Hi,

Does the folder readcounts exist? If so, can you write into it? (can you create a text file under that folder?)

If so, perhaps featureCounts does not accept a path file name, but only file name, although I think it does.

Test if you can create a file under the directory readcounts (assuming that this folder exists), which you can do in linux by (otherwise create it by saving a dummy text file under this folder):

touch readcounts/fake_empty_file.txt

Check if it was created, if it was, try to run the program without giving the folder.

I hope this helps,

António

Problem may be with this

bam files/-.bam 

Is that a directory with a space in the name bam files? That is bad practice. Also -.bam is not how you include all BAM files. Wild card use would be *.bam. You may need to escape the space so try bam\ files/*.bam or ideally change the name of directory and do bam_files/*.bam.