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

Defining minimum ORF length doesn't work #10

genomewalker opened this issue May 5, 2019 · 1 comment


None yet
2 participants
Copy link

commented May 5, 2019

when specifying a --min-length to the assemble workflow to set a minimum ORF length it is used as maximum length as seen here

The output of the extractorfs workflow on commit 53a2eff:

plass assemble tm8_1.truncated.fasta assembly.fas tmp --sub-mat PAM30.out --min-length 10
assemble tm8_1.truncated.fasta assembly.fas tmp --sub-mat PAM30.out --min-length 10
extractorfs /vol/attached/arctic/ORFs/tmp/18009091505483605488/nucl_reads /vol/attached/arctic/ORFs/tmp/18009091505483605488/nucl_6f_start --min-length 20 --max-length 10 --max-gaps 0 --contig-start-mode 1 --contig-end-mode 0 --orf-start-mode 0 --forward-frames 1,2,3 --reverse-frames 1,2,3 --translation-table 1 --use-all-table-starts 0 --id-offset 0 --threads 28 --compressed 0 -v 3


martin-steinegger added a commit that referenced this issue May 11, 2019


This comment has been minimized.

Copy link

commented May 11, 2019

Thank you for reporting this. It should be fixed now.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.