[mira_talk] convert_project not outputting caf files

Hi Bastien and MIRAists,

I used mira 3.4rc2 to do a de novo assembly of a bacterial genome, ~5Mb,
using 600,000 454 reads, unpaired.

The result is a bit puzzling, but I'll come to that in a different
email. I then tried to filter out short, low-covered contigs, as I do
usually. I ran:

convert_project -f caf -t ace -t fasta -t caf -x 500 -y 20 $ASS_ID
\_out.caf $ASS_FILE

Took a very long while, outputting things like that for each contig: 

Generated 0 unique strain ids for 301 reads.
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
Localtime: Thu Jul 14 13:26:22 2011

and at the end:

Data conversion process finished, no obvious errors encountered.
SC Read:: read name issorted (1) capacity 4294967295(4) size 1
SC Read:: scf path name issorted (1) capacity 255(1) size 1
SC Read:: exp path name issorted (1) capacity 255(1) size 1
SC Read:: machine type issorted (1) capacity 255(1) size 1
SC Read:: primer issorted (1) capacity 255(1) size 1
SC Read:: strain issorted (1) capacity 255(1) size 1
SC Read:: base caller issorted (1) capacity 255(1) size 1
SC Read:: dye issorted (1) capacity 255(1) size 1
SC Read:: process status issorted (1) capacity 255(1) size 1
SC Read:: clone vector name issorted (1) capacity 65535(2) size 1
SC Read:: sequencing vector name issorted (1) capacity 65535(2) size 1
SC asped issorted (1) capacity 4294967295(4) size 1


and in the end, it output an ace file, different fasta (AllStrains,
default, and "normal", all with padded and unpadded version) and the
corresponding fasta.qual files, but the .caf file and the
"normal" .fasta (but not the .fasta.qual) are empty... All other files
(fasta qual ace) are fine.

I then found out that if I run only from caf to caf 

convert_project -f caf -t caf -x 500 -y 20 $ASS_ID\_out.caf $ASS_FILE

the debug messages don't show up and the caf file is fine...
Strange, isn't it? I filed a bug report already.

Cheers,

Lionel


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