Stringtie 2.1.4: Error running prepDE.py
1
0
Entering edit mode
12 months ago
venura ▴ 70

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.

Stringtie • 510 views
ADD COMMENT
1
Entering edit mode
12 months ago
venura ▴ 70

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

ADD COMMENT

Login before adding your answer.

Traffic: 1944 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6