Cuffmerge cannot find transcripts.gtf files

Question

[calubr]

Hi Everyone, I'm new to RNAseq and I'm trying to run cuffmerge but I'm encountering the following error message:

[Mon Aug 29 12:09:13 2016] Beginning transcriptome assembly merge

[Mon Aug 29 12:09:13 2016] Preparing output location ./merged_asm/

Traceback (most recent call last):

File "/software/cufflinks/2.2.1/bin/cuffmerge", line 580, in <module>

  sys.exit(main())

File "/software/cufflinks/2.2.1/bin/cuffmerge", line 538, in main

  gtf_input_files = test_input_files(transfrag_list_file)

File "/software/cufflinks/2.2.1/bin/cuffmerge", line 268, in test_input_files

  g = open(line,"r")

IOError: [Errno 2] No such file or directory: './path/to/1_clout/transcripts.gtf'

---

My cuffmerge command is:

cuffmerge -p 8 -g /path/to/gff-file.gff -s /path/to/genome.fa assemblies.txt

and assemblies.txt is a text file that looks like:

./path/to/1_clout/transcripts.gtf

./path/to/2_clout/transcripts.gtf

./path/to/3_clout/transcripts.gtf

./path/to/4_clout/transcripts.gtf

./path/to/5_clout/transcripts.gtf

./path/to/6_clout/transcripts.gtf

It seems to me that cuffmerge can't find the .gtf files made by cufflinks. Is my syntax wrong? I used a reference gff file when running tophat and cufflinks and I'm wondering if my transcripts.gtf files are now wrong?

Thanks for your help!

[GenoMax]

If you are proving full directory paths for files then you would not use the period (.) at the beginning of those paths (like you have in your example for assemblies.txt file above).