Need help using RATT

[Bgansw]

Hi,

I'm new to RATT. I've set it up as specified in the documentation.
This is the error msg I'm getting on running it.

Any help on this would be greatly appreciated. I'm using an embl file as reference, that I downloaded off RAST (Rapid Annotations Subsystems Technology)


ERROR: Reference input does not match delta file
show-coords: show-coords.cc:1118: long int revC(long int, long int): Assertion `Len - Coord + 1 > 0' failed.
/share/scratch/z3321306/ratt/start.ratt.sh: line 73: 14045 Aborted show-coords -clHT $name.delta > $name.coords
show-coords: show-coords.cc:1118: long int revC(long int, long int): Assertion `Len - Coord + 1 > 0' failed.
/share/scratch/z3321306/ratt/start.ratt.sh: line 73: 14046 Aborted show-coords -clHT $name.filter.delta > $name.filter.coords
Use of uninitialized value in print at /share/scratch/z3321306/ratt/main.ratt.pl line 82.
ERROR: Reference input does not match delta file
Nucmer is done. Now transfer the annotation.
perl /share/scratch/z3321306/ratt/main.ratt.pl /share/scratch/z3321306/ratt/embl_file nucmer.506_505_rattResult.snp nucmer.506_505_rattResult.filter.coords 506_505_rattResult
Use of uninitialized value in split at /share/scratch/z3321306/ratt/main.ratt.pl line 1140.
working on 533240.5
1 6691 4780 1911
Overview of transfere of annotation elements:
6 elements found.
6 Elements were transfered.
0 Elements could be transfered partially.
0 Elements split.
0 Parts of elements (i.e.exons tRNA) not transferred.
0 Elements couldn't be transferred.

CDS:
5 Gene models to transfer.
5 Gene models transferred correctly.
0 Gene models partially transferred.
0 Exons not transferred from partial CDS matches.
0 Gene models not transferred.

mkdir: cannot create directory `Sequences': File exists
3050 Sequences where generated
Done.
Nucmer is done. Now Correct the annotation for chromosome .
work on C7773
If you want to start artemis on this replicon:
art 506_505_rattResult.C7773.final.embl + 506_505_rattResult.C7773.Report.gff + Query/506_505_rattResult.C7773.Mutations.gff
work on C7529
If you want to start artemis on this replicon:
art 506_505_rattResult.C7529.final.embl + 506_505_rattResult.C7529.Report.gff + Query/506_505_rattResult.C7529.Mutations.gff

.......


Thanx

Bgansw

[effedi78]

RATT error: no parse delta file

Hi, I am Flavia and I just ran into the same problem... no parse delta file. In my case there was a mistake in the file name of one of the reference files used (an empty space was occurring within the name).
I hope it can help.
Ciao ciao.
Fla