Argument List too Long for cryoSPARC to Relion

Troubleshooting
1

Hi Everyone,

I am attempting to make symbolic link for 3D classification in region, but I keep getting this error.

-bash: /usr/bin/ln: Argument list too long

I’ve tried:
ln -s /directory/extract/job/.mrc .
ln -s /directory/extract/job/.mrc -t .
for file in /directory/extract/job/*.mrc; do ln -s /destination;done

Number of files: 12628
ARG_MAX: 2097152

Any help would be great.

Thanks,
Sean

2

Hi,

I think something like:

`cat list.txt | while read line; do ln -s $line .; done‘

Should work - just make a list of all your files first

3

I tried this. I cannot seem to correctly make the list.txt file. I saw your response in a post from 2020 on this.

EDIT:
dir …/…/…/director/extract/*.mrc > /target/directory/list.txt

I get this also:
-bash: /usr/bin/dir: Argument list too long

4

Nevermind, got this to work. Thank you!!!.

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