Hi,
I am not sure this was discussed before. I am trying to run CTF estimation on aligned images. The job runs through just until almost the end and crushes then. When I terminate the job then, I do not get any results.
There are a couple of images for which I get the error message "Error: a slave has disconnected before all jobs were finished" as was reportet by another user. Since I have a really big dataset I would not mind so much about these few errors, but I would like to get the results for the images where CTF estimation worked. How can I do this?
Ottilie
Hi Ottilie,
At the moment, I'm afraid cisTEM doesn't store results until the job is finished. That means, that if you see "a slave has disconnected before all jobs were finished" then the job will not actually finish. The found defocus values are not written out anywhere, so I'm afraid there is no way to retrieve the results.
CTFFind itself, should not crash however. If there are problem images it should just return 0, so that is a serious bug. It would be very helpful for us if you could provide us with the images that are making it crash (the images for which you don't have results). If we can figure out what is causing it to crash, we can stop this happening in the future.
It sounds like you let the job run to the end, if you look in your Assets/CTF folder there should be missing, or 0 sized files for the images that didn't get a result. If you could identify these images, and give us access to them, then that would be very helpful.
If this is not an option, you can make groups of subset of the images in the assets->images panel of the gui. If you then run the estimation on increasingly small sized groups you should be able to narrow down the problem image(s), although if you have a lot of problem images this might be a bit of a pain.
If you have identified which images are causing problems, you can delete them from the project, or create a group that does not contain them and the CTF estimation should run.
Sorry you are having the problem, I hope you'll be able to provide us with the images which are causing crashes so we can stop this from happening in the future - Thanks!
Tim
Hi Tim,
Thanks this was very useful. I did a test on a small subset and it runs through now. Can I send you the bad images via Zendto (I would need your email for this), or is there a better way?
Thanks a lot for the fast help ;)
Ottilie
Thanks! - I will email you now.
Tim