Ali Mirza

I have the same issue, I also installed using conda.

For some reason, it doesn't want to merge the intermediate contigs. I reran assembly with `--rerun-incomplete` parameter after deleting the empty` final.contigs.fa` file from the `sunbeam_output/assembly/megahit/{sample}_asm` directory hoping it would...

I used MEGAHIT v1.1.3 I couldn't find a similar issue in the megahit github repository. I wonder if to rerun Megahit the intermediate files must be deleted first for megahit...

Great, thank you for the detailed response!

> @aimirza I just need your help in this. Hi @Ankita-1211. I am a user of metaerg, not a developer. Also, I haven't installed it using Docker, I used the...

May you explain how the Abundance (vs count) is calculated for each protein-coding gene function profile?

> No, if you look for usages of the `sample2depth` and `mdepth_values` values in the search and calculated values the depth values are just added together for each step. I...

May you please list all of the tools in the workflow that write partial results? This will help me to know whether or not to delete the output file. I...

Snakemake is a great option. A recent metagenomics pipeline uses Snakemake and it works wonders for me. https://sunbeam.readthedocs.io/en/latest/usage.html

Also, Snakmake makes it easier for me to modify parameters and select which programs to run.