soedinglab
The output file is empty
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
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For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: cmake version 3.16.3
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Server specifications (especially CPU support for AVX2/SSE and amount of system memory): Intel® Core™ i9-9900KF CPU @ 3.60GHz × 16 32g RAM
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Operating system and version: Ubuntu 20.04.1 LTS
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.
