Question: cuffmerge no such file or directory
gravatar for dimitrischat
23 months ago by
dimitrischat70 wrote:

trying to run cuffmerge in mac os. when i had 2 samples it worked. when i had 16 it doesnt. it comes up with this error :

Traceback (most recent call last):
  File "/usr/local/bin/cuffmerge", line 580, in <module>
  File "/usr/local/bin/cuffmerge", line 538, in main
    gtf_input_files = test_input_files(transfrag_list_file)
  File "/usr/local/bin/cuffmerge", line 268, in test_input_files
    g = open(line,"r")
IOError: [Errno 2] No such file or directory: 's1l1transcripts.gtf'

i ran this command : cuffmerge -o /Users/.../cuffmerge/results /Users/.../cuffmerge/merged.txt

i created a folder in which i had all transcripts xxx.gtf files . A .txt file with all names of the xxx.gtf files and a results folder for the cufferge option -o. what is wrong ?

Also tried this command:cuffmerge -o /Users/.../results -p 2 -g /Users/../genes.gtf /Users/../cuffmerge/merged.txt

rna-seq • 703 views
ADD COMMENTlink modified 23 months ago by WouterDeCoster39k • written 23 months ago by dimitrischat70

Where is your file "s1l1transcripts.gtf" located? Where is cuffmerge looking for it? cuffmerge cannot locate the file. maybe an error in path specification?

ADD REPLYlink written 23 months ago by Fabio Marroni2.2k

it was correct. i retyped the name-file and it worked. no idea what was wrong. something with unicode, some character of the file name was an error...dont know

ADD REPLYlink written 23 months ago by dimitrischat70
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