ERROR, output directory my.out/my.out.20 already exists. Delete it or use -f to overwrite it.

[ZeweiSong]

I've spplit the sequence into 20 using ssu-prep
But when I run

ssu-align --merge 20 my.out/my.out.fa.20 my.out/my.out.20

I got the above error, did I miss anything?

I can run with the -f option, but I think that will overwrite the 20th folder, right?

[nawrockie]

@ZeweiSong : if the 20th folder already exists, then it seems like ssu-align already ran and created it, but if you ran it with --merge it should have also performed the merge. So I'm not sure what happened, but if you provide the ssu-prep command that might be helpful towards figuring out what went wrong.

[ZeweiSong]

@nawrockie I followed the User manual:

ssu-prep my.fa my 20 my_script.txt

I've got 20 splitted files, but since the qsub scripts can not run, I ran ssu-align manually on each one, and got 20 folders.

[nawrockie]

Ok, did you run them sequentially or in parallel? If sequentially, the -y option should be used with ssu-prep. If in parallel, the -x option should be used with ssu-prep. Pages 31 and 32 of the user guide provide more detail. The fact that you had 'qsub' in your script means that you did not use -x or -y.

But since you already ran the ssu-align jobs manually: if you ran them sequentially (and not in parallel), the 20th run should have merged them together. If that did not happen, please send me the output in my.out/my.out.20.ssu-align.log and my.out/my.out.20.ssu-align.sum files.

If you ran them in parallel, that may explain why they were not merged.

In any case, if you rerun
ssu-align --merge 20 my.out/my.out.fa.20 my.out/my.out.20
it will redo the 20th ssu-align call and should then merge the output, provided that the other 19 ssu-align runs finished without errors.