Unable to perform merging through cuffmerge

Question

[rajat.pruthi4]

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

[Carlo Yague]

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.

[rajat.pruthi4]

but the files are in this path

[Ram]

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

[Carlo Yague]

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

[rajat.pruthi4]

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

[Carlo Yague]

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
...

[rajat.pruthi4]

its saying no such directory

[Fatima]

in the directory with transcripts.gtf you can use the command pwd to get the path to that directory.

https://www.redhat.com/sysadmin/basic-linux-commands

[rajat.pruthi4]

yes sir i am using window subsytem for linux