update prokka version

README.md

@@ -45,7 +45,7 @@ Before updating, back up your `config-metawrap` file so you do not have to re-do
 conda update -y -c ursky metawrap-mg
 
 # or for a specific version:
-conda install -y -c ursky metawrap-mg=1.3.0
+conda install -y -c ursky metawrap-mg=1.3.1
 ```
 
 If you are using the (recommended) manual instalation of metaWRAP, simply run `git pull` inside the metaWRAP directory.
@@ -118,7 +118,7 @@ conda install -y -c ursky metawrap-mg
 #### Express Installation:
 Directly create a metawrap-specific environment. This accomplishes the same thing as the "Better installation", but with fewer steps.
 ```
- conda create --name metawrap-env --channel ursky --channel bioconda --channel conda-forge metawrap-mg=1.3
+ conda create --name metawrap-env --channel ursky --channel bioconda --channel conda-forge metawrap-mg=1.3.1
  conda activate metawrap-env
 
 # To fix the CONCOCT endless warning messages in metaWRAP=1.2+, run

Usage_tutorial.md

@@ -183,11 +183,13 @@ metawrap bin_refinement -o BIN_REFINEMENT -t 96 -A INITIAL_BINNING/metabat2_bins
 
 In the output directory, you will see the three original bin folders we fed in, as well as `metaWRAP` directory, which contains the final, consilidated bins. You will also see a `Binning_refiner` bin set - this is an internal benchmark for the bins produced by using another consolidation software (Binning_refiner). You can ignore this set - it will likely have low contamination and completion. You will also see .stats files for each one of the bin directories. 
 ```
-concoct_bins.stats maxbin2_bins.stats metabat2_bins.stats metawrap.stats Binning_refiner.stats
-concoct_bins maxbin2_bins metabat2_bins metawrap Binning_refiner
+concoct_bins.stats maxbin2_bins.stats metabat2_bins.stats metawrap_50_10.stats Binning_refiner.stats
+concoct_bins maxbin2_bins metabat2_bins metawrap_50_10_bins Binning_refiner
 ```
 
-The .stat files contain usefull information about each bin, inscuding its completeness and contamination. For example, `cat BIN_REFINEMENT/metawrap.stats`:
+Note that the '_50_10_' part of the naming refers to the `-c` and `-x` options you chose for the algorithm optimization. You can repeat the run with the same output directory using different options to get different results and see what works best on your sample (using '_90_5_' for example to get more near-complete genomes). The re-calculation will use the existing binning outputs, greatly reducing run time.
+
+The .stat files contain usefull information about each bin, inscuding its completeness and contamination. For example, `cat BIN_REFINEMENT/metawrap_50_10.stats`:
 ```
 bin completeness contamination GC lineage N50 size binner
 bin.5 100.0 1.6 0.311 Euryarchaeota 12686 1705532 binsO.checkm
@@ -207,7 +209,7 @@ bin.7 52.94 1.724 0.501 Bacteria 3614 1465011 binsO.checkm
 
 To evaluate how many "good bins" (based on out >50% comp., <10% cont. metric) metaWRAP produced, we can run
 ```
-cat BIN_REFINEMENT/metawrap_bins.stats | awk '$2>50 && $3<10' | wc -l
+cat BIN_REFINEMENT/metawrap_50_10_bins.stats | awk '$2>50 && $3<10' | wc -l
 13
 ```
 
@@ -229,7 +231,7 @@ NOTE: In order to annotate the blobplot with bins with the `--bins` flag, you **
 Note2: You will need R for this module.
 
 ```
-metawrap blobology -a ASSEMBLY/final_assembly.fasta -t 96 -o BLOBOLOGY --bins BIN_REFINEMENT/metawrap_bins CLEAN_READS/ERR*fastq
+metawrap blobology -a ASSEMBLY/final_assembly.fasta -t 96 -o BLOBOLOGY --bins BIN_REFINEMENT/metawrap_50_10_bins CLEAN_READS/ERR*fastq
 ```
 
 You will find that the output has a number of blob plots of our communities, annotated with different levels of taxonomy or their bin membership. Note that to help with visualizing the bins, some of the plots only contain the contigs that were successfully binned (these files have `.binned.blobplot.` in their names). 
@@ -248,7 +250,7 @@ NOTE: In order to run this module, it is **highly** recomended to use the non-re
 
 Lets run the Quant_bins module:
 ```
-metawrap quant_bins -b BIN_REFINEMENT/metawrap_bins -o QUANT_BINS -a ASSEMBLY/final_assembly.fasta CLEAN_READS/ERR*fastq
+metawrap quant_bins -b BIN_REFINEMENT/metawrap_50_10_bins -o QUANT_BINS -a ASSEMBLY/final_assembly.fasta CLEAN_READS/ERR*fastq
 ```
 
 The output contains several usefull files. First, there is the `bin_abundance_heatmap.png` - a quick heatmap made to visualize the bin abundances across the samples. 
@@ -281,7 +283,7 @@ Now that we have our final, consilidated bin set in `BIN_REFINEMENT/metawrap_bin
 
 Let us run the Reassemble_bins module with all the reads we have:
 ```
-metawrap reassemble_bins -o BIN_REASSEMBLY -1 CLEAN_READS/ALL_READS_1.fastq -2 CLEAN_READS/ALL_READS_2.fastq -t 96 -m 800 -c 50 -x 10 -b BIN_REFINEMENT/metawrap_bins
+metawrap reassemble_bins -o BIN_REASSEMBLY -1 CLEAN_READS/ALL_READS_1.fastq -2 CLEAN_READS/ALL_READS_2.fastq -t 96 -m 800 -c 50 -x 10 -b BIN_REFINEMENT/metawrap_50_10_bins
 ```
 
 Looking at the output in `BIN_REASSEMBLY/reassembled_bins.stats`, we can see that 3 bins were improved though strict reassembly, 6 improved thorugh permissive reassembly, and 4 bins could not be improved (`.strict`, `.permissive`, and `.orig` bin extensions, respectively):

bin/metawrap-modules/annotate_bins.sh

@@ -119,7 +119,7 @@ for i in $(ls ${bins}); do
  echo $cmd
  $cmd
 
- if [[ $? -ne 0 ]]; then error "Something went wrong with annotating ${bin_name}. Exiting..."; fi
+ if [[ $? -ne 0 ]]; then warning "Something possibly went wrong with annotating ${bin_name}. Proceeding anyways"; fi
  if [[ ! -s ${out}/prokka_out/${bin_name}/${bin_name}.gff ]]; then error "Something went wrong with annotating ${bin_name}. Exiting..."; fi
  rm ${out}/tmp_bin.fa
 done

conda_pkg/meta.yaml

@@ -1,6 +1,6 @@
 package:
  name: metawrap-mg
- version: "1.3.0"
+ version: "1.3.1"
 
 source:
  git_url: https://github.com/bxlab/metaWRAP.git
@@ -28,7 +28,7 @@ requirements:
  - pandas 0.24.2
  - perl-bioperl
  - pplacer 1.1.alpha19
- - prokka 1.13
+ - prokka 1.*
  - quast 5.0.2
  - r-ggplot2 3.1.0
  - r-reshape2