PenguiN Reproducibility

[MTDouglas]

Expected Behavior

When running the guided_nuclassemble test1_T1.unmapped_1.fastq.gz test1_T1.unmapped_2.fastq.gz test1_T1_NC_004102_genotype_1a.assembly.fasta tmp/ --threads 12 --clust-min-seq-id 0.98 --min-contig-len 8000 --remove-tmp-files command, I am hoping to get the same results every time. I.e., I would expect to get the same number of assemblies every time

Current Behavior

The guided_nuclassemble test1_T1.unmapped_1.fastq.gz test1_T1.unmapped_2.fastq.gz test1_T1_NC_004102_genotype_1a.assembly.fasta tmp/ --threads 12 --clust-min-seq-id 0.98 --min-contig-len 8000 --remove-tmp-files command, is producing inconsistent results despite using a docker container within nextflow. I am getting a different number of assemblies everytime I run PenguiN in my nextflow pipeline.

Steps to Reproduce (for bugs)

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

Plass Output (for bugs)

Please make sure to also post the complete output of Plass. You can use gist.github.com for large output.

Context

Providing context helps us come up with a solution and improve our documentation for the future.
The latest docker container for Plass (5.cf8933) was pulled and converted to singularity. A Nextflow module was created that uses the singularity container. I am running PenguiN within nextflow from that created singularity container, so in theory we should be getting the same output everytime. Is there a random see parameter for PenguiN to make sure I am getting the same result each time?

Your Environment

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

• Git commit used (The string after "Plass Version:" when you execute Plass without any parameters):
• Which Plass version was used (Statically-compiled, self-compiled, Homebrew, etc.):
• For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
• Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
• Operating system and version: