merge_snps

[luoqingqing777]

i have finished the run_species and run_snps steps. there is something wrong with merge_snps

I used midas2 merge_snps --samples_list list_of_samples.tsv --midasdb_name gtdb --midasdb_dir my_midasdb_Escherichia_coli --num_cores 10 --genome_coverage 0.0 --force midas2_output/merge

Here come:
Traceback (most recent call last):
File "/home/luoqingqing/.conda/envs/midas2.0/bin/midas2", line 8, in
sys.exit(main())
File "/home/luoqingqing/.conda/envs/midas2.0/lib/python3.7/site-packages/midas2/main.py", line 24, in main
return subcommand_main(subcommand_args)
File "/home/luoqingqing/.conda/envs/midas2.0/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 664, in main
merge_snps(args)
File "/home/luoqingqing/.conda/envs/midas2.0/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 653, in merge_snps
raise error
File "/home/luoqingqing/.conda/envs/midas2.0/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 617, in merge_snps
assert species_ids_of_interest, f"No (specified) species pass the genome_coverage filter across samples, please adjust the genome_coverage or species_list"
AssertionError: No (specified) species pass the genome_coverage filter across samples, please adjust the genome_coverage or species_list

but i have adjusted the genome_coverage to 0, how can i make it more suitable to get the merge results.
waiting for your kind reply, many thanks

[zhaoc1]

Hi @luoqingqing777 ,

There are three metrics to select species for merge_snps: genome horizontal coverage, genome vertical coverage, and species prevalence. It seems like you also need to adjust the --genome_depth and --sample_counts by your merge_snps command, to compute the population SNPs for low abundant and low prevalent species. Please refer to ReadTheDoc for more details.

Thanks,
Chunyu

[luoqingqing777]

Thanks for your kind reply!