Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

auto.py index out of range #172

Open
alphataubio opened this issue Oct 6, 2023 · 1 comment
Open

auto.py index out of range #172

alphataubio opened this issue Oct 6, 2023 · 1 comment

Comments

@alphataubio
Copy link

i get the following error trying to run fanc auto:

mitch@macmini _hic % fanc auto SRR027956.fastq -i /Users/mitch/_hic/hg18_chr14.fa -g hg18_chr14.bed .
2023-10-06 11:17:09,460 INFO FAN-C version: 0.9.27
2023-10-06 11:17:09,462 INFO Getting regions
2023-10-06 11:17:09,463 INFO Output folder: ./
2023-10-06 11:17:09,463 INFO Input files: SRR027956.fastq
2023-10-06 11:17:09,463 INFO Input file types: fastq
2023-10-06 11:17:09,463 INFO Final basename: SRR027956 (you can change this with the -n option!)
2023-10-06 11:17:09,463 INFO Creating output folders...
Traceback (most recent call last):
File "/usr/local/bin/fanc", line 127, in
Fanc()
File "/usr/local/bin/fanc", line 93, in init
command([sys.argv[0]] + sys.argv[option_ix:], log_level=log_level, verbosity=verbosity)
File "/Users/mitch/Library/Python/3.9/lib/python/site-packages/fanc/commands/fanc_commands.py", line 123, in auto
return fanc.commands.auto.auto(argv, **kwargs)
File "/Users/mitch/Library/Python/3.9/lib/python/site-packages/fanc/commands/auto.py", line 1097, in auto
if not file_types[i + 1] == 'sam':
IndexError: list index out of range

@kaukrise
Copy link
Collaborator

kaukrise commented Oct 9, 2023

You need to supply two FASTQ files, or it is assumed you are using mapped SAM/BAM input. Please have a look at the example in the docs.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants