CTF estimation job fails

CTF Estimation
1

Dear All, I am having this issue:

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 238, in run_ctf_estimation
pool.map(work, selected_exposure_idxs)
File “/gpfs/data/marino_j/cryosparc/v2/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/multiprocessing/pool.py”, line 253, in map
return self.map_async(func, iterable, chunksize).get()
File “/gpfs/data/marino_j/cryosparc/v2/cryosparc/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

I checked and the file pool.py is there, and line 572 indeed contains the raise self._value

I do not really understand what the problem is. I am afraid that my installation got corrupted at some point.

Thank you and best wishes
Jacopo

1 Like
2

It seems like cryosparc cannot find one of your input files. Perhaps double check that the import of your micrographs all went fine?

3

Dear Oli,
thank you, but unfortunately it’s not that. The Import Job finishes correctly. What is more, if I go to a previous project, and I clone the CTF job that once ended correctly, and I now restart it, it gives me the same error. So it’s something related to software and not data, as far as I can see.

Any suggestion is greatly appreciated! I am at the moment unable to use cryosparc :frowning:

best wishes,
Jacopo

4

Hi @marino-j,

Can you please check this post: CTFFind4 jobs fail

If that doesn’t work, you can opt to reinstall cryoSPARC: https://cryosparc.com/docs/reference/install/#forced-update

1 Like
5

A forced update worked for me!

6

Hi all, and thank you for your help. A forced update did not work for me, I get the same error.

Thank you
Jacopo

7

Hi @marino-j,

Can you post your error? Also, did you check this post: CTFFind4 jobs fail?

8

Dear sarulthasan,
thank you for your help. Here is the error:
Traceback (most recent call last):
File “cryosparc2_compute/jobs/ctf/run.py”, line 180, 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 291, 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 “/gpfs/data/marino_j/cryosparc/v2/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/subprocess.py”, line 394, in init
errread, errwrite)
File “/gpfs/data/marino_j/cryosparc/v2/cryosparc/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

On the note, I must say that any other job, including manually curate exposures and 2D classification on this dataset works well. The CTF job was done before I got this error. But I get this error on any other dataset I have.

I checked the link you sent me, but I could not find any advice on what I could do, other than forcing an update. I think I could reinstall the worker. Where do I find the instructions on how to delete the worker installation, and reinstall?
Thank you and best wishes,
Jacopo

9

Dear All,

sorry to keep asking about this issue, but I find interesting that also GCTF fails, despite the fact that no error is reported. Here is the output:

Importing job module for job type ctf_estimation_gctf…

Job ready to run

Wrap of Gctf_v1.06

Zhang, K. (2016). Gctf : Real-time CTF determination and correction. Journal of Structural Biology, 193(1), 1-12. https://doi.org/10.1016/j.jsb.2015.11.003

Using files in wildcard path /gpfs/group/LBR/p007/Jacopo/011118/part1/P14/J10/motioncorrected/FoilHole_9180*.mrc

Writing /gpfs/group/LBR/p007/Jacopo/011118/part1/P14/J10/input_ctfstar.star

Gctf command: /gpfs/data/marino_j/cryosparc/v2/cryosparc/cryosparc2_worker/deps/external/gctf-1.06/bin/Gctf-v1.06_sm_20_cu5.0_x86_64 --apix 0.854 --kV 300.0 --Cs 2.7 --ac 0.1 --ctfstar /gpfs/group/LBR/p007/Jacopo/011118/part1/P14/J10/micrographs_all_gctf.star --input_ctfstar /gpfs/group/LBR/p007/Jacopo/011118/part1/P14/J10/input_ctfstar.star --gid 0 --boxsize 1024 --boxsuffix _automatch.star --logsuffix _gctf.log

ERROR [Errno 2] No such file or directory

exposure_blobpath_to_dsetidx_d {u’J10/motioncorrected/FoilHole_918071_Data_922094_922095_20181101_1715-8456_rigid_aligned.mrc’: 42, u’J10/motioncorrected/FoilHole_918063_Data_922111_922112_20181101_1648-8420_rigid_aligned.mrc’: 6, u’J10/motioncorrected/FoilHole_918080_Data_922111_922112_20181101_1743-8498_rigid_aligned.mrc’: 84, u’J10/motioncorrected/FoilHole_918084_Data_922122_922123_20181101_1755-8515_rigid_aligned.mrc’: 105, u’J10/motioncorrected/FoilHole_918070_Data_921860_921861_20181101_1711-8449_rigid_aligned.mrc’: 36, u’J10/motioncorrected/FoilHole_918065_Data_922111_922112_20181101_1655-8430_rigid_aligned.mrc’: 16, u’J10/motioncorrected/FoilHole_918068_Data_921860_921861_20181101_1705-8439_rigid_aligned.mrc’: 26, u’J10/motioncorrected/FoilHole_918079_Data_922111_922112_20181101_1740-8493_rigid_aligned.mrc’: 79, u’J10/motioncorrected/FoilHole_918062_Data_922122_922123_20181101_1601-8413_rigid_aligned.mrc’: 2, u’J10/motioncorrected/FoilHole_918081_Data_922122_922123_20181101_1745-8500_rigid_aligned.mrc’: 90, u’J10/motioncorrected/FoilHole_918075_Data_922122_922123_20181101_1728-8475_rigid_aligned.mrc’: 65, u’J10/motioncorrected/FoilHole_918074_Data_922094_922095_20181101_1725-8471_rigid_aligned.mrc’: 57, u’J10/motioncorrected/FoilHole_918078_Data_922111_922112_20181101_1737-8488_rigid_aligned.mrc’: 74, u’J10/motioncorrected/FoilHole_918065_Data_922102_922103_20181101_1655-8429_rigid_aligned.mrc’: 15, u’J10/motioncorrected/FoilHole_918073_Data_922102_922103_20181101_1722-8467_rigid_aligned.mrc’: 53, u’J10/motioncorrected/FoilHole_918069_Data_922111_922112_20181101_1710-8448_rigid_aligned.mrc’: 34, u’J10/motioncorrected/FoilHole_918072_Data_922111_922112_20181101_1720-8463_rigid_aligned.mrc’: 49, u’J10/motioncorrected/FoilHole_918078_Data_922102_922103_20181101_1737-8487_rigid_aligned.mrc’: 73, u’J10/motioncorrected/FoilHole_918071_Data_922102_922103_20181101_1716-8457_rigid_aligned.mrc’: 43, u’J10/motioncorrected/FoilHole_918083_Data_922111_922112_20181101_1753-8513_rigid_aligned.mrc’: 99, u’J10/motioncorrected/FoilHole_918065_Data_922122_922123_20181101_1654-8427_rigid_aligned.mrc’: 17, u’J10/motioncorrected/FoilHole_918062_Data_921860_921861_20181101_1601-8412_rigid_aligned.mrc’: 0, u’J10/motioncorrected/FoilHole_918083_Data_921860_921861_20181101_1751-8509_rigid_aligned.mrc’: 96, u’J10/motioncorrected/FoilHole_918073_Data_922111_922112_20181101_1723-8468_rigid_aligned.mrc’: 54, u’J10/motioncorrected/FoilHole_918068_Data_922111_922112_20181101_1706-8443_rigid_aligned.mrc’: 29, u’J10/motioncorrected/FoilHole_918063_Data_921860_921861_20181101_1647-8416_rigid_aligned.mrc’: 3, u’J10/motioncorrected/FoilHole_918079_Data_921860_921861_20181101_1739-8489_rigid_aligned.mrc’: 76, u’J10/motioncorrected/FoilHole_918082_Data_922094_922095_20181101_1749-8506_rigid_aligned.mrc’: 92, u’J10/motioncorrected/FoilHole_918070_Data_922111_922112_20181101_1713-8453_rigid_aligned.mrc’: 39, u’J10/motioncorrected/FoilHole_918072_Data_921860_921861_20181101_1718-8459_rigid_aligned.mrc’: 46, u’J10/motioncorrected/FoilHole_918079_Data_922122_922123_20181101_1739-8490_rigid_aligned.mrc’: 80, u’J10/motioncorrected/FoilHole_918071_Data_922122_922123_20181101_1715-8455_rigid_aligned.mrc’: 45, u’J10/motioncorrected/FoilHole_918079_Data_922102_922103_20181101_1740-8492_rigid_aligned.mrc’: 78, u’J10/motioncorrected/FoilHole_918069_Data_922102_922103_20181101_1709-8447_rigid_aligned.mrc’: 33, u’J10/motioncorrected/FoilHole_918070_Data_922094_922095_20181101_1712-8451_rigid_aligned.mrc’: 37, u’J10/motioncorrected/FoilHole_918070_Data_922122_922123_20181101_1712-8450_rigid_aligned.mrc’: 40, u’J10/motioncorrected/FoilHole_918067_Data_922094_922095_20181101_1702-8436_rigid_aligned.mrc’: 22, u’J10/motioncorrected/FoilHole_918080_Data_922122_922123_20181101_1742-8495_rigid_aligned.mrc’: 85, u’J10/motioncorrected/FoilHole_918068_Data_922122_922123_20181101_1705-8440_rigid_aligned.mrc’: 30, u’J10/motioncorrected/FoilHole_918067_Data_922122_922123_20181101_1702-8435_rigid_aligned.mrc’: 25, u’J10/motioncorrected/FoilHole_918082_Data_921860_921861_20181101_1748-8504_rigid_aligned.mrc’: 91, u’J10/motioncorrected/FoilHole_918072_Data_922122_922123_20181101_1719-8460_rigid_aligned.mrc’: 50, u’J10/motioncorrected/FoilHole_918074_Data_922122_922123_20181101_1725-8470_rigid_aligned.mrc’: 60, u’J10/motioncorrected/FoilHole_918066_Data_922094_922095_20181101_1658-8433_rigid_aligned.mrc’: 19, u’J10/motioncorrected/FoilHole_918078_Data_922094_922095_20181101_1736-8486_rigid_aligned.mrc’: 72, u’J10/motioncorrected/FoilHole_918062_Data_922094_922095_20181101_1601-8414_rigid_aligned.mrc’: 1, u’J10/motioncorrected/FoilHole_918073_Data_921860_921861_20181101_1721-8464_rigid_aligned.mrc’: 51, u’J10/motioncorrected/FoilHole_918068_Data_922102_922103_20181101_1706-8442_rigid_aligned.mrc’: 28, u’J10/motioncorrected/FoilHole_918075_Data_922094_922095_20181101_1729-8476_rigid_aligned.mrc’: 62, u’J10/motioncorrected/FoilHole_918085_Data_921860_921861_20181101_1757-8519_rigid_aligned.mrc’: 106, u’J10/motioncorrected/FoilHole_918084_Data_922111_922112_20181101_1756-8518_rigid_aligned.mrc’: 104, u’J10/motioncorrected/FoilHole_918073_Data_922122_922123_20181101_1722-8465_rigid_aligned.mrc’: 55, u’J10/motioncorrected/FoilHole_918083_Data_922094_922095_20181101_1752-8511_rigid_aligned.mrc’: 97, u’J10/motioncorrected/FoilHole_918075_Data_922102_922103_20181101_1729-8477_rigid_aligned.mrc’: 63, u’J10/motioncorrected/FoilHole_918068_Data_922094_922095_20181101_1705-8441_rigid_aligned.mrc’: 27, u’J10/motioncorrected/FoilHole_918081_Data_921860_921861_20181101_1745-8499_rigid_aligned.mrc’: 86, u’J10/motioncorrected/FoilHole_918082_Data_922102_922103_20181101_1749-8507_rigid_aligned.mrc’: 93, u’J10/motioncorrected/FoilHole_918085_Data_922094_922095_20181101_1758-8521_rigid_aligned.mrc’: 107, u’J10/motioncorrected/FoilHole_918064_Data_922102_922103_20181101_1651-8424_rigid_aligned.mrc’: 10, u’J10/motioncorrected/FoilHole_918076_Data_921860_921861_20181101_1732-8479_rigid_aligned.mrc’: 66, u’J10/motioncorrected/FoilHole_918064_Data_921860_921861_20181101_1650-8421_rigid_aligned.mrc’: 8, u’J10/motioncorrected/FoilHole_918071_Data_921860_921861_20181101_1715-8454_rigid_aligned.mrc’: 41, u’J10/motioncorrected/FoilHole_918066_Data_922122_922123_20181101_1658-8432_rigid_aligned.mrc’: 20, u’J10/motioncorrected/FoilHole_918072_Data_922094_922095_20181101_1719-8461_rigid_aligned.mrc’: 47, u’J10/motioncorrected/FoilHole_918082_Data_922111_922112_20181101_1749-8508_rigid_aligned.mrc’: 94, u’J10/motioncorrected/FoilHole_918075_Data_922111_922112_20181101_1730-8478_rigid_aligned.mrc’: 64, u’J10/motioncorrected/FoilHole_918067_Data_922111_922112_20181101_1703-8438_rigid_aligned.mrc’: 24, u’J10/motioncorrected/FoilHole_918067_Data_921860_921861_20181101_1701-8434_rigid_aligned.mrc’: 21, u’J10/motioncorrected/FoilHole_918063_Data_922102_922103_20181101_1648-8419_rigid_aligned.mrc’: 5, u’J10/motioncorrected/FoilHole_918080_Data_922102_922103_20181101_1743-8497_rigid_aligned.mrc’: 83, u’J10/motioncorrected/FoilHole_918082_Data_922122_922123_20181101_1748-8505_rigid_aligned.mrc’: 95, u’J10/motioncorrected/FoilHole_918074_Data_922102_922103_20181101_1726-8472_rigid_aligned.mrc’: 58, u’J10/motioncorrected/FoilHole_918073_Data_922094_922095_20181101_1722-8466_rigid_aligned.mrc’: 52, u’J10/motioncorrected/FoilHole_918065_Data_922094_922095_20181101_1654-8428_rigid_aligned.mrc’: 14, u’J10/motioncorrected/FoilHole_918074_Data_922111_922112_20181101_1726-8473_rigid_aligned.mrc’: 59, u’J10/motioncorrected/FoilHole_918072_Data_922102_922103_20181101_1719-8462_rigid_aligned.mrc’: 48, u’J10/motioncorrected/FoilHole_918064_Data_922094_922095_20181101_1651-8423_rigid_aligned.mrc’: 9, u’J10/motioncorrected/FoilHole_918076_Data_922111_922112_20181101_1733-8483_rigid_aligned.mrc’: 69, u’J10/motioncorrected/FoilHole_918069_Data_922094_922095_20181101_1709-8446_rigid_aligned.mrc’: 32, u’J10/motioncorrected/FoilHole_918083_Data_922102_922103_20181101_1752-8512_rigid_aligned.mrc’: 98, u’J10/motioncorrected/FoilHole_918081_Data_922111_922112_20181101_1746-8503_rigid_aligned.mrc’: 89, u’J10/motioncorrected/FoilHole_918074_Data_921860_921861_20181101_1725-8469_rigid_aligned.mrc’: 56, u’J10/motioncorrected/FoilHole_918084_Data_922094_922095_20181101_1755-8516_rigid_aligned.mrc’: 102, u’J10/motioncorrected/FoilHole_918079_Data_922094_922095_20181101_1739-8491_rigid_aligned.mrc’: 77, u’J10/motioncorrected/FoilHole_918064_Data_922122_922123_20181101_1650-8422_rigid_aligned.mrc’: 12, u’J10/motioncorrected/FoilHole_918075_Data_921860_921861_20181101_1728-8474_rigid_aligned.mrc’: 61, u’J10/motioncorrected/FoilHole_918064_Data_922111_922112_20181101_1652-8425_rigid_aligned.mrc’: 11, u’J10/motioncorrected/FoilHole_918067_Data_922102_922103_20181101_1702-8437_rigid_aligned.mrc’: 23, u’J10/motioncorrected/FoilHole_918078_Data_921860_921861_20181101_1736-8484_rigid_aligned.mrc’: 71, u’J10/motioncorrected/FoilHole_918081_Data_922094_922095_20181101_1746-8501_rigid_aligned.mrc’: 87, u’J10/motioncorrected/FoilHole_918078_Data_922122_922123_20181101_1736-8485_rigid_aligned.mrc’: 75, u’J10/motioncorrected/FoilHole_918084_Data_922102_922103_20181101_1755-8517_rigid_aligned.mrc’: 103, u’J10/motioncorrected/FoilHole_918066_Data_921860_921861_20181101_1657-8431_rigid_aligned.mrc’: 18, u’J10/motioncorrected/FoilHole_918063_Data_922122_922123_20181101_1647-8417_rigid_aligned.mrc’: 7, u’J10/motioncorrected/FoilHole_918069_Data_922122_922123_20181101_1709-8445_rigid_aligned.mrc’: 35, u’J10/motioncorrected/FoilHole_918085_Data_922102_922103_20181101_1758-8522_rigid_aligned.mrc’: 108, u’J10/motioncorrected/FoilHole_918084_Data_921860_921861_20181101_1754-8514_rigid_aligned.mrc’: 101, u’J10/motioncorrected/FoilHole_918085_Data_922111_922112_20181101_1759-8523_rigid_aligned.mrc’: 109, u’J10/motioncorrected/FoilHole_918085_Data_922122_922123_20181101_1758-8520_rigid_aligned.mrc’: 110, u’J10/motioncorrected/FoilHole_918071_Data_922111_922112_20181101_1716-8458_rigid_aligned.mrc’: 44, u’J10/motioncorrected/FoilHole_918080_Data_921860_921861_20181101_1742-8494_rigid_aligned.mrc’: 81, u’J10/motioncorrected/FoilHole_918063_Data_922094_922095_20181101_1648-8418_rigid_aligned.mrc’: 4, u’J10/motioncorrected/FoilHole_918076_Data_922094_922095_20181101_1732-8481_rigid_aligned.mrc’: 67, u’J10/motioncorrected/FoilHole_918080_Data_922094_922095_20181101_1743-8496_rigid_aligned.mrc’: 82, u’J10/motioncorrected/FoilHole_918081_Data_922102_922103_20181101_1746-8502_rigid_aligned.mrc’: 88, u’J10/motioncorrected/FoilHole_918069_Data_921860_921861_20181101_1708-8444_rigid_aligned.mrc’: 31, u’J10/motioncorrected/FoilHole_918070_Data_922102_922103_20181101_1713-8452_rigid_aligned.mrc’: 38, u’J10/motioncorrected/FoilHole_918076_Data_922122_922123_20181101_1732-8480_rigid_aligned.mrc’: 70, u’J10/motioncorrected/FoilHole_918065_Data_921860_921861_20181101_1654-8426_rigid_aligned.mrc’: 13, u’J10/motioncorrected/FoilHole_918076_Data_922102_922103_20181101_1733-8482_rigid_aligned.mrc’: 68, u’J10/motioncorrected/FoilHole_918083_Data_922122_922123_20181101_1752-8510_rigid_aligned.mrc’: 100}

initial fail_idx_set set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110])

ERROR: Gctf failed: [’/gpfs/data/marino_j/cryosparc/v2/cryosparc/cryosparc2_worker/deps/external/gctf-1.06/bin/Gctf-v1.06_sm_20_cu5.0_x86_64’, ‘–apix’, ‘0.854’, ‘–kV’, ‘300.0’, ‘–Cs’, ‘2.7’, ‘–ac’, ‘0.1’, ‘–ctfstar’, ‘/gpfs/group/LBR/p007/Jacopo/011118/part1/P14/J10/micrographs_all_gctf.star’, ‘–input_ctfstar’, ‘/gpfs/group/LBR/p007/Jacopo/011118/part1/P14/J10/input_ctfstar.star’, ‘–gid’, ‘0’, ‘–boxsize’, ‘1024’, ‘–boxsuffix’, ‘_automatch.star’, ‘–logsuffix’, ‘_gctf.log’]

ERROR: 111 exposures failed: [’/gpfs/data/marino_j/cryosparc/v2/cryosparc/cryosparc2_worker/deps/external/gctf-1.06/bin/Gctf-v1.06_sm_20_cu5.0_x86_64’, ‘–apix’, ‘0.854’, ‘–kV’, ‘300.0’, ‘–Cs’, ‘2.7’, ‘–ac’, ‘0.1’, ‘–ctfstar’, ‘/gpfs/group/LBR/p007/Jacopo/011118/part1/P14/J10/micrographs_all_gctf.star’, ‘–input_ctfstar’, ‘/gpfs/group/LBR/p007/Jacopo/011118/part1/P14/J10/input_ctfstar.star’, ‘–gid’, ‘0’, ‘–boxsize’, ‘1024’, ‘–boxsuffix’, ‘_automatch.star’, ‘–logsuffix’, ‘_gctf.log’]

Completed CTF Estimation using Gctf

Zhang, K. (2016). Gctf : Real-time CTF determination and correction. Journal of Structural Biology, 193(1), 1-12. https://doi.org/10.1016/j.jsb.2015.11.003

Compiling job outputs…

Passing through outputs for output group exposures_success from input group exposures

This job outputted results [‘ctf’, ‘ctf_plotdata’]

Loaded output dset with 0 items

Passthrough results [‘movie_blob’, ‘micrograph_blob_non_dw’, ‘micrograph_blob’, ‘mscope_params’, ‘background_blob’, ‘rigid_motion’, ‘gain_ref_blob’]

Loaded passthrough dset with 111 items

Intersection of output and passthrough has 0 items

Passing through outputs for output group exposures_fail from input group exposures

This job outputted results [‘ctf’, ‘ctf_plotdata’]

Loaded output dset with 111 items

Passthrough results [‘movie_blob’, ‘micrograph_blob_non_dw’, ‘micrograph_blob’, ‘mscope_params’, ‘background_blob’, ‘rigid_motion’, ‘gain_ref_blob’]

Loaded passthrough dset with 111 items

Intersection of output and passthrough has 111 items

Passing through outputs for output group particles_success from input group particles

This job outputted results [‘ctf’]

Loaded output dset with 0 items

Passthrough results []

Passing through outputs for output group particles_fail from input group particles

This job outputted results [‘ctf’]

Loaded output dset with 0 items

Passthrough results []

Checking outputs for output group exposures_success

Checking outputs for output group exposures_fail

Checking outputs for output group particles_success

Checking outputs for output group particles_fail

Job complete. Total time 0.68s

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Dear Jacopo @marino-j ,

I just deleted the worker folder, and reinstalled it like this:

INSTP=< cryoSPARC install path here>

cryosparcm stop
rm -rf cryosparc2_worker

LICENSE_ID=
PORT=
USER_NAME=""
USER_EMAIL=""
USER_PASS=""

cd $INSTP

curl -L https://get.cryosparc.com/download/worker-latest/$LICENSE_ID > cryosparc2_worker.tar.gz
tar -xf cryosparc2_worker.tar.gz

Then connect the worker to cluster, if you are using one.

Best wishes,
Valtteri

P.S. as always when using “rm -rf” command in linux, pay attention to write the folder name correctly as it is a very powerful command.

13

Another question is: to re-install the CTFfind and GCTF, one would need to reinstall the worker only, or the master is also needed?

Thank you

14

Only the worker needs to be reinstalled for compute dependencies (CUDA, CTFFIND, GCTF, etc.)

15

Dear Ali, thank you for your answer.
I have now deleted my installation and reinstalled it, and it works well.

Thank you all for your help!
Jacopo

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