)
Fatal Error (may be due to problems of the input data):
"TraceInfo XML file not found for loading: test_traceinfo_in.454.xml"
->Thrown: void NCBIInfoXML::readXMLFile(string filename)
->Caught: void ReadPool::mergeXMLTraceInfo(const string & filename)
Program aborted, probably due to error in the input data or parametrisation.
Please check the output log for more information.
Cheers
Shab
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