celera assembler to .ace with multiple .frg files

[agroster]

Hi,
I have used Celera assembler to produce an assembly with three sets of data:
1. unpaired 454 FLX reads
2. unpaired 454 Tit reads
3. paired-end 454 Tit reads (10 Kb)

I used the sffToCA utility individually on each of these data sets, and then runCA to assemble the three data sets. It produced a fairly nice set of contigs, up to 480 Kbp in size.

Now I'd like to visualize the assembly with EagleView or hawkeye, and then to analyze with consed using the .ace file format.

I run this line:
$ perl ca2ace.pl CB1190WGS10kb.asm

I then get the error: CB1190WGS10kb.frg: No such file or directory

This file has never existed, as I used three separate .frg files as input for runCA (*.frg). I've noticed that trying to convert to AMOS file formats produces similar errors, where it is looking for an inappropriate .frg file.

Has anyone encountered this? Are there any work-arounds?

[blu78]

Hi,

I am having the same problem, anyone can hint how to sort this?

Thanks

Hi,
I have used Celera assembler to produce an assembly with three sets of data:
1. unpaired 454 FLX reads
2. unpaired 454 Tit reads
3. paired-end 454 Tit reads (10 Kb)

I used the sffToCA utility individually on each of these data sets, and then runCA to assemble the three data sets. It produced a fairly nice set of contigs, up to 480 Kbp in size.

Now I'd like to visualize the assembly with EagleView or hawkeye, and then to analyze with consed using the .ace file format.

I run this line:
$ perl ca2ace.pl CB1190WGS10kb.asm

I then get the error: CB1190WGS10kb.frg: No such file or directory

This file has never existed, as I used three separate .frg files as input for runCA (*.frg). I've noticed that trying to convert to AMOS file formats produces similar errors, where it is looking for an inappropriate .frg file.

Has anyone encountered this? Are there any work-arounds?

[sklages]

Well, this FRG file has been written defaultly in assembler versions prior to 5.0.
Now you need to create this file after the assembly freshly by hand from the gatekeeper store, e.g.

$ gatekeeper -dumpfrg PROJECT.gkpStore | grep -v 'No source' > PROJECT.frg

ca2ace.pl is not further developed AFAIK ..

hth, Sven

[blu78]

Well, this FRG file has been written defaultly in assembler versions prior to 5.0.
Now you need to create this file after the assembly freshly by hand from the gatekeeper store, e.g.

$ gatekeeper -dumpfrg PROJECT.gkpStore | grep -v 'No source' > PROJECT.frg

ca2ace.pl is not further developed AFAIK ..

hth, Sven

yes that helped, thanks a lot!