Relion3 ami gives error running CTFFIND4

234 views

Skip to first unread message

Rick Baker

unread,

Sep 12, 2018, 1:40:07 PM9/12/18

to Cryo-EM in the cloud

Hi Mike,

thanks for making a Relion3 install on AWS.

I was running it just now and I got an error when I tried to run CTFFIND4. Gctf ran fine, however, so I didn't investigate too thoroughly.

Thanks!

Rick

sh: 1: csh: not found

WARNING: there was an error in executing: csh CtfFind/job003/Movies/18sep11b_grid_00014gr_00004sq_00005hl_00002en_frames_ctffind4.com

sh: 1: csh: not found

WARNING: there was an error in executing: csh CtfFind/job003/Movies/18sep11b_grid_00008gr_00005sq_00005hl_00001en_frames_ctffind4.com

WARNING: there was an error in executing: csh CtfFind/job003/Movies/18sep11b_grid_00008gr_00005sq_00008hl_00001en_frames_ctffind4.com

sh: 1: csh: not found

WARNING: there was an error in executing: csh CtfFind/job003/Movies/18sep11b_grid_00008gr_00005sq_00004hl_00002en_frames_ctffind4.com

sh: 1: csh: not found

WARNING: there was an error in executing: csh CtfFind/job003/Movies/18sep11b_grid_00008gr_00005sq_00006hl_00002en_frames_ctffind4.com

sh: 1: csh: not found

WARNING: there was an error in executing: csh CtfFind/job003/Movies/18sep11b_grid_00008gr_00005sq_00010hl_00001en_frames_ctffind4.com

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00014hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00008hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00005hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00014gr_00004sq_00002hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00012hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00003hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00003hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00005hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00008hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00014gr_00004sq_00004hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00014gr_00004sq_00003hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00004hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00009hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00009hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00014gr_00004sq_00005hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00007hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00010hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00010hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00007hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00009gr_00003sq_00002hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00006hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00011hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00009gr_00003sq_00005hl_00002en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00008gr_00005sq_00011hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11b_grid_00009gr_00003sq_00003hl_00001en_frames.mrc

WARNING: skipping, since cannot get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00006hl_00002en_frames.mrc

Did not find any of the expected EPS files to generate a PDF file

+ Will make an empty PDF-file in CtfFind/job003/logfile.pdf CtfFind/job003/logfile.pdft get CTF values for MotionCorr/job002/Movies/18sep11a_grid_00012gr_00007sq_00007hl_00001en_frames.mrc