Trim galore error - directory completely empty

Question

[x]

I'm trying to run trim galore on multiple files (24), but I haven't gotten it to work. The code I'm using is:

 trim_galore /home/name/sequences -j 4 *.fastq.gz -o /home/name --paired

The last message produced is:

Output will be written into the directory: /home/name/
Input file '/home/name/sequences' seems to be completely empty. Consider respecifying!

I know for sure the folder is not empty. All the files are zipped (.fastq.gz). I made a separate folder with unzipped files (.fastq), and it's the same result. I've moved the position of --paired, because I saw somewhere it might work, but it didn't.

I'm running Linux Ubuntu on my Windows computer.

[Ram]

What is the output to file /home/name/sequences?

[x]

-bash: /home/name/sequences: Is a directory

Answer 1

[GenoMax]

I am not a trim galore user but I don't think you can provide trimgalore with a directory name like you did. Based on the usage statement trimgalore is expecting options to follow the program name with input files at the end of the command.

Can you try the following

trim_galore  -j 4 -o /home/name/ --paired /home/name/sequences/*.fastq.gz 

[x]

This seems to be working. Thanks!