Error in Deep Enhancer

Troubleshooting
#1

Hello,

I set the paths for my deep Enhancer job, but every time that I run it, I face this error:

Subprocess existed with status -11 …

Can anyone help me how I can fix this?

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#2

Please post additional messages from the Event and Job logs.

#3

I added a picture of it, thank you!

#4

Please post the text (to facilitate searches of the forum) of the error message in the picture, and text of relevant entries in the job log.

#5

double check the path(s). inside /opt/miniconda3/envs/deepEMhancer_env/lib are there three files for tightTarget, highRes, and wideTarget? do you need a slash after lib? What happens if you provide a mask and set mask type to 2 (areas outside mask set to 0)? This will ignore the 3 “types” of mask generation above.

#6

Thank you!
I still face this error:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 93, in cryosparc_compute.run.main
File “/opt/cryosparc3/cryosparc_worker/cryosparc_compute/jobs/deepemhancer/run.py”, line 158, in run_deepemhancer_wrapper
assert process.returncode == 0, f"Subprocess exited with status {process.returncode} ({str_command})"
AssertionError: Subprocess exited with status 1 (/opt/miniconda3/envs/deepEMhancer_env/bin/deepemhancer -i /data/data_jylee/femr_202112_krios/P3/J349/map_half_A_filtered.mrc -i2 /data/data_jylee/femr_202112_krios/P3/J349/map_half_B_filtered.mrc -o /data/data_jylee/femr_202112_krios/P3/J349/J349_map_sharp.mrc -g 1 --deepLearningModelPath /home/jyleelab/Desktop/deepEMhancerModels/production_checkpoints/deepEMhancer_tightTarget.hd5 -p wideTarget)

#7

This is a new error that I get every time, I run it:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 93, in cryosparc_compute.run.main
File “/opt/cryosparc3/cryosparc_worker/cryosparc_compute/jobs/deepemhancer/run.py”, line 158, in run_deepemhancer_wrapper
assert process.returncode == 0, f"Subprocess exited with status {process.returncode} ({str_command})"
AssertionError: Subprocess exited with status 1 (/opt/miniconda3/envs/deepEMhancer_env/bin/deepemhancer -i /data/data_jylee/femr_202112_krios/P3/J349/map_half_A_filtered.mrc -i2 /data/data_jylee/femr_202112_krios/P3/J349/map_half_B_filtered.mrc -o /data/data_jylee/femr_202112_krios/P3/J349/J349_map_sharp.mrc -g 1 --deepLearningModelPath /home/jyleelab/Desktop/deepEMhancerModels/production_checkpoints/deepEMhancer_tightTarget.hd5 -p wideTarget)

#8

to be sure, are you filling out both the path to the executable AND a different path to the folder containing the 3 models? wtempel wants you to go the log of the job and post that text so they can see more information than just the error message.

#9

I filled both paths. But unfortunately still got this error. I will post the log tomorrow.

#10

Does deepEMhancer run successfully with the same parameters outside of cryoSPARC?