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soedinglab / plass

sensitive and precise assembly of short sequencing reads
https://plass.mmseqs.com
GNU General Public License v3.0
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Defining minimum ORF length doesn't work #10

Closed genomewalker closed 5 years ago

genomewalker commented 5 years ago

Hi 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 53a2eff54d26d24ec3c9486020ebf15add15af9f:

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

Thanks Antonio

martin-steinegger commented 5 years ago

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