cuffmerge error: IOError: [Errno 2] No such file or directory: '\xe2\x80\x93g'

Question

[pedereri]

Hi

I am trying to run cuffmerge in Linux mint directly from the program script instead of installing, since I cannot figure out how to install the correct version on Linux mint (./cuffmerge .. ..). When I sudo apt-get install cuffmerge, I get a very outdated version, so this is my fix, which has worked with cufflinks (./cufflinks .. ..).

Anyways when I run cuffmerge:

./cuffmerge -o "./wtC" –g /directory/Ppatens_251_v3.0.gene.gff3 -s /directory3/ppatens3.fa merged_asm assembly_gtf_merge_C.txt

I get this error:

Beginning transcriptome assembly merge
-------------------------------------------

[date] Preparing output location ./directory/
Traceback (most recent call last):
  File "./cuffmerge", line 580, in <module>
    sys.exit(main())
  File "./cuffmerge", line 530, in main
    transfrag_list_file = open(args[0], "r")
IOError: [Errno 2] No such file or directory: '\xe2\x80\x93g'

So what I am asking is either how to fix this, or how to install the newest version of cuffmerge on linux mint, preferably the initial though.

[pedereri]

I guess I should say I am using cufflinks-2.2.1.Linux_x86_64 on linux mint 17

Answer 1

[Cytosine]

Don't use quotation marks (") when making an output folder.

[pedereri]

That doesn't seem to do anything.

I had quotation marks when I was using both Tophat and cufflinks, but I didn't get an error

[Cytosine]

Thought it was the quotations, but Alex Reynolds seems to have a good lead.

\xe2\x80\x93g is the encoding for ‒g, which may be the problem when you really want the short hyphen -g

[anjyou.80]

I am getting this error ... please suggest solution

cuffmerge ‑g gene.gtf assemblies.txt

Traceback (most recent call last):
  File "/usr/bin/cuffmerge", line 580, in <module>
    sys.exit(main())
  File "/usr/bin/cuffmerge", line 530, in main
    transfrag_list_file = open(args[0], "r")
IOError: [Errno 2] No such file or directory: '\xe2\x80\x91g'

Answer 2

[Alex Reynolds]

Here's your command:

$ ./cuffmerge -o "./wtC" –g /directory/Ppatens_251_v3.0.gene.gff3 -s /directory3/ppatens3.fa merged_asm assembly_gtf_merge_C.txt

Here's the problem, probably:

$ ./cuffmerge -o "./wtC" –g /directory/Ppatens_251_v3.0.gene.gff3 -s /directory3/ppatens3.fa merged_asm assembly_gtf_merge_C.txt
_________________________^

Try replacing that en-dash before the g with a hyphen. They look similar, but only a hyphen will likely be interpreted as an option specifier.

[pedereri]

....Wow, ok thanks, I would have never seen that.

I just ran it and it worked

Cheers

[anjyou.80]

It's not working. Can you please type the exact command which you have used.

Thank you