The output file is empty

[Sami-Altayyar]

I have one nucleotide fasta file (nuc1.fasta) and I run the following command

plass assemble nuc1.fasta result.fasta tmp

from my understanding the final output should be result.fasta

but the result.fasta is empty

Current Behavior

result.fasta is empty

Steps to Reproduce (for bugs)

Please make sure to execute the reproduction steps with newly recreated and empty tmp folders. checked

Plass Output (for bugs)

Please make sure to also post the complete output of Plass. You can use gist.github.com for large output. no results

Context

Providing context helps us come up with a solution and improve our documentation for the future.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

Plass Version: 41d03ca639be3086bbe6719fb1930db4d8cf60b4 compiled version

• For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: cmake version 3.16.3

• Server specifications (especially CPU support for AVX2/SSE and amount of system memory): Intel® Core™ i9-9900KF CPU @ 3.60GHz × 16 32g RAM

• Operating system and version: Ubuntu 20.04.1 LTS

[martin-steinegger]

How long are the reads in your nuc1.fasta? In default Plass tries to extract protein fragments of at least 30 length (90 nucleotides). If you want to lower the size, you can adjust the --min-length parameter.