[mira_talk] Re: bug

Lionel Guy a écrit :

Hi Laurent,

Your qual input seems OK.
Have you checked that read FUJ9VHQ01DRU97 has actually 242 bp, and the corresponding quality has also 242 values? Otherwise it might be an upstream problem, maybe from the clipping process? 

HTH,

Lionel
yes, you are right the FUJ9VHQ01DRU97 sequence has 242bp whereas the corresponding quality file has 245 qualities values. the i have 450000 sequences to test, is there an option to ignore the difference between the number of bases and the number of quality values ? 



On 4 May 2009, at 12:43 , Laurent MANCHON wrote:


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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