No thumbnails in html report

[tarhil]

Hi,
I just installed the latest scipion version from git on a debian stretch system.
To evaluate microscope performance I started a standard workflow of import movies, motioncor2, gctf and monitor summary.
Everything runs like a charm, however I have no thumbnails in the index.html
All thumbnail folders are empty.

Any ideas?

[azazellochg]

Hi @tarhil, my guess would be you are missing eman2 which is now used to make thumbnails. If you install it and rerun monitor it should work

[tarhil]

Hi @tarhil, my guess would be you are missing eman2 which is now used to make thumbnails. If you install it and rerun monitor it should work

Thanks for the reply, sadly eman2.3 was installed via the plugin manager.

[pconesa]

Hi! @tarhil Scipion should be able to use eman2.3 for the thumbnails

[tarhil]

Hi! @tarhil Scipion should be able to use eman2.3 for the thumbnails

Oh, that was misleading. Just wanted to make clear that eman is installed and the problem must be something else...

[pconesa]

I see....Do you see any hint in the logs of the monitor summary?

[tarhil]

no errors, seems everything ok.

[pconesa]

Do you see any log lines like:

"Generating images for mic xxxxx" ?

[tarhil]

Do you see any log lines like:

"Generating images for mic xxxxx" ?

no

[azazellochg]

Could you please attach full run.stdout?

…

On Fri, Sep 20, 2019, 12:22 tarhil ***@***.***> wrote: Do you see any log lines like: "Generating images for mic xxxxx" ? no — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2052?email_source=notifications&email_token=ABVBPJUAZTWE7ENHNSTAL63QKSI55A5CNFSM4IX77URKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7GD5XI#issuecomment-533479133>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABVBPJWSSTWNYCSQJ33Z57LQKSI55ANCNFSM4IX77URA> .

[tarhil]

ESC[32mRUNNING PROTOCOL -----------------ESC[0m
HostName: sambia
PID: 17644
Scipion: v2.0 (2019-04-23) Diocletian
currentDir: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS
workingDir: Runs/000190_ProtMonitorSummary
runMode: Restart
MPI: 1
threads: 1
Starting at step: 1
Running steps
ESC[35mSTARTEDESC[0m: monitorStep, step 1
2019-09-25 09:37:32.239072
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
ESC[32mRUNNING PROTOCOL -----------------ESC[0m
HostName: sambia
PID: 20732
Scipion: v2.0 (2019-04-23) Diocletian
currentDir: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS
workingDir: Runs/000190_ProtMonitorSummary
runMode: Continue
MPI: 1
threads: 1
len(steps) 1 len(prevSteps) 1
Starting at step: 1
Running steps
ESC[35mSTARTEDESC[0m: monitorStep, step 1
2019-09-25 09:40:47.504419
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
(END)

[pconesa]

Which protocols did you select in the summary monitor?

[tarhil]

I included results from import, motioncor, gctf.

[pconesa]

Thank you tarhil. I fail to see what can be wrong there. Is there any chance we can ssh your machine to check more technical stuff? El jue., 26 sept. 2019 20:51, tarhil <notifications@github.com> escribió:

…

I included results from import, motioncor, gctf. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2052?email_source=notifications&email_token=AAF7ZYNMPB6XOLPQ6534HHLQLUACNA5CNFSM4IX77URKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7WTBHY#issuecomment-535638175>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAF7ZYMTYV6XI5TWUBJWBJTQLUACNANCNFSM4IX77URA> .

[azazellochg]

@tarhil above is run.log, could you paste run.stdout which is more detailed?
Also, by no thumbnails you mean Micrographs table has no images or the whole report page has no images/plots? Maybe a screenshot? :)

[azazellochg]

@pconesa if I use a default browser (Konqueror) on a remote host then I have no plots/images at all - I guess JS is not enabled/working there. But in Firefox/Chrome all is ok. However, I think @tarhil has a different issue here..