/gannet/Atumefaciens/20190416_metagenomics_pgen_metagenemark

Gene prediction using MetaGeneMark on Mox with pH-specific (pH=7.1 and pH=8.2) MEGAHIT assemblies.

Input FastA files were from MEGAHIT assembly on 20190415:

https://robertslab.github.io/sams-notebook/2019/04/15/Metagenome-Assemblies-P.generosa-Water-Samples-Trimmed-HiSeqX-Data-Using-Megahit-on-Mox-to-Compare-pH-Treatments.html



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FILES

-- 20190416_metagenomics_pgen_metagenemark.sh: SBATCH script to run MetaGeneMark on Mox.

- fastas.list.txt: List of input FastAs used for MetaGeneMark.

- pH71.mgm.gff: GFF of pH=7.1 assembly.

- pH71.mgm-nucleotides.fasta: Predicted nucleotides FastA of pH=7.1 assembly.

- pH71.mgm-nucleotides.fasta.fai: FastA index.

- pH71.mgm-proteins.fasta: Predicted proteins FastA of pH=7.1 assembly.

- pH71.mgm-proteins.fasta.fai: FastA index.

- pH82.mgm.gff: GFF of pH=7.1 assembly.

- pH82.mgm-nucleotides.fasta: Predicted nucleotides FastA of pH=8.2 assembly.

- pH82.mgm-nucleotides.fasta.fai: FastA index.

- pH82.mgm-proteins.fasta: Predicted proteins FastA of pH=8.2 assembly.

- pH82.mgm-proteins.fasta.fai: FastA index.

- slurm-754006.out: SLURM output file (contains stderr/stdout)

- system_path.log: Log of Sam's Mox system $PATH contents.


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Notebook:

https://robertslab.github.io/sams-notebook/2019/04/16/Metagenomics-Gene-Prediction-P.generosa-Water-Samples-Using-MetaGeneMark-on-Mox-to-Compare-pH-Treatments.html