doall stall about gapseq HOT 6 CLOSED

hi Adrien,
great to hear that it is running now!
The difference in the number of pathways is caused by a new setting that restricts metacyc pathway to bacteria-related pathways.

gapseq_find.sh -b 200 -p all -m bacteria fasta

If you remove -m bacteria you will get the old number of pathways again.

from gapseq.

Not sure if it helps but I found out that the update_sequence.sh did not unpack the sequence.tar.gz files. I will have a closer look at this issue next week.

from gapseq.

good avise! I added a parameter for this.
Could you try ./gapseq -n doall and report where it hangs?

from gapseq.

ok let's continue next week! thanks for your input :)

from gapseq.

Hello Johannes,

I finally had time to go back to the Gapseq tool. I have updated the tool to the latest github version and rerun with your command.
It worked fine and generated all the files nicely, except for the sbml conversion where for the life of me I can't install SybilSbml (I have opened an issue on BacArena but it's probably the wrong place to do so).

One thing though, on the version I used a month ago gapseq was going through 2738 pathways and now it only goes through 1682. Why the switch? And is there somewhere the possibility to have the previous database? I have annotated a few genomes with the old DB and would like to keep using it for the next ones.

from gapseq.

please reopen if still an issue

from gapseq.