Kegg API error

[Ueli von Ah]

Hi,

I got a Kegg API error in dgenome when using your tutorial (see
below). Therefore, some of the following steps did not work properly.
Not sure whether it might be sth with the connection. 
Other question: Would it be possible to use MetaCyc as well or instead
of Kegg? This DB is still not behind a paywall. Only if you want to use
it specific like in biocyc.

Here's the error:


2017-10-01 00:19:14 - ductape.kegg - [WARNING] - link (reaction)
failed!
2017-10-01 00:19:15 - ductape.kegg - [DEBUG] - http://rest.kegg.jp/link
/reaction/ko%3AK01609%3C/td%3E%2Bko%3AK02066%3C/td%3E%2Bko%3AK01887%3C/
td%3E%2Bko%3AK00766%3C/td%3E%2Bko%3AK02110%3C/td%3E%2Bko%3AK13013%3C/td
%3E%2Bko%3AK10233%3C/td%3E%2Bko%3AK03579%3C/td%3E%2Bko%3AK01752%3C/td%3
E%2Bko%3AK07110%3C/td%3E%2Bko%3AK02619%3C/td%3E%2Bko%3AK00161%3C/td%3E%
2Bko%3AK01704%3C/td%3E%2Bko%3AK00012%3C/td%3E%2Bko%3AK00299%3C/td%3E%2B
ko%3AK01004%3C/td%3E%2Bko%3AK02031%3C/td%3E%2Bko%3AK00102%3C/td%3E%2Bko
%3AK01430%3C/td%3E%2Bko%3AK01448%3C/td%3E%2Bko%3AK02114%3C/td%3E%2Bko%3
AK02027%3C/td%3E%2Bko%3AK01644%3C/td%3E%2Bko%3AK01506%3C/td%3E%2Bko%3AK
07032%3C/td%3E%2Bko%3AK03704%3C/td%3E%2Bko%3AK06890%3C/td%3E%2Bko%3AK10
441%3C/td%3E%2Bko%3AK01652%3C/td%3E%2Bko%3AK03829%3C/td%3E%2Bko%3AK0033
7%3C/td%3E%2Bko%3AK02963%3C/td%3E%2Bko%3AK02410%3C/td%3E%2Bko%3AK00457%
3C/td%3E%2Bko%3AK02379%3C/td%3E%2Bko%3AK01740%3C/td%3E%2Bko%3AK03071%3C
/td%3E%2Bko%3AK00962%3C/td%3E%2Bko%3AK14058%3C/td%3E%2Bko%3AK06896%3C/t
d%3E%2Bko%3AK05833%3C/td%3E%2Bko%3AK01885%3C/td%3E%2Bko%3AK03501%3C/td%
3E%2Bko%3AK02992%3C/td%3E%2Bko%3AK14659%3C/td%3E%2Bko%3AK06959%3C/td%3E
%2Bko%3AK09971%3C/td%3E%2Bko%3AK03324%3C/td%3E%2Bko%3AK01113%3C/td%3E%2
Bko%3AK00662%3C/td%3E%2Bko%3AK00899%3C/td%3E%2Bko%3AK09123%3C/td%3E%2Bk
o%3AK07171%3C/td%3E%2Bko%3AK03070%3C/td%3E%2Bko%3AK00860%3C/td%3E%2Bko%
3AK07106%3C/td%3E%2Bko%3AK11754%3C/td%3E%2Bko%3AK01464%3C/td%3E%2Bko%3A
K02427%3C/td%3E%2Bko%3AK03408%3C/td%3E%2Bko%3AK09862%3C/td%3E%2Bko%3AK1
0544%3C/td%3E%2Bko%3AK03499%3C/td%3E%2Bko%3AK00930%3C/td%3E%2Bko%3AK096
88%3C/td%3E%2Bko%3AK03684%3C/td%3E%2Bko%3AK13821%3C/td%3E%2Bko%3AK01119
%3C/td%3E%2Bko%3AK03758%3C/td%3E%2Bko%3AK15408%3C/td%3E%2Bko%3AK01903%3
C/td%3E%2Bko%3AK03187%3C/td%3E%2Bko%3AK00606%3C/td%3E%2Bko%3AK04782%3C/
td%3E%2Bko%3AK00891%3C/td%3E%2Bko%3AK02072%3C/td%3E%2Bko%3AK07793%3C/td
%3E%2Bko%3AK06902%3C/td%3E%2Bko%3AK00309%3C/td%3E%2Bko%3AK02258%3C/td%3
E
2017-10-01 00:19:15 - ductape.kegg - [WARNING] - link (reaction)
failed!
2017-10-01 00:19:15 - ductape.kegg - [ERROR] - KEGG API error, aborting
2017-10-01 00:19:15 - ductape.terminal - [ERROR] - Failure! KEGG API
error
2017-10-01 00:19:15 - ductape - [ERROR] - Genome(s) could not be mapped
to kegg!

Best Regards

Ueli

[Marco Galardini]

Hi Ueli,

is your computer connected to the internet? Can you access the kegg website from where you are? Could try to ping the following address: http://rest.kegg.jp/?

I'm afraid that implementing metacyc support would require time and effort that I don't have at the moment, I'm sorry. I'm happy to review any code contribution if you have any.

Best,
Marco

[Ueli von Ah]

Hi Marco,

yep, it's connected to the net and I can access http://rest.kegg.jp over the browser. But pinging seems not working. Either unknown host (if I use http://rest.kegg.jp/) or only rest.kegg.jp gives no answer. I'll try another time when I'm not sleeping during the run ;).

I understand that it would take time. This is a limitation here as well. But I thought I'd ask. I guess creating an inreractive activity ring will fail with the same issue.

Ueli

[Ueli von Ah]

Hi again,

it seems that it was a network error. It worked today.

Ueli