This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Unable to perform merging through cuffmerge

Can anybody how to overcome this error in Cuffmerge

command = 

cuffmerge -g /mnt/c/Data/Week4/gencommand_proj4/athal_genes.gtf -p 8 -s /mnt/c/Data/Week4/gencommand_proj4/athal_chr.fa assembly.txt
assembly.txt = /mnt/c/Data/Week4/gencommand_proj4/Day8/transcripts.gtf
                        /mnt/c/Data/Week4/gencommand_proj4/Day16/transcripts.gtf

[Fri Apr 17 13:24:22 2020] Preparing output location ./merged_asm/
Traceback (most recent call last):
  File "/usr/bin/cuffmerge", line 580, in <module>
    sys.exit(main())
  File "/usr/bin/cuffmerge", line 538, in main
    gtf_input_files = test_input_files(transfrag_list_file)
  File "/usr/bin/cuffmerge", line 268, in test_input_files
    g = open(line,"r")
IOError: [Errno 2] No such file or directory: '/mnt/c/Data/Week4/gencommand_proj4/Day8/transcripts.gtf

I would be very thankful

rna-seq
• 2,277 views • link
written by rajat.pruthi4 • rajat.pruthi4

This should be a "question", not a tutorial, but to give you a quick answer, it looks like your /mnt/c/Data/Week4/gencommand_proj4/Day8/transcripts.gtf is missing or that the path is incorrect.

• 0 views • link
written by Carlo Yague Carlo Yague

Are you working on Windows Subsystem for Linux? That might add a layer of complications.

• 0 views • link
written by Ram Ram

Then try the command head /mnt/c/Data/Week4/gencommand_proj4/Day8/transcripts.gtf in terminal. Does it work ?

• 0 views • link
written by Carlo Yague Carlo Yague

no it did not worked, can you provide me answer because i am just a beginner

• 0 views • link
written by rajat.pruthi4 • rajat.pruthi4

I see three possibilities: the file does not exist, the file exists but the path is wrong, or you do not have the permissions to access the file (although I think the error message would have been different in that last case). To make sure that the path is correct, try to navigate step by step from your home directory using ls. Like this:

ls /mnt
ls /mnt/c
ls /mnt/c/Data
ls /mnt/c/Data/Week4
...
• 0 views • link
written by Carlo Yague Carlo Yague

0 answers

No answers yet.

Log in to answer this question.

More posts like this