Question: cuffmerge error: IOError: [Errno 2] No such file or directory: '\xe2\x80\x93g'
0
gravatar for pedereri
3.9 years ago by
pedereri0
Sweden/Uppsala/UU
pedereri0 wrote:

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 When I sudo apt-get install cuffmerge, I get a very outdated version, so this is my fix, which has worked with cufflinks (./cufflinks ....).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.

 

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by pedereri0

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

ADD REPLYlink written 3.9 years ago by pedereri0

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

ADD REPLYlink written 3.9 years ago by pedereri0

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'

ADD REPLYlink written 3.9 years ago by Cytosine440

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

I just ran it and it worked

Cheers

ADD REPLYlink written 3.9 years ago by pedereri0

it's not working .. can you please type the exact command which you have used .

Thank you

ADD REPLYlink written 3.4 years ago by anjyou.800
0
gravatar for Cytosine
3.9 years ago by
Cytosine440
Ljubljana, Slovenia
Cytosine440 wrote:

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

ADD COMMENTlink written 3.9 years ago by Cytosine440

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'

ADD REPLYlink written 3.4 years ago by anjyou.800
0
gravatar for Alex Reynolds
3.9 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

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, in bold:

$ ./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.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Alex Reynolds28k
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