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---
title: "Tree building, bin refinement, ADA clade addition"
author: "Paul Den Uyl"
date: "2023-11-02"
output: html_document
---
Dependencies
```{r setup, include=FALSE}
#rm(list=ls());if(is.null(dev.list()["RStudioGD"])){} else {dev.off(dev.list()["RStudioGD"])};cat("\014")
library(tidyverse)
library(dplyr)
library(here)
library(vroom)
library(ggmap)
library(googledrive)
library(readxl)
library(Biostrings)
library(lubridate)
library(ggplot2)
library(ggpmisc)
knitr::opts_knit$set(root.dir = here::here(""))
#Load postgres server running on Alpena
pg <- DBI::dbConnect(RPostgres::Postgres(),dbname = "glamr_data", host = "localhost", port = "5432", user = "glamr_admin", password = "glamr2023")
#Load GLAMR GTDBTK data
gtdb <- tbl(pg, "GTDB") %>%
collect() %>%
mutate(sample = str_extract(user_genome, "samp_\\d+")) %>%
relocate(user_genome, sample)
#Load GLAMR CheckM data
checkM <- tbl(pg, "checkm") %>%
collect() %>%
mutate(sample = str_extract(`Bin Id`, "samp_\\d+")) %>%
relocate(`Bin Id`, sample)
```
---Outline---
1.) GToTree preparation (drep 95, 97, 98, 99)
2.) GTDBTK (re)run preparation
3.) GToTree building
-------------
1.) Prep for (re)run of GTDBTK on MAGs/Genomes for tree building - future labels
```{r}
###conda config --set channel_priority strict
###snakemake run_gtdbtk_GToTree --profile config/snakemake_profiles/alpena --rerun-incomplete --dry-run
gtdbtk_summary <- read_tsv("/geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/ada_bins/gtdbtk/output/gtdbtk.bac120.summary.tsv") #also called in step 2
```
2a.) GToTree preparation initial (drep 95, 97, 98, 99)
```{r}
#Gather all ADA MAG paths to prepare for GToTree building, sym link to new path
for (i in c("95", "97", "98", "99")) {
ada_mag_paths <- system(paste0("ls /geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/ada_bins/drep_",i,"/dereplicated_genomes/"), intern = TRUE) %>%
tibble(mag = .) %>%
mutate(mag = mag %>% str_remove(".fa"),
mag_path = paste0("/geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/ada_bins/drep_",i,"/dereplicated_genomes/",mag,".fa"),
new_mag_path = str_glue(paste0("/geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/ada_bins/drep_",i,"/GToTree/{mag}_drep_",i,".fna")),
new_file_name = new_mag_path %>% str_remove(".*GToTree/"))
ada_mag_paths_bind <- ada_mag_paths[,c(4, 1)]
#add new MAG paths to fasta_files.txt list for tree building
fasta_files <- read_tsv(paste0("/geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/ada_bins/drep_",i,"/GToTree/fasta_files.txt"), col_names = "new_file_name")
fasta_files_new <- bind_rows(fasta_files[,1], ada_mag_paths_bind[,1]) %>% distinct()
write_tsv(fasta_files_new, paste0("/geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/ada_bins/drep_",i,"/GToTree/fasta_files.txt"), col_names = FALSE)
#add new MAG paths and names to genome_to_id_map.tsv for tree building
genome_to_id_map <- read_tsv(paste0("/geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/ada_bins/drep_",i,"/GToTree/genome_to_id_map.tsv"), col_names = c("new_file_name", "mag"))
genome_to_id_map_new <- bind_rows(genome_to_id_map, ada_mag_paths_bind) %>% distinct()
#add gtdbtk annotations to genome_to_id_map.tsv names
genome_to_id_map_new_gtdbtk <- read_tsv("/geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/ada_bins/gtdbtk/output/gtdbtk.bac120.summary.tsv") %>%
mutate(new_file_name = paste0(user_genome, ".fna") %>% str_replace("drep_99", paste0("drep_",i)),
genus_species = classification %>% str_remove(".*;g__") %>% str_replace(";s__", "_") %>% str_replace(" ", "_"),
genus_species = sapply(strsplit(genus_species, "_"), function(parts) {
if (length(parts) > 1) {parts[2] <- tolower(parts[2])}
paste(parts, collapse = "_")})) %>%
inner_join(genome_to_id_map_new, ., by = "new_file_name") %>%
mutate(mag = paste0(mag, "---", genus_species)) %>%
select(new_file_name, mag)
write_tsv(genome_to_id_map_new_gtdbtk, paste0("/geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/ada_bins/drep_",i,"/GToTree/genome_to_id_map.tsv"), col_names = FALSE)
#symbolic link ada_mag_paths
file.symlink(ada_mag_paths$mag_path, ada_mag_paths$new_mag_path)
}
```
3.) GToTree building
```{bash}
#For each GToTree directory, independently, run:
comics -i sid
cp -r /usr/local/lib/GToTree-1.7.05/hmm_sets/ ./
export GToTree_HMM_dir=hmm_sets/
export TAXONKIT_DB=ncbi-taxdump
conda deactivate
GToTree -f fasta_files.txt -H Cyanobacteria -t -m genome_to_id_map.tsv -j 40 -o Tree_output_drep_99
```
#Generate Anvi'o profiles
#References - Metagenomic workflow (primary- LOOK HERE FIRST!): https://merenlab.org/2016/06/22/anvio-tutorial-v2/
# Mapping: https://merenlab.org/tutorials/assembly-based-metagenomics/
# Running on servers: https://merenlab.org/2015/11/28/visualizing-from-a-server/
# Anvi'o snakemake workflows: https://merenlab.org/2018/07/09/anvio-snakemake-workflows/
1.) Setup terminal and screen session to run and visualize Anvi'o
```{bash}
#The following direction are directly performed in terminal or VS Code
ssh -L 8720:localhost:8720 pdenuyl@earth-gateway.earth.lsa.umich.edu
#ENTER PASSWORD
ssh -L 8720:localhost:8720 vondamm
#ENTER PASSWORD
#****Change port to be unique*****
screen -S anvio
cd /geomicro/data2/pdenuyl2/neurotoxin_thesis/FINAL2/anvio
```
2.) Run snakemake file to setup and generate Anvi'o sample profiles
```{bash}
#Run create anvio profiles for MAGs of interest (ADA non-sp000312705 drep98) (ADA sp000312705 drep99)
#MAGs of interest determined from drep output analysis through tree building above
snakemake \
samples/samp_471/anvio_db/profiles/.samp_471_done_primary \
samples/samp_481/anvio_db/profiles/.samp_481_done_primary \ #no compliments
samples/samp_2047/anvio_db/profiles/.samp_2047_done_primary \ #no compliments
samples/samp_2073/anvio_db/profiles/.samp_2073_done_primary \ #no compliments, looks good
samples/samp_4417/anvio_db/profiles/.samp_4417_done_primary \ #no compliments, looks decent w/compliments #Low final completeness, not used
samples/samp_477/anvio_db/profiles/.samp_477_done_primary \ #no compliments, looks decent w/compliments
samples/samp_4344/anvio_db/profiles/.samp_4344_done_primary \ #no compliments, looks good
samples/samp_3937/anvio_db/profiles/.samp_3937_done_primary \ #no compliments, looks good
samples/samp_468/anvio_db/profiles/.samp_468_done_primary \
samples/samp_4304/anvio_db/profiles/.samp_4304_done_primary \ # THAMES
samples/samp_4326/anvio_db/profiles/.samp_4326_done_primary \ # KENYA
samples/samp_4380/anvio_db/profiles/.samp_4380_done_primary \
samples/samp_507/anvio_db/profiles/.samp_507_done_primary \
samples/samp_4305/anvio_db/profiles/.samp_4305_done_primary \
samples/samp_2059/anvio_db/profiles/.samp_2059_done_primary \
--profile config/snakemake_profiles/cayman/
#Run create complimentary anvio profiles for MAGs of interest (all grouped by secondary_cluster (drep_99))
snakemake \
samples/samp_471/anvio_db/profiles/.samp_470_done \
samples/samp_471/anvio_db/profiles/.samp_472_done \ #not in secondary_cluster, BUT has sxt and from same date
samples/samp_471/anvio_db/profiles/.samp_511_done \
samples/samp_471/anvio_db/profiles/.samp_2047_done
snakemake \
samples/samp_468/anvio_db/profiles/.samp_1001_done \
samples/samp_468/anvio_db/profiles/.samp_1324_done \
samples/samp_468/anvio_db/profiles/.samp_2116_done \
samples/samp_468/anvio_db/profiles/.samp_2138_done \
samples/samp_4304/anvio_db/profiles/.samp_2109_done \
samples/samp_4304/anvio_db/profiles/.samp_2141_done \
samples/samp_4304/anvio_db/profiles/.samp_470_done \
samples/samp_4304/anvio_db/profiles/.samp_508_done \
samples/samp_4326/anvio_db/profiles/.samp_4308_done \
samples/samp_4326/anvio_db/profiles/.samp_4311_done \
samples/samp_4326/anvio_db/profiles/.samp_4317_done \
samples/samp_4326/anvio_db/profiles/.samp_4319_done \
samples/samp_4326/anvio_db/profiles/.samp_4321_done \
samples/samp_4326/anvio_db/profiles/.samp_4323_done \
samples/samp_4326/anvio_db/profiles/.samp_4325_done \
samples/samp_4380/anvio_db/profiles/.samp_2014_done \
samples/samp_4380/anvio_db/profiles/.samp_4333_done \
samples/samp_4380/anvio_db/profiles/.samp_4366_done \
samples/samp_4380/anvio_db/profiles/.samp_4376_done \
samples/samp_4380/anvio_db/profiles/.samp_4385_done \
samples/samp_4380/anvio_db/profiles/.samp_4387_done \
samples/samp_4380/anvio_db/profiles/.samp_4425_done \
samples/samp_507/anvio_db/profiles/.samp_2155_done \
samples/samp_507/anvio_db/profiles/.samp_2157_done \
samples/samp_507/anvio_db/profiles/.samp_2161_done \
--profile config/snakemake_profiles/cayman/ \
--rerun-incomplete
#Run create complimentary anvio profiles for MAGs of interest WITHOUT secondary_clustor compliments (all grouped by primary_cluster (drep_99))
snakemake \
samples/samp_481/anvio_db/profiles/.samp_477_done \
samples/samp_481/anvio_db/profiles/.samp_484_done \
samples/samp_2047/anvio_db/profiles/.samp_470_done \
samples/samp_2047/anvio_db/profiles/.samp_471_done \
samples/samp_2047/anvio_db/profiles/.samp_2073_done \
samples/samp_2047/anvio_db/profiles/.samp_4417_done \
samples/samp_4417/anvio_db/profiles/.samp_470_done \
samples/samp_4417/anvio_db/profiles/.samp_471_done \
samples/samp_4417/anvio_db/profiles/.samp_2047_done \
samples/samp_4417/anvio_db/profiles/.samp_2073_done \
samples/samp_477/anvio_db/profiles/.samp_481_done \
samples/samp_477/anvio_db/profiles/.samp_484_done \
samples/samp_4344/anvio_db/profiles/.samp_507_done \
samples/samp_4344/anvio_db/profiles/.samp_2059_done \
samples/samp_4344/anvio_db/profiles/.samp_4367_done \
samples/samp_4344/anvio_db/profiles/.samp_4375_done \
samples/samp_4344/anvio_db/profiles/.samp_2013_done \
samples/samp_3937/anvio_db/profiles/.samp_506_done \
samples/samp_3937/anvio_db/profiles/.samp_481_done \
samples/samp_3937/anvio_db/profiles/.samp_4356_done \
samples/samp_4305/anvio_db/profiles/.samp_462_done \
samples/samp_4305/anvio_db/profiles/.samp_463_done \
samples/samp_4305/anvio_db/profiles/.samp_1328_done \
--profile config/snakemake_profiles/cayman/
```
3.) Merge Anvi'o profiles, import collections, interact, visualize, and refine bins
samp_471
```{bash}
module load anvio/7
anvi-merge \
samples/samp_471/anvio_db/profiles/*_profile/PROFILE.db \
-o samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all \
-c samples/samp_471/anvio_db/contigs.db \
--sample-name samp_471_pls_compliments
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-merge samples/samp_471/anvio_db/profiles/*_profile/PROFILE.db -o samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all -c samples/samp_471/anvio_db/contigs.db --sample-name samp_471_pls_compliments
############
#Import bins
############
mkdir samples/samp_471/anvio_db/collections
cp /geomicro/data2/kiledal/GLAMR/data/omics/metagenomes/samp_471/bins/das_tool/*.tsv \
samples/samp_471/anvio_db/collections/
#imports contig assignments from the following binners: concoct, maxbin, metabat2, metadecoder, semibin, VAMB
anvi-import-collection \
samples/samp_471/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_471/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_471/anvio_db/collections/concoct_contigs.txt -p samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_471/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
anvi-interactive \
-p samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_471/anvio_db/contigs.db \
-C concoct \
--server-only \
-P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-interactive -p samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_471/anvio_db/contigs.db -C concoct --server-only -P 8720
anvi-refine \
-p samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_471/anvio_db/contigs.db \
-C concoct \
-b samp_471_concoct_280 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_471/anvio_db/contigs.db -C concoct -b samp_471_concoct_280 --server-only -P 8720
#############################################
Summarize bins / export new refine bin fasta+
#############################################
anvi-summarize \
-p samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_471/anvio_db/contigs.db \
-C concoct \
-o samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-summarize -p samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_471/anvio_db/contigs.db -C concoct -o samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER
#New fasta for refined bin located:
#samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER/bin_by_bin/samp_471_concoct_280_refine_FINAL2/samp_471_concoct_280_refine_FINAL2-contigs.fa
#Check final refined profile
anvi-refine -p samples/samp_471/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_471/anvio_db/contigs.db -C concoct -b samp_471_concoct_280_refine_FINAL2 --server-only -P 8720
```
4.) Merge Anvi'o profiles, import collections, interact, visualize, and refine bins
samp_481
```{bash}
module load anvio/7
#no secondary_cluster compliments to merge
############
#Import bins
############
mkdir samples/samp_481/anvio_db/collections
cp /geomicro/data2/kiledal/GLAMR/data/omics/metagenomes/samp_481/bins/das_tool/*.tsv \
samples/samp_481/anvio_db/collections/
#imports contig assignments from the following binners: concoct, maxbin, metabat2, metadecoder, semibin, VAMB
anvi-import-collection \
samples/samp_481/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_481/anvio_db/profiles/samp_481_profile/PROFILE.db \
-c samples/samp_481/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_481/anvio_db/collections/concoct_contigs.txt -p samples/samp_481/anvio_db/profiles/samp_481_profile/PROFILE.db -c samples/samp_481/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
#no secondary_cluster compliments
#no need to run anvi-interactive
anvi-refine \
-p samples/samp_481/anvio_db/profiles/samp_481_profile/PROFILE.db \
-c samples/samp_481/anvio_db/contigs.db \
-C concoct \
-b samp_481_concoct_764 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_481/anvio_db/profiles/samp_481_profile/PROFILE.db -c samples/samp_481/anvio_db/contigs.db -C concoct -b samp_481_concoct_764 --server-only -P 8720
#Looks bad, let's add in some primary_cluster compliments
anvi-merge \
samples/samp_481/anvio_db/profiles/*_profile/PROFILE.db \
-o samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all \
-c samples/samp_481/anvio_db/contigs.db \
--sample-name samp_481_pls_compliments
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-merge samples/samp_481/anvio_db/profiles/*_profile/PROFILE.db -o samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all -c samples/samp_481/anvio_db/contigs.db --sample-name samp_481_pls_compliments
############
#Import bins
############
anvi-import-collection \
samples/samp_481/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_481/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection \
samples/samp_481/anvio_db/collections/concoct_contigs.txt -p samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_481/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-interactive \
-p samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_481/anvio_db/contigs.db \
-C concoct \
--server-only \
-P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-interactive -p samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_481/anvio_db/contigs.db -C concoct --server-only -P 8720
anvi-refine \
-p samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_481/anvio_db/contigs.db \
-C concoct \
-b samp_481_concoct_764 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_481/anvio_db/contigs.db -C concoct -b samp_481_concoct_764 --server-only -P 8720
#############################################
Summarize bins / export new refine bin fasta+
#############################################
anvi-summarize \
-p samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_481/anvio_db/contigs.db \
-C concoct \
-o samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-summarize -p samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_481/anvio_db/contigs.db -C concoct -o samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER
#New fasta for refined bin located:
#samples/samp_481/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER/bin_by_bin/samp_481_concoct_764_refine_FINAL2/samp_481_concoct_764_refine_FINAL2-contigs.fa
#Check final refined profile
s
```
5.) Merge Anvi'o profiles, import collections, interact, visualize, and refine bins
samp_2047
```{bash}
module load anvio/7
#no secondary_cluster compliments to merge
############
#Import bins
############
mkdir samples/samp_2047/anvio_db/collections
cp /geomicro/data2/kiledal/GLAMR/data/omics/metagenomes/samp_2047/bins/das_tool/*.tsv \
samples/samp_2047/anvio_db/collections/
#imports contig assignments from the following binners: concoct, maxbin, metabat2, metadecoder, semibin, VAMB
anvi-import-collection \
samples/samp_2047/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_2047/anvio_db/profiles/samp_2047_profile/PROFILE.db \
-c samples/samp_2047/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_2047/anvio_db/collections/concoct_contigs.txt -p samples/samp_2047/anvio_db/profiles/samp_2047_profile/PROFILE.db -c samples/samp_2047/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
#no secondary_cluster compliments
#no need to run anvi-interactive
anvi-refine \
-p samples/samp_2047/anvio_db/profiles/samp_2047_profile/PROFILE.db \
-c samples/samp_2047/anvio_db/contigs.db \
-C concoct \
-b samp_2047_concoct_1911 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_2047/anvio_db/profiles/samp_2047_profile/PROFILE.db -c samples/samp_2047/anvio_db/contigs.db -C concoct -b samp_2047_concoct_1911 --server-only -P 8720
#Looks bad, let's add in some primary_cluster compliments
anvi-merge \
samples/samp_2047/anvio_db/profiles/*_profile/PROFILE.db \
-o samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all \
-c samples/samp_2047/anvio_db/contigs.db \
--sample-name samp_2047_pls_compliments
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-merge samples/samp_2047/anvio_db/profiles/*_profile/PROFILE.db -o samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all -c samples/samp_2047/anvio_db/contigs.db --sample-name samp_2047_pls_compliments
############
#Import bins
############
anvi-import-collection \
samples/samp_2047/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_2047/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_2047/anvio_db/collections/concoct_contigs.txt -p samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_2047/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-interactive \
-p samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_2047/anvio_db/contigs.db \
-C concoct \
--server-only \
-P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-interactive -p samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_2047/anvio_db/contigs.db -C concoct --server-only -P 8720
anvi-refine \
-p samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_2047/anvio_db/contigs.db \
-C concoct \
-b samp_2047_concoct_1911 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_2047/anvio_db/contigs.db -C concoct -b samp_2047_concoct_1911 --server-only -P 8720
#############################################
Summarize bins / export new refine bin fasta+
#############################################
anvi-summarize \
-p samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_2047/anvio_db/contigs.db \
-C concoct \
-o samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-summarize -p samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_2047/anvio_db/contigs.db -C concoct -o samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER
#New fasta for refined bin located:
#samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER/bin_by_bin/samp_2047_concoct_1911_refine_FINAL2/samp_2047_concoct_1911_refine_FINAL2-contigs.fa
#Check final refined profile
anvi-refine -p samples/samp_2047/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_2047/anvio_db/contigs.db -C concoct -b samp_2047_concoct_1911_refine_FINAL2 --server-only -P 8720
```
6.) Merge Anvi'o profiles, import collections, interact, visualize, and refine bins
samp_2073
```{bash}
module load anvio/7
#no secondary_cluster compliments to merge
############
#Import bins
############
mkdir samples/samp_2073/anvio_db/collections
cp /geomicro/data2/kiledal/GLAMR/data/omics/metagenomes/samp_2073/bins/das_tool/*.tsv \
samples/samp_2073/anvio_db/collections/
#imports contig assignments from the following binners: concoct, maxbin, metabat2, metadecoder, semibin, VAMB
anvi-import-collection \
samples/samp_2073/anvio_db/collections/semibin_contigs.txt \
-p samples/samp_2073/anvio_db/profiles/samp_2073_profile/PROFILE.db \
-c samples/samp_2073/anvio_db/contigs.db \
-C semibin \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_2073/anvio_db/collections/semibin_contigs.txt -p samples/samp_2073/anvio_db/profiles/samp_2073_profile/PROFILE.db -c samples/samp_2073/anvio_db/contigs.db -C semibin --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
#no secondary_cluster compliments
#no need to run anvi-interactive
anvi-refine \
-p samples/samp_2073/anvio_db/profiles/samp_2073_profile/PROFILE.db \
-c samples/samp_2073/anvio_db/contigs.db \
-C semibin \
-b samp_2073_semibin_92 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_2073/anvio_db/profiles/samp_2073_profile/PROFILE.db -c samples/samp_2073/anvio_db/contigs.db -C semibin -b samp_2073_semibin_92 --server-only -P 8720
#Looks good, not much reason to refine further
```
7.) Merge Anvi'o profiles, import collections, interact, visualize, and refine bins
samp_4417
```{bash}
module load anvio/7
#no secondary_cluster compliments to merge
############
#Import bins
############
mkdir samples/samp_4417/anvio_db/collections
cp /geomicro/data2/kiledal/GLAMR/data/omics/metagenomes/samp_4417/bins/das_tool/*.tsv \
samples/samp_4417/anvio_db/collections/
#imports contig assignments from the following binners: concoct, maxbin, metabat2, metadecoder, semibin, VAMB
anvi-import-collection \
samples/samp_4417/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_4417/anvio_db/profiles/samp_4417_profile/PROFILE.db \
-c samples/samp_4417/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_4417/anvio_db/collections/concoct_contigs.txt -p samples/samp_4417/anvio_db/profiles/samp_4417_profile/PROFILE.db -c samples/samp_4417/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
#no secondary_cluster compliments
#no need to run anvi-interactive
anvi-refine \
-p samples/samp_4417/anvio_db/profiles/samp_4417_profile/PROFILE.db \
-c samples/samp_4417/anvio_db/contigs.db \
-C semibin \
-b samp_4417_concoct_106 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_4417/anvio_db/profiles/samp_4417_profile/PROFILE.db -c samples/samp_4417/anvio_db/contigs.db -C concoct -b samp_4417_concoct_106 --server-only -P 8720
#Looks pretty good, let's still try to add in some primary_cluster compliments
anvi-merge \
samples/samp_4417/anvio_db/profiles/*_profile/PROFILE.db \
-o samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all \
-c samples/samp_4417/anvio_db/contigs.db \
--sample-name samp_4417_pls_compliments
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-merge samples/samp_4417/anvio_db/profiles/*_profile/PROFILE.db -o samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all -c samples/samp_4417/anvio_db/contigs.db --sample-name samp_4417_pls_compliments
############
#Import bins
############
anvi-import-collection \
samples/samp_4417/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_4417/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_4417/anvio_db/collections/concoct_contigs.txt -p samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_4417/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
anvi-refine \
-p samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_4417/anvio_db/contigs.db \
-C concoct \
-b samp_4417_concoct_106 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_4417/anvio_db/contigs.db -C concoct -b samp_4417_concoct_106 --server-only -P 8720
#############################################
Summarize bins / export new refine bin fasta+
#############################################
anvi-summarize \
-p samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_4417/anvio_db/contigs.db \
-C concoct \
-o samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-summarize -p samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_4417/anvio_db/contigs.db -C concoct -o samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER
#New fasta for refined bin located:
#samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/SUMMARY_FOLDER/bin_by_bin/samp_4417_concoct_106_refine_FINAL2/samp_4417_concoct_106_refine_FINAL2-contigs.fa
#Check final refined profile
anvi-refine -p samples/samp_4417/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_4417/anvio_db/contigs.db -C concoct -b samp_4417_concoct_106_refine_FINAL2 --server-only -P 8720
```
8.) Merge Anvi'o profiles, import collections, interact, visualize, and refine bins
samp_477
```{bash}
module load anvio/7
#no secondary_cluster compliments to merge
############
#Import bins
############
mkdir samples/samp_477/anvio_db/collections
cp /geomicro/data2/kiledal/GLAMR/data/omics/metagenomes/samp_477/bins/das_tool/*.tsv \
samples/samp_477/anvio_db/collections/
#imports contig assignments from the following binners: concoct, maxbin, metabat2, metadecoder, semibin, VAMB
anvi-import-collection \
samples/samp_477/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_477/anvio_db/profiles/samp_477_profile/PROFILE.db \
-c samples/samp_477/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_477/anvio_db/collections/concoct_contigs.txt -p samples/samp_477/anvio_db/profiles/samp_477_profile/PROFILE.db -c samples/samp_477/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
#no secondary_cluster compliments
#no need to run anvi-interactive
anvi-refine \
-p samples/samp_477/anvio_db/profiles/samp_477_profile/PROFILE.db \
-c samples/samp_477/anvio_db/contigs.db \
-C concoct \
-b samp_477_concoct_589 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_477/anvio_db/profiles/samp_477_profile/PROFILE.db -c samples/samp_477/anvio_db/contigs.db -C concoct -b samp_477_concoct_589 --server-only -P 8720
#Looks pretty good, let's still try to add in some primary_cluster compliments
anvi-merge \
samples/samp_477/anvio_db/profiles/*_profile/PROFILE.db \
-o samples/samp_477/anvio_db/profiles/SAMPLES-MERGED_all \
-c samples/samp_477/anvio_db/contigs.db \
--sample-name samp_477_pls_compliments
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-merge samples/samp_477/anvio_db/profiles/*_profile/PROFILE.db -o samples/samp_477/anvio_db/profiles/SAMPLES-MERGED_all -c samples/samp_477/anvio_db/contigs.db --sample-name samp_477_pls_compliments
############
#Import bins
############
anvi-import-collection \
samples/samp_477/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_477/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_477/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_477/anvio_db/collections/concoct_contigs.txt -p samples/samp_477/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_477/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
anvi-refine \
-p samples/samp_477/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_477/anvio_db/contigs.db \
-C concoct \
-b samp_477_concoct_589 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_477/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_477/anvio_db/contigs.db -C concoct -b samp_477_concoct_589 --server-only -P 8720
#Still looks good, no refine!
```
8.) Merge Anvi'o profiles, import collections, interact, visualize, and refine bins
samp_4344
```{bash}
module load anvio/7
#no secondary_cluster compliments to merge
############
#Import bins
############
mkdir samples/samp_4344/anvio_db/collections
cp /geomicro/data2/kiledal/GLAMR/data/omics/metagenomes/samp_4344/bins/das_tool/*.tsv \
samples/samp_4344/anvio_db/collections/
#imports contig assignments from the following binners: concoct, maxbin, metabat2, metadecoder, semibin, VAMB
anvi-import-collection \
samples/samp_4344/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_4344/anvio_db/profiles/samp_477_profile/PROFILE.db \
-c samples/samp_4344/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_4344/anvio_db/collections/concoct_contigs.txt -p samples/samp_4344/anvio_db/profiles/samp_4344_profile/PROFILE.db -c samples/samp_4344/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
#no secondary_cluster compliments
#no need to run anvi-interactive
anvi-refine \
-p samples/samp_4344/anvio_db/profiles/samp_477_profile/PROFILE.db \
-c samples/samp_4344/anvio_db/contigs.db \
-C concoct \
-b samp_4344_concoct_197 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_4344/anvio_db/profiles/samp_4344_profile/PROFILE.db -c samples/samp_4344/anvio_db/contigs.db -C concoct -b samp_4344_concoct_197 --server-only -P 8720
#Looks very good, let's still try to add in some primary_cluster compliments
anvi-merge \
samples/samp_4344/anvio_db/profiles/*_profile/PROFILE.db \
-o samples/samp_4344/anvio_db/profiles/SAMPLES-MERGED_all \
-c samples/samp_4344/anvio_db/contigs.db \
--sample-name samp_4344_pls_compliments
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-merge samples/samp_4344/anvio_db/profiles/*_profile/PROFILE.db -o samples/samp_4344/anvio_db/profiles/SAMPLES-MERGED_all -c samples/samp_4344/anvio_db/contigs.db --sample-name samp_4344_pls_compliments
############
#Import bins
############
anvi-import-collection \
samples/samp_4344/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_4344/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_4344/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_4344/anvio_db/collections/concoct_contigs.txt -p samples/samp_4344/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_4344/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
anvi-refine \
-p samples/samp_4344/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_4344/anvio_db/contigs.db \
-C concoct \
-b samp_4344_concoct_197 \ \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_4344/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_4344/anvio_db/contigs.db -C concoct -b samp_4344_concoct_197 --server-only -P 8720
#Still looks good, no refine!
```
9.) Merge Anvi'o profiles, import collections, interact, visualize, and refine bins
samp_3937
```{bash}
module load anvio/7
#no secondary_cluster compliments to merge
############
#Import bins
############
mkdir samples/samp_3937/anvio_db/collections
cp /geomicro/data2/kiledal/GLAMR/data/omics/metagenomes/samp_3937/bins/das_tool/*.tsv \
samples/samp_3937/anvio_db/collections/
#imports contig assignments from the following binners: concoct, maxbin, metabat2, metadecoder, semibin, VAMB
anvi-import-collection \
samples/samp_3937/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_3937/anvio_db/profiles/samp_3937_profile/PROFILE.db \
-c samples/samp_3937/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_3937/anvio_db/collections/concoct_contigs.txt -p samples/samp_3937/anvio_db/profiles/samp_3937_profile/PROFILE.db -c samples/samp_3937/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
#no secondary_cluster compliments
#no need to run anvi-interactive
anvi-refine \
-p samples/samp_3937/anvio_db/profiles/samp_3937_profile/PROFILE.db \
-c samples/samp_3937/anvio_db/contigs.db \
-C concoct \
-b samp_3937_concoct_558 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_3937/anvio_db/profiles/samp_3937_profile/PROFILE.db -c samples/samp_3937/anvio_db/contigs.db -C concoct -b samp_3937_concoct_558 --server-only -P 8720 #Looks very good, let's still try to add in some primary_cluster compliments
anvi-merge \
samples/samp_3937/anvio_db/profiles/*_profile/PROFILE.db \
-o samples/samp_3937/anvio_db/profiles/SAMPLES-MERGED_all \
-c samples/samp_3937/anvio_db/contigs.db \
--sample-name samp_3937_pls_compliments
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-merge samples/samp_3937/anvio_db/profiles/*_profile/PROFILE.db -o samples/samp_3937/anvio_db/profiles/SAMPLES-MERGED_all -c samples/samp_3937/anvio_db/contigs.db --sample-name samp_3937_pls_compliments
############
#Import bins
############
anvi-import-collection \
samples/samp_3937/anvio_db/collections/concoct_contigs.txt \
-p samples/samp_3937/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_3937/anvio_db/contigs.db \
-C concoct \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection samples/samp_3937/anvio_db/collections/concoct_contigs.txt -p samples/samp_3937/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_3937/anvio_db/contigs.db -C concoct --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
anvi-refine \
-p samples/samp_3937/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_3937/anvio_db/contigs.db \
-C concoct \
-b samp_3937_concoct_558 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_3937/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_3937/anvio_db/contigs.db -C concoct -b samp_3937_concoct_558 --server-only -P 8720
#Still looks good, no refine!
```
10.) Merge Anvi'o profiles, import collections, interact, visualize, and refine bins
samp_468
```{bash}
module load anvio/7
anvi-merge \
samples/samp_468/anvio_db/profiles/*_profile/PROFILE.db \
-o samples/samp_468/anvio_db/profiles/SAMPLES-MERGED_all \
-c samples/samp_468/anvio_db/contigs.db \
--sample-name samp_468_pls_compliments
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-merge samples/samp_468/anvio_db/profiles/*_profile/PROFILE.db -o samples/samp_468/anvio_db/profiles/SAMPLES-MERGED_all -c samples/samp_468/anvio_db/contigs.db --sample-name samp_468_pls_compliments
############
#Import bins
############
mkdir samples/samp_468/anvio_db/collections
cp /geomicro/data2/kiledal/GLAMR/data/omics/metagenomes/samp_468/bins/das_tool/*.tsv \
samples/samp_468/anvio_db/collections/
#imports contig assignments from the following binners: concoct, maxbin, metabat2, metadecoder, semibin, VAMB
anvi-import-collection \
samples/samp_468/anvio_db/collections/metabat2_contigs.txt \
-p samples/samp_468/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_468/anvio_db/contigs.db \
-C metabat2 \
--contigs-mode
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-import-collection \
samples/samp_468/anvio_db/collections/metabat2_contigs.txt -p samples/samp_468/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_468/anvio_db/contigs.db -C metabat2 --contigs-mode
#####################################
#Interact, visualize, and refine bins
#####################################
anvi-interactive -p samples/samp_468/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_468/anvio_db/contigs.db -C metabat2 --server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-interactive \
-p samples/samp_468/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_468/anvio_db/contigs.db \
-C metabat2 \
--server-only \
-P 8720
anvi-refine \
-p samples/samp_468/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \
-c samples/samp_468/anvio_db/contigs.db \
-C metabat2 \
-b samp_468_metabat2_39 \
--server-only -P 8720
#Example: NOTE - Needed to run in single line or files couldn't be found by Anvi'o
anvi-refine -p samples/samp_468/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db -c samples/samp_468/anvio_db/contigs.db -C metabat2 -b samp_468_metabat2_39 --server-only -P 8720
#############################################
Summarize bins / export new refine bin fasta+
#############################################
anvi-summarize \
-p samples/samp_468/anvio_db/profiles/SAMPLES-MERGED_all/PROFILE.db \