Is "doall" command quite by default?

[maringos]

Hi,

I was wondering if the command ./gapseq doall toy/myb71.fna.gz should print anything else than the following info or I do something wrong:

index file myb71.fna.tmp.fai not found, generating...
Predicted taxonomy: Bacteria
Checking updates for Bacteria /home/*****/software/gapseq/src/../dat/seq/Bacteria
2022-03-02 11:55:06 URL: ftp://ftp.rz.uni-kiel.de/pub/medsystbio/Bacteria/rev/sequences.tar.gz [193] -> ".listing" [1]
2022-03-02 11:55:07 URL: ftp://ftp.rz.uni-kiel.de/pub/medsystbio/Bacteria/unrev/sequences.tar.gz [194] -> ".listing" [1]
2022-03-02 11:55:07 URL: ftp://ftp.rz.uni-kiel.de/pub/medsystbio/Bacteria/rxn/sequences.tar.gz [193] -> ".listing" [1]
Bacteria reviewed sequences already up-to-date
Bacteria unreviewed sequences already up-to-date
Bacteria additional reaction sequences already up-to-date

Regards,
Georgios

[silvtal]

Hi,

I think it is (or if it isn't, I have the same bug)
If it is, I wanted to ask - is there any way of making it verbose?

Thanks in advance,
Silvia

[jotech]

./gapseq -n should enable the verbose mode

[jotech]

there should be more printing especially from the gapfilling step! Something like this:

Starting gap filling
Loading model files /work_beegfs/sukem066/cembio.ext/out/MYb45-draft.RDS                                             
using media file /work_beegfs/sukem066/gapseq/dat/media/TSBmed.csv


1. Initial gapfilling: Make model grow on given media using all reactions
Utilized candidate reactions:  73
Gapfill summary:
Added reactions:       73
Added core reactions:  15
Final growth rate:     1.233
[...]