We seem to be having a similar issue with v2.6.4 the ctffind job fails using the test dataset but complains that some file can’t be found?
Processed 0 of 20 micrographs in 0.06s
=== Running CTFFIND for micrograph 000001 ( J2/motioncorrected/14sep05c_00024sq_00003hl_00005es.frames_rigid_aligned.mrc )
Running thread Thread-1…
=== Running CTFFIND for micrograph 000000 ( J2/motioncorrected/14sep05c_00024sq_00003hl_00002es.frames_rigid_aligned.mrc )
Running thread Thread-2…
=== Running CTFFIND for micrograph 000002 ( J2/motioncorrected/14sep05c_00024sq_00004hl_00002es.frames_rigid_aligned.mrc )
Running thread Thread-3…
=== Running CTFFIND for micrograph 000004 ( J2/motioncorrected/14sep05c_c_00003gr_00014sq_00002hl_00005es.frames_rigid_aligned.mrc )
Running thread Thread-5…
=== Running CTFFIND for micrograph 000003 ( J2/motioncorrected/14sep05c_00024sq_00006hl_00003es.frames_rigid_aligned.mrc )
Running thread Thread-4…
=== Running CTFFIND for micrograph 000006 ( J2/motioncorrected/14sep05c_c_00003gr_00014sq_00005hl_00002es.frames_rigid_aligned.mrc )
Running thread Thread-7…
=== Running CTFFIND for micrograph 000005 ( J2/motioncorrected/14sep05c_c_00003gr_00014sq_00004hl_00004es.frames_rigid_aligned.mrc )
Running thread Thread-6…
=== Running CTFFIND for micrograph 000007 ( J2/motioncorrected/14sep05c_c_00003gr_00014sq_00005hl_00003es.frames_rigid_aligned.mrc )
Running thread Thread-8…
Traceback (most recent call last):
File “cryosparc2_compute/jobs/ctf/run.py”, line 173, in work
resample=params[‘resample’]
File “cryosparc2_compute/jobs/ctf/ctf_wrapper.py”, line 398, in run_ctf_wrapper
**kwargs)
File “cryosparc2_compute/jobs/ctf/ctf_wrapper.py”, line 375, in run_ctffind
proc = rc.start_external_process([ctffind_bin_path_abs], log_path_abs) # starts and registers subprocess
File “cryosparc2_compute/jobs/runcommon.py”, line 671, in start_external_process
process = com.start_external_process(command, log_file_path)
File “cryosparc2_compute/jobs/common.py”, line 200, in start_external_process
close_fds = True ) # NOTES close_fds is critical! otherwise child process will keep the webserver’s sockets open and cause all kinds of problems!
File “/home/cryosparc_user/cryosparc2_worker/deps/anaconda/lib/python2.7/subprocess.py”, line 394, in init
errread, errwrite)
File “/home/cryosparc_user/cryosparc2_worker/deps/anaconda/lib/python2.7/subprocess.py”, line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
=== Running CTFFIND for micrograph 000008 ( J2/motioncorrected/14sep05c_c_00003gr_00014sq_00005hl_00005es.frames_rigid_aligned.mrc )
Running thread Thread-3…
Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/ctf/run.py”, line 231, in run_ctf_estimation
pool.map(work, selected_exposure_idxs)
File “/home/cryosparc_user/cryosparc2_worker/deps/anaconda/lib/python2.7/multiprocessing/pool.py”, line 253, in map
return self.map_async(func, iterable, chunksize).get()
File “/home/cryosparc_user/cryosparc2_worker/deps/anaconda/lib/python2.7/multiprocessing/pool.py”, line 572, in get
raise self._value
OSError: [Errno 2] No such file or directory
all the logs are 0b files; but the ctffind bins are in the correct path:
[cryosparc_user@gpu1 root]$ ls /home/cryosparc_user/cryosparc2_worker/deps/ext/ctffind/bin -lah
total 28M
drwxr-xr-x 2 root root 52 Dec 13 09:35 .
drwxrwxr-x 4 cryosparc_user cryosparc_user 55 Dec 13 09:35 …
-rwxr-xr-x 1 cryosparc_user cryosparc_user 28M Jun 7 2017 ctffind
-rwxr-xr-x 1 cryosparc_user cryosparc_user 4.9K Jun 7 2017 ctffind_plot_results.sh