Stringtie 2.1.4: Error running prepDE.py

Question

[venura]

Hi ,

When I run prepDE.py job exit with the following error. I am using StringTie/2.1.4 with Python/2.7.18.

Traceback (most recent call last): File "/sw/eb/software/StringTie/2.1.4-GCC-9.3.0/bin/prepDE.py", line 58, in samples = [(i,glob.iglob(os.path.join(opts.input,i,"*.gtf")).next()) for i in next(os.walk(opts.input))[1] if re.search(opts.pattern,i)] StopIteration

I have a directory structure as follows (since formatting looks messed up I added image as well)

├── ballgown
│   ├── PVX_2d_1
│   │   ├── e2t.ctab
│   │   ├── e_data.ctab
│   │   ├── i2t.ctab
│   │   ├── i_data.ctab
│   │   ├── PVX_2d_1.gtf
│   │   └── t_data.ctab
│   ├── PVX_2d_2
│   │   ├── e2t.ctab
│   │   ├── e_data.ctab
│   │   ├── i2t.ctab
│   │   ├── i_data.ctab
│   │   ├── PVX_2d_2.gtf
│   │   └── t_data.ctab
│   ├── PVX_2d_3
│   │   ├── e2t.ctab
│   │   ├── e_data.ctab
│   │   ├── i2t.ctab
│   │   ├── i_data.ctab
│   │   ├── PVX_2d_3.gtf
│   │   └── t_data.ctab

Can someone help me in this regard? Thanks in advance.

Answer 1

[venura]

I ran prepDE.py -i ballgown and got the output.