[EMBOSS] fndadist : data read error

[christophe caron]

Hello

We run EMBOSS 5.0 and fdnadist on output files from mpi-clustalw (phylip 
format). Actually i could not post the original private data file.

So I run
# fdnadist -sequence nok2.phylip -outfile distance.matrix -method f
But i get this message
Nucleic acid sequence Distance Matrix program
Error: Sequence is not nucleic

Error: Unable to read sequence 'nok2.phylip'
Died: fdnadist terminated: Bad value for '-sequence' and no prompt



**Then i try with -debug option and from the debug file :

  - Phylip format seems to be correctly detected :
...
  Free: 0 Last: -1
seqRead:try format 22 (phylip)
++seqReadFmt format 22 (phylip) 'nok2.phylip' feat No
seqReadPhylip seqin->Data 0
ajFileBuffBuff nok2.phylip buffsize: 5000
....


  - Then i have this message:

seqMsfTabDel key: 'lcl2X90834' item: 'lcl2X90834'
Testing input buffer: IsBuff: Yes Eof: No
Format 22 (phylip) failed, file buffer reset by seqReadFmt
++seqReadFmt failed - nothing read
seqRead: (b1) seqReadFmt stat == FAIL *failed*
Trace buffer file 'nok2.phylip'
              Pos: 0 Size: 5000 FreeSize: 0 Fpos: 339808 End: N
  Lines:
   Curr:        0 544e10 548200 < 3713 1453
 >
   From:        0 544e10 548200 < 3713 1453
 >
     To:   339808 5fbb20 0 <             t--------- ------attt 
cat-ac-ttt -atgc-ta-a aaa-------
 >
  Free: 0 Last: -1
seqRead:try format 24 (acedb)
++seqReadFmt format 24 (acedb) 'nok2.phylip' feat No
seqReadAcedb
first line:
' 3713 1453


I think tha fdnadist could not read one line and then try others format 
(acedb...)
How could i use the 3713/1453 information. Lines number ?



**Finally the last 10 lines from the debug file

EOF ajFileGetsL file nok2.phylip
End of file - data in buffer - return ajFalse
read 115137 lines
ajFileBuffClear (0) Nobuff: No
size 0: Lines: 5476c0 Curr: 1518600  Prev: 15185a0 Last: 1518600 Free: 
5476c0 Freelast: 1518600
ajFileBuffClear 'nok2.phylip' (0 lines)
      N size: 0 pos: 0 removed 115137 lines add to free: 115137
Trace buffer file 'nok2.phylip'
              Pos: 0 Size: 0 FreeSize: 0 Fpos: 7388914 End: Y
  Free: 115137 Last: 115137
seqReadFmt success with format 43 (raw)
seqQueryMatch '' id '' acc '' Sv '' Gi '' Des '' Key '' Org '' Case No 
Done No
ajSeqTypeCheckIn type 'gapdnaphylo' found (DNA sequence with gaps and 
queries)
Convert gaps to '-'
ajSeqIsNuc Type ''
ajSeqTypeGapnucS test
seqTypeTest, len 5412078 goodchars 'ACGTUBDHKMNRSVWXY?.~O-'
seqTypeTest, Sequence had bad character 'l' (6c) at 0 of 5412078/5412078
ajSeqIsNuc failed
ajSeqTypeCheckIn: rejected - not nucleic
seqRead: (a1) seqReadFmt stat == BADTYPE *failed*
ajSeqRead: open buffer  usa: 'nok2.phylip' returns: No


Error with the sequence type ?? I have only 'l' in the header and not 
the sequence data (may be because fdnadist mode is RAW after the first 
error ?)



And a last information:  Phylip dnadist version runs fine on this file.


Any clue ?

thanks.


cc
-- 


**************************************************************************
Christophe Caron - INRA 	    | Tél: (+33) 013465 2888
Mathematique, Informatique et Genome| Fax: (+33) 013465 2901
Domaine de Vilvert 		    | Email: christophe.caron at jouy.inra.fr
F-78350 Jouy-en-Josas		    | http://migale.jouy.inra.fr/
**************************************************************************

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