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 When I sudo apt-get install cuffmerge, I get a very outdated version, so this is my fix, which has worked with cufflinks (./cufflinks ..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.
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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
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pedereri •
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'
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.
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Alex Reynolds
....Wow, ok thanks, I would have never seen that.
I just ran it and it worked
Cheers
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pedereri •
It's not working. Can you please type the exact command which you have used.
Thank you
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anjyou.80 •
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I guess I should say I am using cufflinks-2.2.1.Linux_x86_64 on linux mint 17