cannot locate input file: –r [likely solution]

[bassanio]

Error while executing the below command

gffcompare -R –r Reference.gtf –o merged stringtie_merged.gtf
Error: cannot locate input file: –r

Reference.gtf is available in the same folder with full permission

Version: gffcompare v0.9.7

[afkoeppel]

I had this same issue initially but it turned out it was because I had copied & pasted the command from an example on a website. The "-" were in a different text format. I deleted the "-" (in -r and -o etc.) and replaced them with my own dashes and then it worked.

[gpertea]

Wow - thank you so much for taking the time to provide a (possible and very likely) explanation for that puzzling behavior! I've never been able to reproduce the problem that the original poster had, but this makes a lot of sense now. I guess I could close this issue but perhaps it's better served if I leave it open so other users stumbling into the same problem might see it if they come here to post.
Thanks again!

[aWormGuy]

I had the same issue and the tip from afkoeppel solved my problem too! I had originally copy-pasted the command from the page 1659 in the pdf version of Pertea et al. 2016 Nature 2016!

[ehhill]

I've just had the same issue, but changing the dashes and writing the command from scratch yield the same error. I've tried with all files in the working directory and specifying paths etc.

Error: cannot locate input file: Chromosome_01 StringTie transcript 2312 2610 1000 - gene_id "CS10_MSTRG.1"; transcript_id "CS10_MSTRG.1.1";

Would you have any idea on what's causing this?

Thanks!

[mycecilia]

I'm having the same problem as ehhill. It looks like the input file triggered a bug.

[gpertea]

I realized I ignored ehhill's error because it really looked like a basic user error in which the -i option was somehow misused.. Clearly the -i option should be immediately followed by the name of a text file which contains the list of GTF files to analyze. The error reported by ehhill suggested that -i was followed by the name of a GTF file instead.
What was your exact command line which gave you that "same problem" like ehhill ? Also, what is the content of the file given with the -i option? Make sure that's just a list of files in there, not directly GTF lines.. (in the latter case it's likely that the command used to build that file might be the problem, perhaps concatenating the content of those GTF files instead of simply listing their names..).

[gpertea]

OK, maybe I jumped the gun here assuming that you (and ehhill) used the -i option when perhaps you didn't. In any case, I need details about the exact command line used and the exact error message you received.