[mira_talk] bug
- From: Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 04 May 2009 12:43:45 +0200
i have installed mira_2.9.43_dev_linux-gnu_x86_64 on my server.
when i use this command:
mira -project=ESTUR -job=denovo,est,normal,454 --notraceinfo GE:not=2
-CO:asir=yes 454_SETTINGS
-AL:mrs=95:egp=yes:egpl=reject_codongaps:megpp=100 -CO:rodirs=10 -AL:mo=60
it returns:
Warning: "Read FUJ9VHQ01DRU97: tried to set 245 qualities although the
read has 242 bases.
"
->Thrown: void Read::setQuality(vector<base_quality_t> & quals)
->Caught: void ReadPool::loadDataFromFASTA(const string & filename,
const string & qualfilename, const bool generatefilenames, const uint8
seqtype)
..../....
Loaded 434802 reads, 345575 of which have quality accounted for.
Fatal Error: "Fatal error encountered during load of data (see log),
aborting.
"
->Thrown: void ReadPool::loadDataFromFASTA(const string & filename,
const string & qualfilename, const bool generatefilenames, const uint8
seqtype)
->Caught: Assembly::loadFASTA(const string & fastafile, const string &
fastaqualfile)
Program aborted.
CWD: /sfs1/home/frt/lmanchon/mira_2.9.43_dev_linux-gnu_x86_64
Abort (core dumped)
and when i suppress the quality file it works fine.
This is the format of my quality file:
>FUJ9VHQ01C3893 length = 60
37 37 37 37 37 37 40 40 39 37 37 37 37 37 37 33 28 27 27 27
37 37 38 38 35 35 35 35 35 37 37 37 37 34 34 30 27 27 27 37
37 37 35 35 38 37 37 37 35 35 33 32 32 30 30 28 21 18 14 14
>FUJ9VHQ01ED7WN length = 37
37 37 37 37 37 37 40 40 40 40 39 37 35 34 32 32 32 32 32 32
20 20 19 19 27 27 27 32 30 30 28 15 15 15 29 28 27
>FUJ9VHQ01DX8T3 length = 35
37 37 37 37 37 37 39 39 36 30 31 31 30 35 33 33 33 33 32 30
24 23 19 19 19 27 27 28 23 21 22 24 24 18 19
.../...
it seems to be solexa quality score, so is it understanding by Mira ?
and in other way how to convert those solexa score to correct quality file ?
Laurent --
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