I was in the middle of an ab intio refinement and got a no Heartbeat error. I decided to stop cryosparc and restart it. On restart I got the following message.
Creating Upload directory at /srv/home/johnf/cryosparc/run/bulk/.cryosparc_output_dir/cryosparc_output_data/uploads
mkdir: cannot create directory ‘/srv/home/johnf/cryosparc/run/bulk/.cryosparc_output_dir’: File exists
John
Thanks for reporting. Did you perhaps have a file in your cryosparc_output_data folder called ‘uploads’?
This error is happening because in the new version of cryoSPARC, you can directly upload volumes and masks through the web interface, so when cryosparc starts it makes sure that the uploads directory where files are stored exists.
Can you do:
cryosparc configure bulk list
And also:
ls -l /srv/home/johnf/cryosparc/run/bulk/.cryosparc_output_dir/cryosparc_output_data/
If there is an uploads folder in cryosparc_output_data, can you do:
cryosparc configure bulk add /srv/home/johnf/cryosparc/run/bulk/.cryosparc_output_dir/cryosparc_output_data/uploads uploads
Please let me know what happens.
Ali
johnf@dilbert:~$ cryosparc start
Starting cryoSPARC…
Creating Upload directory at /srv/home/johnf/cryosparc/run/bulk/.cryosparc_output_dir/cryosparc_output_data/uploads
mkdir: cannot create directory ‘/srv/home/johnf/cryosparc/run/bulk/.cryosparc_output_dir’: File exists
johnf@dilbert:~$
Hi back again. I was running cryosparc using a mask that I created in relion. It kept falling over. So I exited chrome and stopped cryosparc. When I went to restart the program it gave me that error. I then went through the series of commands that you posted previously. There was no uploads folder in cryosparc_output_data. There was however,
johnf@dilbert:~$ cryosparc configure bulk list
Bulk directory contents:
total 1
lrwxrwxrwx 1 johnf johnf 1 Feb 22 09:40 local_fs -> /
lrwxrwxrwx 1 johnf johnf 27 Feb 22 09:40 uploads -> /d3/johnf/cryoSparc/uploads
and on executing the second command (as expected since uploads was in the directory above:
johnf@dilbert:~$ ls -l /srv/home/johnf/cryosparc/run/bulk/.cryosparc_output_dir/cryosparc_output_data/
ls: cannot access /srv/home/johnf/cryosparc/run/bulk/.cryosparc_output_dir/cryosparc_output_data/: No such file or directory
johnf@dilbert:~$
Based upon that the third command was superfluous.
Of note, but perhaps irrelevant I just installed the newest version of the program today.
Cheers and thank you in advance.
John
Hi
I tracked this down. It turns out that someone rebooted the computer where this information is located. In my case cryosparc was installed on one computer the data on another and all of the files were on a third. A bit of a mess but when i remounted the correct disc it worked.
Cheers
John