mOTU extender

The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data. The mOTU extender is a companion tool used to extend the current mOTUs database with user provided genomes.

If you are using mOTUs, please cite:

Hans-Joachim Ruscheweyh, Alessio Milanese, Lucas Paoli, Nicolai Karcher, Quentin Clayssen, Marisa Isabell Metzger, Jakob Wirbel, Peer Bork, Daniel R. Mende, Georg Zeller & Shinichi Sunagawa. Reference genome-independent taxonomic profiling of microbiomes with mOTUs3; BioRxiv, doi: 0.1101/2021.04.20.440600

Pre-requisites

The mOTU extender was tested with:

python 3.6.7
- biopython 1.79
- numpy 1.18.2
- scipy 1.1.0
bwa 0.7.17-r1188
samtools 1.9
snakemake 6.15.5
vsearch 2.14.1
prodigal 2.6.3
fetchMGs 1.2 (link)

Installation

The mOTUs extender can be installed via GitHub:

git clone https://github.com/motu-tool/mOTUs-extender.git

Basic example

To use the mOTU extender you will need to provide 2 input data:

A folder with genomes, one file per genome with the .fa file suffix.
A 7 rank taxonomy (NCBI) file which contains the taxonomic assignation of each genome (see here for an example: mOTUs-extender/mOTUs-extender/test/genomes.tax)

We provide a test dataset with 50 genomes taken from (Buck et. al, 2021).

The mOTUs extender is a 3 step pipeline which (1) prepares the current database, (2) checks what user genomes are already part of the current database and (3) adds genomes with novel taxonomic information to the database.

0. Test Data

mkdir -p test_extension/genomes/
cp mOTUs-extender/mOTUs-extender/test/genomes/*gz test_extension/genomes/
gunzip test_extension/genomes/*gz

1. mOTUs extender - prepare

python mOTUs-extender/mOTUs-extender/motus-extender.py prepare -w test_extension/extension

Note This command will download the current mOTUs database (~3.5GB).

Commandline stdout

python mOTUs-extender/mOTUs-extender/motus-extender.py prepare -w test_extension/extension
2022-08-12 10:17:50,392 INFO: Starting mOTUs-extender
2022-08-12 10:17:50,393 INFO: Creating work folder test_extension/extension
2022-08-12 10:17:50,395 INFO: Downloading mOTUs 3.0.1 database
2022-08-12 10:17:50,396 INFO: Executing: curl https://zenodo.org/record/5140350/files/db_mOTU_v3.0.1.tar.gz -o test_extension/extension/orig_db/db_mOTU_v3.0.1.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 3342M  100 3342M    0     0  29.7M      0  0:01:52  0:01:52 --:--:-- 35.8M
2022-08-12 10:19:42,904 INFO: Uncompressing mOTUs 3.0.1 database
2022-08-12 10:19:42,904 INFO: Executing: tar -xzvf test_extension/extension/orig_db/db_mOTU_v3.0.1.tar.gz -C test_extension/extension/orig_db
db_mOTU/
db_mOTU/db_mOTU_bam_header_NR
db_mOTU/db_mOTU_padding_coordinates_NR.tsv
db_mOTU/db_mOTU_MAP_MGCs_to_mOTUs.tsv
db_mOTU/db_mOTU_taxonomy_ref-mOTUs.tsv
db_mOTU/db_mOTU_taxonomy_CAMI.tsv
db_mOTU/db_mOTU_DB_CEN.fasta.ann
db_mOTU/db_mOTU_DB_CEN.fasta.bwt
db_mOTU/db_mOTU_versions
db_mOTU/public_profiles/
db_mOTU/public_profiles/mOTUs.profiles_environments.gz
db_mOTU/public_profiles/mOTUs.profiles.gz
db_mOTU/db_mOTU_padding_coordinates_CEN.tsv
db_mOTU/db_mOTU_DB_NR.fasta.bwt
db_mOTU/db_mOTU_DB_NR.fasta.ann
db_mOTU/db_mOTU_bam_header_CEN
db_mOTU/db_mOTU_taxonomy_ref-mOTUs_short_names.tsv
db_mOTU/db_mOTU_MAP_genes_to_MGCs.tsv
db_mOTU/README
db_mOTU/db_mOTU_taxonomy_meta-mOTUs.tsv
db_mOTU/db_mOTU_DB_CEN.fasta
db_mOTU/db_mOTU_test/
db_mOTU/db_mOTU_test/test1.motus
db_mOTU/db_mOTU_test/test1_single.fastq
db_mOTU/db_mOTU_DB_NR.fasta.amb
db_mOTU/db_mOTU_DB_NR.fasta.sa
db_mOTU/db_mOTU_DB_NR.fasta.pac
db_mOTU/db_mOTU_DB_CEN.fasta.annotations
db_mOTU/db_mOTU_DB_CEN.fasta.pac
db_mOTU/db_mOTU_DB_CEN.fasta.sa
db_mOTU/db_mOTU_DB_NR.fasta
db_mOTU/db_mOTU_genes_length_NR
db_mOTU/db_mOTU_DB_CEN.fasta.amb
db_mOTU/db_mOTU_MAP_MGCs_to_mOTUs_in-line.tsv
2022-08-12 10:21:07,307 INFO: Preparing mOTUs 3.0.1 database for extension
2022-08-12 10:21:07,308 INFO: Executing: python mOTUs-extender/mOTUs-extender/prepare_mOTUs.py test_extension/extension/orig_db/db_mOTU/ test_extension/extension/temp_db_folder
####################################
#### Checking db_mOTU_versions #####
####################################
Version of motus is 2.6.0. Correct version. Continue
Version of nr is 2.6.0. Correct version. Continue
Version of cen is 2.6.0. Correct version. Continue
Version of append is 2.6.0. Correct version. Continue
Version of map_genes_to_mOTUs is 2.6.0. Correct version. Continue
Version of map_mOTUs_to_LGs is 2.6.0. Correct version. Continue
Version of runBWA is 2.6.0. Correct version. Continue
Version of specI_tax is 2.6.0. Correct version. Continue
Version of mOTULG_tax is 2.6.0. Correct version. Continue
###################################################
##### Processing db_mOTU_MAP_MGCs_to_mOTUs.tsv ####
###################################################
Found 521780 MGCs of which 213652 MGCs belong to unassigned
###################################################
#### Processing db_mOTU_MAP_genes_to_MGCs.tsv #####
###################################################
Found 1184175 MGs of which 222782 MGs belong to unassigned
####################################################
# Processing db_mOTU_MAP_MGCs_to_mOTUs_in-line.tsv #
####################################################
unassigned mOTU written: 1
ref-mOTU/meta-mOTU mOTUs written: 33570
####################################################
## Processing db_mOTU_padding_coordinates_NR.tsv ###
####################################################
-1 MGs written: 222782
ref-mOTU/meta-mOTU MGs written: 961393
####################################################
## Processing db_mOTU_padding_coordinates_CEN.tsv ##
####################################################
unassigned MGs written: 213652
ref-mOTU/meta-mOTU MGs written: 308128
#####################################################
Copying db_mOTU_taxonomy_ref-mOTUs_short_names.tsv
#####################################################
#####################################################
Copying db_mOTU_taxonomy_CAMI.tsv
#####################################################
#####################################################
Copying db_mOTU_taxonomy_ref-mOTUs.tsv
#####################################################
#####################################################
Copying README
#####################################################
#####################################################
Copying db_mOTU_taxonomy_meta-mOTUs.tsv
#####################################################
#####################################################
Copying db_mOTU_test
#####################################################
#####################################################
Processing db_mOTU_genes_length_NR
#####################################################
unassigned MGs written: 222782
ref-mOTU/meta-mOTU MGs written: 961393
#####################################################
Processing db_mOTU_DB_CEN.fasta.annotations
#####################################################
unassigned MGs written: 213652
ref-mOTU/meta-mOTU MGs written: 308128
#####################################################
Processing db_mOTU_bam_header_CEN
#####################################################
unassigned MGs written: 213652
ref-mOTU/meta-mOTU MGs written: 308128
#####################################################
Processing db_mOTU_bam_header_NR
#####################################################
unassigned MGs written: 222782
ref-mOTU/meta-mOTU MGs written: 961393
####################################
### Processing db_mOTU_DB_NR.fasta ####
####################################
50000/1184175 MGs read
100000/1184175 MGs read
150000/1184175 MGs read
200000/1184175 MGs read
250000/1184175 MGs read
300000/1184175 MGs read
350000/1184175 MGs read
400000/1184175 MGs read
450000/1184175 MGs read
500000/1184175 MGs read
550000/1184175 MGs read
600000/1184175 MGs read
650000/1184175 MGs read
700000/1184175 MGs read
750000/1184175 MGs read
800000/1184175 MGs read
850000/1184175 MGs read
900000/1184175 MGs read
950000/1184175 MGs read
1000000/1184175 MGs read
1050000/1184175 MGs read
1100000/1184175 MGs read
1150000/1184175 MGs read
unassigned MGs written: 222782
ref-mOTU/meta-mOTU MGs written: 961393
####################################
### Processing db_mOTU_DB_CEN.fasta ####
####################################
50000/163789 MGs read
100000/163789 MGs read
150000/163789 MGs read
200000/163789 MGs read
250000/163789 MGs read
300000/163789 MGs read
350000/163789 MGs read
400000/163789 MGs read
450000/163789 MGs read
500000/163789 MGs read
unassigned MGs written: 213652
ref-mOTU/meta-mOTU MGs written: 308128
Start building vsearch database on test_extension/extension/temp_db_folder/db_mOTU//db_mOTU_DB_NR.fasta
vsearch v2.14.1_linux_x86_64, 2011.3GB RAM, 256 cores
https://github.com/torognes/vsearch

Reading file test_extension/extension/temp_db_folder/db_mOTU//db_mOTU_DB_NR.fasta 100%
1647961589 nt in 961393 seqs, min 403, max 9725, avg 1714
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Writing UDB file 100%
Finished building vsearch database on test_extension/extension/temp_db_folder/db_mOTU//db_mOTU_DB_NR.fasta
####################################
### Finished mOTUs DB preparation ##
####################################
2022-08-12 10:30:51,695 INFO: mOTUs-extender finished successfully

2. mOTUs extender - membership

python mOTUs-extender/mOTUs-extender/motus-extender.py membership -w test_extension/extension/ -g test_extension/genomes/ -t 32

Commandline stdout

python mOTUs-extender/mOTUs-extender/motus-extender.py membership -w test_extension/extension/ -g test_extension/genomes/ -t 32
2022-08-12 11:20:36,781 INFO: Starting mOTUs-extender
2022-08-12 11:20:36,783 INFO: Executing: gunzip -c mOTUs-extender/mOTUs-extender/mOTU.v3.0.mOTU-LG.map.gz > test_extension/extension/mOTU.v3.0.mOTU-LG.map
2022-08-12 11:20:37,188 INFO: Found 50 genomes in test_extension/genomes path
2022-08-12 11:20:37,250 INFO: Executing: snakemake -s mOTUs-extender/mOTUs-extender/0prod_fetchMGs.py --config mapfile=test_extension/extension/mOTU.v3.0.mOTU-LG.map infolder=test_extension/genomes/ outfolder=test_extension/extension/ temp_db_folder=test_extension/extension/temp_db_folder/ scriptfolder=mOTUs-extender/mOTUs-extender genomes=test_extension/genomes/GCA_903824045.1.fa,test_extension/genomes/GCA_903824635.1.fa,test_extension/genomes/GCA_903824795.1.fa,test_extension/genomes/GCA_903826635.1.fa,test_extension/genomes/GCA_903835685.1.fa,test_extension/genomes/GCA_903839445.1.fa,test_extension/genomes/GCA_903841135.1.fa,test_extension/genomes/GCA_903842315.1.fa,test_extension/genomes/GCA_903843765.1.fa,test_extension/genomes/GCA_903845665.1.fa,test_extension/genomes/GCA_903853455.1.fa,test_extension/genomes/GCA_903853495.1.fa,test_extension/genomes/GCA_903854225.1.fa,test_extension/genomes/GCA_903854255.1.fa,test_extension/genomes/GCA_903857725.1.fa,test_extension/genomes/GCA_903869175.1.fa,test_extension/genomes/GCA_903869725.1.fa,test_extension/genomes/GCA_903871585.1.fa,test_extension/genomes/GCA_903875175.1.fa,test_extension/genomes/GCA_903879295.1.fa,test_extension/genomes/GCA_903883715.1.fa,test_extension/genomes/GCA_903884585.1.fa,test_extension/genomes/GCA_903888055.1.fa,test_extension/genomes/GCA_903894295.1.fa,test_extension/genomes/GCA_903895255.1.fa,test_extension/genomes/GCA_903899515.1.fa,test_extension/genomes/GCA_903900705.1.fa,test_extension/genomes/GCA_903902845.1.fa,test_extension/genomes/GCA_903902895.1.fa,test_extension/genomes/GCA_903907865.1.fa,test_extension/genomes/GCA_903907955.1.fa,test_extension/genomes/GCA_903913555.1.fa,test_extension/genomes/GCA_903914905.1.fa,test_extension/genomes/GCA_903915725.1.fa,test_extension/genomes/GCA_903915855.1.fa,test_extension/genomes/GCA_903918315.1.fa,test_extension/genomes/GCA_903920605.1.fa,test_extension/genomes/GCA_903920995.1.fa,test_extension/genomes/GCA_903924625.1.fa,test_extension/genomes/GCA_903928895.1.fa,test_extension/genomes/GCA_903934285.1.fa,test_extension/genomes/GCA_903935095.1.fa,test_extension/genomes/GCA_903936775.1.fa,test_extension/genomes/GCA_903937725.1.fa,test_extension/genomes/GCA_903939965.1.fa,test_extension/genomes/GCA_903945225.1.fa,test_extension/genomes/GCA_903945495.1.fa,test_extension/genomes/GCA_903953565.1.fa,test_extension/genomes/GCA_903959825.1.fa,test_extension/genomes/GCA_903961455.1.fa -j 32 -k
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 32
Rules claiming more threads will be scaled down.
Job stats:
job                 count    min threads    max threads
----------------  -------  -------------  -------------
all                     1              1              1
prodigalfetchMgs       50              1              1
total                  51              1              1

Select jobs to execute...

[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903920605.1.fa
    output: test_extension/extension/genes/GCA_903920605.1/GCA_903920605.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903920605.1/GCA_903920605.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903920605.1/GCA_903920605.1.prodigal_fetchMGs.command
    jobid: 37
    benchmark: test_extension/extension/genes/GCA_903920605.1/GCA_903920605.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903920605.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903857725.1.fa
    output: test_extension/extension/genes/GCA_903857725.1/GCA_903857725.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903857725.1/GCA_903857725.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903857725.1/GCA_903857725.1.prodigal_fetchMGs.command
    jobid: 15
    benchmark: test_extension/extension/genes/GCA_903857725.1/GCA_903857725.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903857725.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903939965.1.fa
    output: test_extension/extension/genes/GCA_903939965.1/GCA_903939965.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903939965.1/GCA_903939965.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903939965.1/GCA_903939965.1.prodigal_fetchMGs.command
    jobid: 45
    benchmark: test_extension/extension/genes/GCA_903939965.1/GCA_903939965.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903939965.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903842315.1.fa
    output: test_extension/extension/genes/GCA_903842315.1/GCA_903842315.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903842315.1/GCA_903842315.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903842315.1/GCA_903842315.1.prodigal_fetchMGs.command
    jobid: 8
    benchmark: test_extension/extension/genes/GCA_903842315.1/GCA_903842315.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903842315.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903888055.1.fa
    output: test_extension/extension/genes/GCA_903888055.1/GCA_903888055.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903888055.1/GCA_903888055.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903888055.1/GCA_903888055.1.prodigal_fetchMGs.command
    jobid: 23
    benchmark: test_extension/extension/genes/GCA_903888055.1/GCA_903888055.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903888055.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903920995.1.fa
    output: test_extension/extension/genes/GCA_903920995.1/GCA_903920995.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903920995.1/GCA_903920995.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903920995.1/GCA_903920995.1.prodigal_fetchMGs.command
    jobid: 38
    benchmark: test_extension/extension/genes/GCA_903920995.1/GCA_903920995.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903920995.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903869175.1.fa
    output: test_extension/extension/genes/GCA_903869175.1/GCA_903869175.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903869175.1/GCA_903869175.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903869175.1/GCA_903869175.1.prodigal_fetchMGs.command
    jobid: 16
    benchmark: test_extension/extension/genes/GCA_903869175.1/GCA_903869175.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903869175.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903907955.1.fa
    output: test_extension/extension/genes/GCA_903907955.1/GCA_903907955.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903907955.1/GCA_903907955.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903907955.1/GCA_903907955.1.prodigal_fetchMGs.command
    jobid: 31
    benchmark: test_extension/extension/genes/GCA_903907955.1/GCA_903907955.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903907955.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903824635.1.fa
    output: test_extension/extension/genes/GCA_903824635.1/GCA_903824635.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903824635.1/GCA_903824635.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903824635.1/GCA_903824635.1.prodigal_fetchMGs.command
    jobid: 2
    benchmark: test_extension/extension/genes/GCA_903824635.1/GCA_903824635.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903824635.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903945225.1.fa
    output: test_extension/extension/genes/GCA_903945225.1/GCA_903945225.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903945225.1/GCA_903945225.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903945225.1/GCA_903945225.1.prodigal_fetchMGs.command
    jobid: 46
    benchmark: test_extension/extension/genes/GCA_903945225.1/GCA_903945225.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903945225.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903843765.1.fa
    output: test_extension/extension/genes/GCA_903843765.1/GCA_903843765.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903843765.1/GCA_903843765.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903843765.1/GCA_903843765.1.prodigal_fetchMGs.command
    jobid: 9
    benchmark: test_extension/extension/genes/GCA_903843765.1/GCA_903843765.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903843765.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903945495.1.fa
    output: test_extension/extension/genes/GCA_903945495.1/GCA_903945495.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903945495.1/GCA_903945495.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903945495.1/GCA_903945495.1.prodigal_fetchMGs.command
    jobid: 47
    benchmark: test_extension/extension/genes/GCA_903945495.1/GCA_903945495.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903945495.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903902895.1.fa
    output: test_extension/extension/genes/GCA_903902895.1/GCA_903902895.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903902895.1/GCA_903902895.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903902895.1/GCA_903902895.1.prodigal_fetchMGs.command
    jobid: 29
    benchmark: test_extension/extension/genes/GCA_903902895.1/GCA_903902895.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903902895.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903826635.1.fa
    output: test_extension/extension/genes/GCA_903826635.1/GCA_903826635.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903826635.1/GCA_903826635.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903826635.1/GCA_903826635.1.prodigal_fetchMGs.command
    jobid: 4
    benchmark: test_extension/extension/genes/GCA_903826635.1/GCA_903826635.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903826635.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903875175.1.fa
    output: test_extension/extension/genes/GCA_903875175.1/GCA_903875175.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903875175.1/GCA_903875175.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903875175.1/GCA_903875175.1.prodigal_fetchMGs.command
    jobid: 19
    benchmark: test_extension/extension/genes/GCA_903875175.1/GCA_903875175.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903875175.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903915725.1.fa
    output: test_extension/extension/genes/GCA_903915725.1/GCA_903915725.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903915725.1/GCA_903915725.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903915725.1/GCA_903915725.1.prodigal_fetchMGs.command
    jobid: 34
    benchmark: test_extension/extension/genes/GCA_903915725.1/GCA_903915725.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903915725.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903959825.1.fa
    output: test_extension/extension/genes/GCA_903959825.1/GCA_903959825.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903959825.1/GCA_903959825.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903959825.1/GCA_903959825.1.prodigal_fetchMGs.command
    jobid: 49
    benchmark: test_extension/extension/genes/GCA_903959825.1/GCA_903959825.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903959825.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903853495.1.fa
    output: test_extension/extension/genes/GCA_903853495.1/GCA_903853495.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903853495.1/GCA_903853495.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903853495.1/GCA_903853495.1.prodigal_fetchMGs.command
    jobid: 12
    benchmark: test_extension/extension/genes/GCA_903853495.1/GCA_903853495.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903853495.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903900705.1.fa
    output: test_extension/extension/genes/GCA_903900705.1/GCA_903900705.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903900705.1/GCA_903900705.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903900705.1/GCA_903900705.1.prodigal_fetchMGs.command
    jobid: 27
    benchmark: test_extension/extension/genes/GCA_903900705.1/GCA_903900705.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903900705.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903935095.1.fa
    output: test_extension/extension/genes/GCA_903935095.1/GCA_903935095.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903935095.1/GCA_903935095.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903935095.1/GCA_903935095.1.prodigal_fetchMGs.command
    jobid: 42
    benchmark: test_extension/extension/genes/GCA_903935095.1/GCA_903935095.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903935095.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903879295.1.fa
    output: test_extension/extension/genes/GCA_903879295.1/GCA_903879295.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903879295.1/GCA_903879295.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903879295.1/GCA_903879295.1.prodigal_fetchMGs.command
    jobid: 20
    benchmark: test_extension/extension/genes/GCA_903879295.1/GCA_903879295.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903879295.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903835685.1.fa
    output: test_extension/extension/genes/GCA_903835685.1/GCA_903835685.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903835685.1/GCA_903835685.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903835685.1/GCA_903835685.1.prodigal_fetchMGs.command
    jobid: 5
    benchmark: test_extension/extension/genes/GCA_903835685.1/GCA_903835685.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903835685.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903915855.1.fa
    output: test_extension/extension/genes/GCA_903915855.1/GCA_903915855.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903915855.1/GCA_903915855.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903915855.1/GCA_903915855.1.prodigal_fetchMGs.command
    jobid: 35
    benchmark: test_extension/extension/genes/GCA_903915855.1/GCA_903915855.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903915855.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903961455.1.fa
    output: test_extension/extension/genes/GCA_903961455.1/GCA_903961455.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903961455.1/GCA_903961455.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903961455.1/GCA_903961455.1.prodigal_fetchMGs.command
    jobid: 50
    benchmark: test_extension/extension/genes/GCA_903961455.1/GCA_903961455.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903961455.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903854255.1.fa
    output: test_extension/extension/genes/GCA_903854255.1/GCA_903854255.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903854255.1/GCA_903854255.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903854255.1/GCA_903854255.1.prodigal_fetchMGs.command
    jobid: 14
    benchmark: test_extension/extension/genes/GCA_903854255.1/GCA_903854255.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903854255.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903854225.1.fa
    output: test_extension/extension/genes/GCA_903854225.1/GCA_903854225.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903854225.1/GCA_903854225.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903854225.1/GCA_903854225.1.prodigal_fetchMGs.command
    jobid: 13
    benchmark: test_extension/extension/genes/GCA_903854225.1/GCA_903854225.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903854225.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:38 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903902845.1.fa
    output: test_extension/extension/genes/GCA_903902845.1/GCA_903902845.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903902845.1/GCA_903902845.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903902845.1/GCA_903902845.1.prodigal_fetchMGs.command
    jobid: 28
    benchmark: test_extension/extension/genes/GCA_903902845.1/GCA_903902845.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903902845.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:39 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903936775.1.fa
    output: test_extension/extension/genes/GCA_903936775.1/GCA_903936775.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903936775.1/GCA_903936775.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903936775.1/GCA_903936775.1.prodigal_fetchMGs.command
    jobid: 43
    benchmark: test_extension/extension/genes/GCA_903936775.1/GCA_903936775.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903936775.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:39 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903839445.1.fa
    output: test_extension/extension/genes/GCA_903839445.1/GCA_903839445.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903839445.1/GCA_903839445.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903839445.1/GCA_903839445.1.prodigal_fetchMGs.command
    jobid: 6
    benchmark: test_extension/extension/genes/GCA_903839445.1/GCA_903839445.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903839445.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:39 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903883715.1.fa
    output: test_extension/extension/genes/GCA_903883715.1/GCA_903883715.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903883715.1/GCA_903883715.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903883715.1/GCA_903883715.1.prodigal_fetchMGs.command
    jobid: 21
    benchmark: test_extension/extension/genes/GCA_903883715.1/GCA_903883715.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903883715.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:39 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903918315.1.fa
    output: test_extension/extension/genes/GCA_903918315.1/GCA_903918315.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903918315.1/GCA_903918315.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903918315.1/GCA_903918315.1.prodigal_fetchMGs.command
    jobid: 36
    benchmark: test_extension/extension/genes/GCA_903918315.1/GCA_903918315.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903918315.1
    resources: tmpdir=/tmp


[Fri Aug 12 11:20:39 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903937725.1.fa
    output: test_extension/extension/genes/GCA_903937725.1/GCA_903937725.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903937725.1/GCA_903937725.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903937725.1/GCA_903937725.1.prodigal_fetchMGs.command
    jobid: 44
    benchmark: test_extension/extension/genes/GCA_903937725.1/GCA_903937725.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903937725.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903854225.1/GCA_903854225.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:30 2022]
Finished job 13.
1 of 51 steps (2%) done
Select jobs to execute...

[Fri Aug 12 11:21:30 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903934285.1.fa
    output: test_extension/extension/genes/GCA_903934285.1/GCA_903934285.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903934285.1/GCA_903934285.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903934285.1/GCA_903934285.1.prodigal_fetchMGs.command
    jobid: 41
    benchmark: test_extension/extension/genes/GCA_903934285.1/GCA_903934285.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903934285.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903853495.1/GCA_903853495.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:34 2022]
Finished job 12.
2 of 51 steps (4%) done
Select jobs to execute...

[Fri Aug 12 11:21:34 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903841135.1.fa
    output: test_extension/extension/genes/GCA_903841135.1/GCA_903841135.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903841135.1/GCA_903841135.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903841135.1/GCA_903841135.1.prodigal_fetchMGs.command
    jobid: 7
    benchmark: test_extension/extension/genes/GCA_903841135.1/GCA_903841135.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903841135.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903888055.1/GCA_903888055.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:45 2022]
Finished job 23.
3 of 51 steps (6%) done
Select jobs to execute...

[Fri Aug 12 11:21:45 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903924625.1.fa
    output: test_extension/extension/genes/GCA_903924625.1/GCA_903924625.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903924625.1/GCA_903924625.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903924625.1/GCA_903924625.1.prodigal_fetchMGs.command
    jobid: 39
    benchmark: test_extension/extension/genes/GCA_903924625.1/GCA_903924625.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903924625.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903826635.1/GCA_903826635.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:47 2022]
Finished job 4.
4 of 51 steps (8%) done
Select jobs to execute...

[Fri Aug 12 11:21:47 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903953565.1.fa
    output: test_extension/extension/genes/GCA_903953565.1/GCA_903953565.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903953565.1/GCA_903953565.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903953565.1/GCA_903953565.1.prodigal_fetchMGs.command
    jobid: 48
    benchmark: test_extension/extension/genes/GCA_903953565.1/GCA_903953565.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903953565.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903939965.1/GCA_903939965.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:50 2022]
Finished job 45.
5 of 51 steps (10%) done
Select jobs to execute...

[Fri Aug 12 11:21:50 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903824795.1.fa
    output: test_extension/extension/genes/GCA_903824795.1/GCA_903824795.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903824795.1/GCA_903824795.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903824795.1/GCA_903824795.1.prodigal_fetchMGs.command
    jobid: 3
    benchmark: test_extension/extension/genes/GCA_903824795.1/GCA_903824795.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903824795.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903835685.1/GCA_903835685.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:50 2022]
Finished job 5.
6 of 51 steps (12%) done
Select jobs to execute...

[Fri Aug 12 11:21:50 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903845665.1.fa
    output: test_extension/extension/genes/GCA_903845665.1/GCA_903845665.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903845665.1/GCA_903845665.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903845665.1/GCA_903845665.1.prodigal_fetchMGs.command
    jobid: 10
    benchmark: test_extension/extension/genes/GCA_903845665.1/GCA_903845665.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903845665.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903945225.1/GCA_903945225.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:50 2022]
Finished job 46.
7 of 51 steps (14%) done
Select jobs to execute...

[Fri Aug 12 11:21:50 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903895255.1.fa
    output: test_extension/extension/genes/GCA_903895255.1/GCA_903895255.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903895255.1/GCA_903895255.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903895255.1/GCA_903895255.1.prodigal_fetchMGs.command
    jobid: 25
    benchmark: test_extension/extension/genes/GCA_903895255.1/GCA_903895255.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903895255.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903935095.1/GCA_903935095.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:50 2022]
Finished job 42.
8 of 51 steps (16%) done
Select jobs to execute...

[Fri Aug 12 11:21:51 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903928895.1.fa
    output: test_extension/extension/genes/GCA_903928895.1/GCA_903928895.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903928895.1/GCA_903928895.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903928895.1/GCA_903928895.1.prodigal_fetchMGs.command
    jobid: 40
    benchmark: test_extension/extension/genes/GCA_903928895.1/GCA_903928895.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903928895.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903879295.1/GCA_903879295.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:51 2022]
Finished job 20.
9 of 51 steps (18%) done
Select jobs to execute...

[Fri Aug 12 11:21:51 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903871585.1.fa
    output: test_extension/extension/genes/GCA_903871585.1/GCA_903871585.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903871585.1/GCA_903871585.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903871585.1/GCA_903871585.1.prodigal_fetchMGs.command
    jobid: 18
    benchmark: test_extension/extension/genes/GCA_903871585.1/GCA_903871585.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903871585.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903959825.1/GCA_903959825.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:51 2022]
Finished job 49.
10 of 51 steps (20%) done
Select jobs to execute...

[Fri Aug 12 11:21:51 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903914905.1.fa
    output: test_extension/extension/genes/GCA_903914905.1/GCA_903914905.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903914905.1/GCA_903914905.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903914905.1/GCA_903914905.1.prodigal_fetchMGs.command
    jobid: 33
    benchmark: test_extension/extension/genes/GCA_903914905.1/GCA_903914905.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903914905.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903824635.1/GCA_903824635.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:52 2022]
Finished job 2.
11 of 51 steps (22%) done
Select jobs to execute...

[Fri Aug 12 11:21:52 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903913555.1.fa
    output: test_extension/extension/genes/GCA_903913555.1/GCA_903913555.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903913555.1/GCA_903913555.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903913555.1/GCA_903913555.1.prodigal_fetchMGs.command
    jobid: 32
    benchmark: test_extension/extension/genes/GCA_903913555.1/GCA_903913555.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903913555.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903883715.1/GCA_903883715.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:52 2022]
Finished job 21.
12 of 51 steps (24%) done
Select jobs to execute...

[Fri Aug 12 11:21:52 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903869725.1.fa
    output: test_extension/extension/genes/GCA_903869725.1/GCA_903869725.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903869725.1/GCA_903869725.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903869725.1/GCA_903869725.1.prodigal_fetchMGs.command
    jobid: 17
    benchmark: test_extension/extension/genes/GCA_903869725.1/GCA_903869725.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903869725.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903900705.1/GCA_903900705.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:53 2022]
Finished job 27.
13 of 51 steps (25%) done
Select jobs to execute...

[Fri Aug 12 11:21:53 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903824045.1.fa
    output: test_extension/extension/genes/GCA_903824045.1/GCA_903824045.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903824045.1/GCA_903824045.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903824045.1/GCA_903824045.1.prodigal_fetchMGs.command
    jobid: 1
    benchmark: test_extension/extension/genes/GCA_903824045.1/GCA_903824045.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903824045.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903842315.1/GCA_903842315.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:53 2022]
Finished job 8.
14 of 51 steps (27%) done
Select jobs to execute...

[Fri Aug 12 11:21:53 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903907865.1.fa
    output: test_extension/extension/genes/GCA_903907865.1/GCA_903907865.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903907865.1/GCA_903907865.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903907865.1/GCA_903907865.1.prodigal_fetchMGs.command
    jobid: 30
    benchmark: test_extension/extension/genes/GCA_903907865.1/GCA_903907865.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903907865.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903937725.1/GCA_903937725.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:54 2022]
Finished job 44.
15 of 51 steps (29%) done
Select jobs to execute...

[Fri Aug 12 11:21:54 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903853455.1.fa
    output: test_extension/extension/genes/GCA_903853455.1/GCA_903853455.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903853455.1/GCA_903853455.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903853455.1/GCA_903853455.1.prodigal_fetchMGs.command
    jobid: 11
    benchmark: test_extension/extension/genes/GCA_903853455.1/GCA_903853455.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903853455.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903857725.1/GCA_903857725.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:54 2022]
Finished job 15.
16 of 51 steps (31%) done
Select jobs to execute...

[Fri Aug 12 11:21:54 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903899515.1.fa
    output: test_extension/extension/genes/GCA_903899515.1/GCA_903899515.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903899515.1/GCA_903899515.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903899515.1/GCA_903899515.1.prodigal_fetchMGs.command
    jobid: 26
    benchmark: test_extension/extension/genes/GCA_903899515.1/GCA_903899515.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903899515.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903902845.1/GCA_903902845.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:54 2022]
Finished job 28.
17 of 51 steps (33%) done
Select jobs to execute...

[Fri Aug 12 11:21:54 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903884585.1.fa
    output: test_extension/extension/genes/GCA_903884585.1/GCA_903884585.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903884585.1/GCA_903884585.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903884585.1/GCA_903884585.1.prodigal_fetchMGs.command
    jobid: 22
    benchmark: test_extension/extension/genes/GCA_903884585.1/GCA_903884585.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903884585.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903918315.1/GCA_903918315.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:54 2022]
Finished job 36.
18 of 51 steps (35%) done
Select jobs to execute...

[Fri Aug 12 11:21:54 2022]
rule prodigalfetchMgs:
    input: test_extension/genomes/GCA_903894295.1.fa
    output: test_extension/extension/genes/GCA_903894295.1/GCA_903894295.1.prodigal_fetchMGs.done
    log: test_extension/extension/genes/GCA_903894295.1/GCA_903894295.1.prodigal_fetchMGs.log, test_extension/extension/genes/GCA_903894295.1/GCA_903894295.1.prodigal_fetchMGs.command
    jobid: 24
    benchmark: test_extension/extension/genes/GCA_903894295.1/GCA_903894295.1.prodigal_fetchMGs.benchmark
    wildcards: sample=GCA_903894295.1
    resources: tmpdir=/tmp

Touching output file test_extension/extension/genes/GCA_903907955.1/GCA_903907955.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:54 2022]
Finished job 31.
19 of 51 steps (37%) done
Touching output file test_extension/extension/genes/GCA_903869175.1/GCA_903869175.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:55 2022]
Finished job 16.
20 of 51 steps (39%) done
Touching output file test_extension/extension/genes/GCA_903843765.1/GCA_903843765.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:55 2022]
Finished job 9.
21 of 51 steps (41%) done
Touching output file test_extension/extension/genes/GCA_903920605.1/GCA_903920605.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:56 2022]
Finished job 37.
22 of 51 steps (43%) done
Touching output file test_extension/extension/genes/GCA_903875175.1/GCA_903875175.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:56 2022]
Finished job 19.
23 of 51 steps (45%) done
Touching output file test_extension/extension/genes/GCA_903915725.1/GCA_903915725.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:56 2022]
Finished job 34.
24 of 51 steps (47%) done
Touching output file test_extension/extension/genes/GCA_903945495.1/GCA_903945495.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:56 2022]
Finished job 47.
25 of 51 steps (49%) done
Touching output file test_extension/extension/genes/GCA_903902895.1/GCA_903902895.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:57 2022]
Finished job 29.
26 of 51 steps (51%) done
Touching output file test_extension/extension/genes/GCA_903839445.1/GCA_903839445.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:57 2022]
Finished job 6.
27 of 51 steps (53%) done
Touching output file test_extension/extension/genes/GCA_903920995.1/GCA_903920995.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:57 2022]
Finished job 38.
28 of 51 steps (55%) done
Touching output file test_extension/extension/genes/GCA_903961455.1/GCA_903961455.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:21:58 2022]
Finished job 50.
29 of 51 steps (57%) done
Touching output file test_extension/extension/genes/GCA_903915855.1/GCA_903915855.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:06 2022]
Finished job 35.
30 of 51 steps (59%) done
Touching output file test_extension/extension/genes/GCA_903936775.1/GCA_903936775.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:07 2022]
Finished job 43.
31 of 51 steps (61%) done
Touching output file test_extension/extension/genes/GCA_903854255.1/GCA_903854255.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:20 2022]
Finished job 14.
32 of 51 steps (63%) done
Touching output file test_extension/extension/genes/GCA_903841135.1/GCA_903841135.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:45 2022]
Finished job 7.
33 of 51 steps (65%) done
Touching output file test_extension/extension/genes/GCA_903869725.1/GCA_903869725.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:48 2022]
Finished job 17.
34 of 51 steps (67%) done
Touching output file test_extension/extension/genes/GCA_903894295.1/GCA_903894295.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:55 2022]
Finished job 24.
35 of 51 steps (69%) done
Touching output file test_extension/extension/genes/GCA_903914905.1/GCA_903914905.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:56 2022]
Finished job 33.
36 of 51 steps (71%) done
Touching output file test_extension/extension/genes/GCA_903824045.1/GCA_903824045.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:57 2022]
Finished job 1.
37 of 51 steps (73%) done
Touching output file test_extension/extension/genes/GCA_903884585.1/GCA_903884585.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:58 2022]
Finished job 22.
38 of 51 steps (75%) done
Touching output file test_extension/extension/genes/GCA_903953565.1/GCA_903953565.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:22:59 2022]
Finished job 48.
39 of 51 steps (76%) done
Touching output file test_extension/extension/genes/GCA_903913555.1/GCA_903913555.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:00 2022]
Finished job 32.
40 of 51 steps (78%) done
Touching output file test_extension/extension/genes/GCA_903934285.1/GCA_903934285.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:01 2022]
Finished job 41.
41 of 51 steps (80%) done
Touching output file test_extension/extension/genes/GCA_903845665.1/GCA_903845665.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:01 2022]
Finished job 10.
42 of 51 steps (82%) done
Touching output file test_extension/extension/genes/GCA_903928895.1/GCA_903928895.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:01 2022]
Finished job 40.
43 of 51 steps (84%) done
Touching output file test_extension/extension/genes/GCA_903871585.1/GCA_903871585.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:02 2022]
Finished job 18.
44 of 51 steps (86%) done
Touching output file test_extension/extension/genes/GCA_903824795.1/GCA_903824795.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:03 2022]
Finished job 3.
45 of 51 steps (88%) done
Touching output file test_extension/extension/genes/GCA_903853455.1/GCA_903853455.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:03 2022]
Finished job 11.
46 of 51 steps (90%) done
Touching output file test_extension/extension/genes/GCA_903899515.1/GCA_903899515.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:06 2022]
Finished job 26.
47 of 51 steps (92%) done
Touching output file test_extension/extension/genes/GCA_903907865.1/GCA_903907865.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:08 2022]
Finished job 30.
48 of 51 steps (94%) done
Touching output file test_extension/extension/genes/GCA_903895255.1/GCA_903895255.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:15 2022]
Finished job 25.
49 of 51 steps (96%) done
Touching output file test_extension/extension/genes/GCA_903924625.1/GCA_903924625.1.prodigal_fetchMGs.done.
[Fri Aug 12 11:23:18 2022]
Finished job 39.
50 of 51 steps (98%) done
Select jobs to execute...

[Fri Aug 12 11:23:18 2022]
localrule all:
    input: test_extension/extension/genes/GCA_903824045.1/GCA_903824045.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903824635.1/GCA_903824635.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903824795.1/GCA_903824795.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903826635.1/GCA_903826635.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903835685.1/GCA_903835685.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903839445.1/GCA_903839445.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903841135.1/GCA_903841135.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903842315.1/GCA_903842315.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903843765.1/GCA_903843765.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903845665.1/GCA_903845665.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903853455.1/GCA_903853455.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903853495.1/GCA_903853495.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903854225.1/GCA_903854225.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903854255.1/GCA_903854255.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903857725.1/GCA_903857725.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903869175.1/GCA_903869175.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903869725.1/GCA_903869725.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903871585.1/GCA_903871585.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903875175.1/GCA_903875175.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903879295.1/GCA_903879295.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903883715.1/GCA_903883715.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903884585.1/GCA_903884585.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903888055.1/GCA_903888055.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903894295.1/GCA_903894295.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903895255.1/GCA_903895255.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903899515.1/GCA_903899515.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903900705.1/GCA_903900705.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903902845.1/GCA_903902845.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903902895.1/GCA_903902895.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903907865.1/GCA_903907865.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903907955.1/GCA_903907955.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903913555.1/GCA_903913555.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903914905.1/GCA_903914905.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903915725.1/GCA_903915725.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903915855.1/GCA_903915855.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903918315.1/GCA_903918315.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903920605.1/GCA_903920605.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903920995.1/GCA_903920995.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903924625.1/GCA_903924625.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903928895.1/GCA_903928895.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903934285.1/GCA_903934285.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903935095.1/GCA_903935095.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903936775.1/GCA_903936775.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903937725.1/GCA_903937725.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903939965.1/GCA_903939965.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903945225.1/GCA_903945225.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903945495.1/GCA_903945495.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903953565.1/GCA_903953565.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903959825.1/GCA_903959825.1.prodigal_fetchMGs.done, test_extension/extension/genes/GCA_903961455.1/GCA_903961455.1.prodigal_fetchMGs.done
    jobid: 0
    resources: tmpdir=/tmp

[Fri Aug 12 11:23:18 2022]
Finished job 0.
51 of 51 steps (100%) done
Complete log: .snakemake/log/2022-08-12T112037.598847.snakemake.log
2022-08-12 11:23:18,293 INFO: Processing genome assignation
2022-08-12 11:23:18,571 INFO: Processed 50 / 50
2022-08-12 11:23:18,575 INFO: Total genomes: 50
2022-08-12 11:23:18,575 INFO: 	 Assigned to refmotus 			0
2022-08-12 11:23:18,575 INFO: 	 Assigned to metamotus 			0
2022-08-12 11:23:18,575 INFO: 	 Assigned to extmotus 			0
2022-08-12 11:23:18,575 INFO: 	 Genomes not assigned to any mOTU 	50
2022-08-12 11:23:18,575 INFO: 	 Filtered genomes (<6 MGs) 		0
2022-08-12 11:23:18,577 INFO: mOTUs-extender finished successfully

The membership file will show whether a genome is already represented by an existing mOTU of if it represents taxonomic novelty.

cat test_extension/extension/mOTUs.membership.tsv

GCA_903824045.1	Novel	10
GCA_903824635.1	Novel	10
GCA_903824795.1	Novel	10
GCA_903826635.1	Novel	10
GCA_903835685.1	Novel	10
GCA_903839445.1	Novel	10
GCA_903841135.1	Novel	10
GCA_903842315.1	Novel	10
GCA_903843765.1	Novel	10
GCA_903845665.1	Novel	10
GCA_903853455.1	Novel	10
GCA_903853495.1	Novel	8
GCA_903854225.1	Novel	9
GCA_903854255.1	Novel	10
...

Note: This step can, depending on the number of genomes, take from minutes to hours.

3. mOTUs extender - createdb

python mOTUs-extender/mOTUs-extender/motus-extender.py createdb  -w test_extension/extension/ -a mOTUs-extender/mOTUs-extender/test/genomes.tax -p NEWDB -t 32

Commandline stdout


python mOTUs-extender/mOTUs-extender/motus-extender.py createdb  -w test_extension/extension/ -a mOTUs-extender/mOTUs-extender/test/genomes.tax -p NEWDB -t 32
2022-08-12 14:44:05,495 INFO: Starting mOTUs-extender
2022-08-12 14:44:05,502 INFO: Executing: sh mOTUs-extender/mOTUs-extender/extend_mOTUs_generateDB.sh test_extension/extension/genomes.list NEWDB mOTUs-extender/mOTUs-extender/test/genomes.tax test_extension/extension/extension/ mOTUs-extender/mOTUs-extender/ test_extension/extension/temp_db_folder/ 32
+ fileListGenomes=test_extension/extension/genomes.list
+ newDBName=NEWDB
+ taxonomyFile=mOTUs-extender/mOTUs-extender/test/genomes.tax
+ new_database_folder=test_extension/extension/extension/
+ scriptDir=mOTUs-extender/mOTUs-extender/
+ mOTU_folder=test_extension/extension/temp_db_folder/
+ threads=32
+ cutoffsFile=mOTUs-extender/mOTUs-extender//cutoffs_fscore_specIAsRef.csv
+ mOTU_MG_file=mOTUs-extender/mOTUs-extender//10RefMGs.IDs
+ cutoff=99.0
+ fileListGenomes2=test_extension/extension/extension//NEWDB.newGenomes.filteredMissingMGs.txt
+ touch test_extension/extension/extension//NEWDB.newGenomes.filteredMissingMGs.txt
+ rm test_extension/extension/extension//NEWDB.newGenomes.filteredMissingMGs.txt
+ touch test_extension/extension/extension//NEWDB.newGenomes.filteredMissingMGs.txt
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903824045.1/GCA_903824045.1.map ']'
+ echo GCA_903824045.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903824635.1/GCA_903824635.1.map ']'
+ echo GCA_903824635.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903824795.1/GCA_903824795.1.map ']'
+ echo GCA_903824795.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903826635.1/GCA_903826635.1.map ']'
+ echo GCA_903826635.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903835685.1/GCA_903835685.1.map ']'
+ echo GCA_903835685.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903839445.1/GCA_903839445.1.map ']'
+ echo GCA_903839445.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903841135.1/GCA_903841135.1.map ']'
+ echo GCA_903841135.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903842315.1/GCA_903842315.1.map ']'
+ echo GCA_903842315.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903843765.1/GCA_903843765.1.map ']'
+ echo GCA_903843765.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903845665.1/GCA_903845665.1.map ']'
+ echo GCA_903845665.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903853455.1/GCA_903853455.1.map ']'
+ echo GCA_903853455.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903853495.1/GCA_903853495.1.map ']'
+ echo GCA_903853495.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903854225.1/GCA_903854225.1.map ']'
+ echo GCA_903854225.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903854255.1/GCA_903854255.1.map ']'
+ echo GCA_903854255.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903857725.1/GCA_903857725.1.map ']'
+ echo GCA_903857725.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903869175.1/GCA_903869175.1.map ']'
+ echo GCA_903869175.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903869725.1/GCA_903869725.1.map ']'
+ echo GCA_903869725.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903871585.1/GCA_903871585.1.map ']'
+ echo GCA_903871585.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903875175.1/GCA_903875175.1.map ']'
+ echo GCA_903875175.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903879295.1/GCA_903879295.1.map ']'
+ echo GCA_903879295.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903883715.1/GCA_903883715.1.map ']'
+ echo GCA_903883715.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903884585.1/GCA_903884585.1.map ']'
+ echo GCA_903884585.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903888055.1/GCA_903888055.1.map ']'
+ echo GCA_903888055.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903894295.1/GCA_903894295.1.map ']'
+ echo GCA_903894295.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903895255.1/GCA_903895255.1.map ']'
+ echo GCA_903895255.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903899515.1/GCA_903899515.1.map ']'
+ echo GCA_903899515.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903900705.1/GCA_903900705.1.map ']'
+ echo GCA_903900705.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903902845.1/GCA_903902845.1.map ']'
+ echo GCA_903902845.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903902895.1/GCA_903902895.1.map ']'
+ echo GCA_903902895.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903907865.1/GCA_903907865.1.map ']'
+ echo GCA_903907865.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903907955.1/GCA_903907955.1.map ']'
+ echo GCA_903907955.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903913555.1/GCA_903913555.1.map ']'
+ echo GCA_903913555.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903914905.1/GCA_903914905.1.map ']'
+ echo GCA_903914905.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903915725.1/GCA_903915725.1.map ']'
+ echo GCA_903915725.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903915855.1/GCA_903915855.1.map ']'
+ echo GCA_903915855.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903918315.1/GCA_903918315.1.map ']'
+ echo GCA_903918315.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903920605.1/GCA_903920605.1.map ']'
+ echo GCA_903920605.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903920995.1/GCA_903920995.1.map ']'
+ echo GCA_903920995.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903924625.1/GCA_903924625.1.map ']'
+ echo GCA_903924625.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903928895.1/GCA_903928895.1.map ']'
+ echo GCA_903928895.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903934285.1/GCA_903934285.1.map ']'
+ echo GCA_903934285.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903935095.1/GCA_903935095.1.map ']'
+ echo GCA_903935095.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903936775.1/GCA_903936775.1.map ']'
+ echo GCA_903936775.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903937725.1/GCA_903937725.1.map ']'
+ echo GCA_903937725.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903939965.1/GCA_903939965.1.map ']'
+ echo GCA_903939965.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903945225.1/GCA_903945225.1.map ']'
+ echo GCA_903945225.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903945495.1/GCA_903945495.1.map ']'
+ echo GCA_903945495.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903953565.1/GCA_903953565.1.map ']'
+ echo GCA_903953565.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903959825.1/GCA_903959825.1.map ']'
+ echo GCA_903959825.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//dbs/GCA_903961455.1/GCA_903961455.1.map ']'
+ echo GCA_903961455.1
+ read genome_ID
+ '[' -s test_extension/extension/extension//NEWDB.newGenomes.filteredMissingMGs.txt ']'
+ echo 'Adding genomes to database.'
Adding genomes to database.
+ mkdir -p test_extension/extension/extension//NEWDB/vsearch
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903824045.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903824635.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903824795.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903826635.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903835685.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903839445.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903841135.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903842315.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903843765.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903845665.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903853455.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903853495.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903854225.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903854255.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903857725.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903869175.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903869725.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903871585.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903875175.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903879295.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903883715.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903884585.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903888055.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903894295.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903895255.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903899515.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903900705.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903902845.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903902895.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903907865.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903907955.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903913555.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903914905.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903915725.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903915855.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903918315.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903920605.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903920995.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903924625.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903928895.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903934285.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903935095.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903936775.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903937725.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903939965.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903945225.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903945495.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903953565.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903959825.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903961455.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ python mOTUs-extender/mOTUs-extender//extend_mOTUs_filterGenomesByDistance.py --cutoff 99.0 test_extension/extension/extension//NEWDB/vsearch/combined.normalized.distances_vs_db.m8 test_extension/extension/extension//NEWDB.newGenomes.filteredMissingMGs.txt
+ '[' -s test_extension/extension/extension//NEWDB/genomes.filtered.list ']'
+ echo 'Adding genomes listed in test_extension/extension/extension//NEWDB/genomes.filtered.list.'
Adding genomes listed in test_extension/extension/extension//NEWDB/genomes.filtered.list.
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903843765.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903913555.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903842315.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903835685.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903841135.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903884585.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903853455.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903937725.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903883715.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903914905.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903894295.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903936775.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903854225.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903953565.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903915855.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903857725.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903824635.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903875175.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903902845.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903853495.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903854255.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903934285.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903839445.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903945225.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903918315.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903826635.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903915725.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903924625.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903879295.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903920995.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903939965.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903824045.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903845665.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903907865.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903900705.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903869725.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903895255.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903935095.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903888055.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903871585.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903824795.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903907955.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903959825.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903920605.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903928895.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903945495.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903869175.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903902895.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903899515.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903961455.1/vsearch/combined.normalized.distances_vs_db.m8
+ read genome_ID
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903843765.1/GCA_903843765.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903913555.1/GCA_903913555.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903842315.1/GCA_903842315.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903835685.1/GCA_903835685.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903841135.1/GCA_903841135.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903884585.1/GCA_903884585.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903853455.1/GCA_903853455.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903937725.1/GCA_903937725.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903883715.1/GCA_903883715.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903914905.1/GCA_903914905.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903894295.1/GCA_903894295.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903936775.1/GCA_903936775.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903854225.1/GCA_903854225.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903953565.1/GCA_903953565.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903915855.1/GCA_903915855.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903857725.1/GCA_903857725.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903824635.1/GCA_903824635.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903875175.1/GCA_903875175.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903902845.1/GCA_903902845.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903853495.1/GCA_903853495.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903854255.1/GCA_903854255.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903934285.1/GCA_903934285.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903839445.1/GCA_903839445.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903945225.1/GCA_903945225.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903918315.1/GCA_903918315.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903826635.1/GCA_903826635.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903915725.1/GCA_903915725.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903924625.1/GCA_903924625.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903879295.1/GCA_903879295.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903920995.1/GCA_903920995.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903939965.1/GCA_903939965.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903824045.1/GCA_903824045.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903845665.1/GCA_903845665.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903907865.1/GCA_903907865.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903900705.1/GCA_903900705.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903869725.1/GCA_903869725.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903895255.1/GCA_903895255.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903935095.1/GCA_903935095.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903888055.1/GCA_903888055.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903871585.1/GCA_903871585.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903824795.1/GCA_903824795.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903907955.1/GCA_903907955.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903959825.1/GCA_903959825.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903920605.1/GCA_903920605.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903928895.1/GCA_903928895.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903945495.1/GCA_903945495.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903869175.1/GCA_903869175.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903902895.1/GCA_903902895.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903899515.1/GCA_903899515.1.map
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903961455.1/GCA_903961455.1.map
+ read genome_ID
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903843765.1/GCA_903843765.1.map2genome
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903913555.1/GCA_903913555.1.map2genome
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903842315.1/GCA_903842315.1.map2genome
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903835685.1/GCA_903835685.1.map2genome
+ read genome_ID
+ cat test_extension/extension/extension//dbs/GCA_903841135.1/GCA_903841135.1.map2genome
+ read ge

Name		Name	Last commit message	Last commit date
Latest commit History 11 Commits
mOTUs-extender		mOTUs-extender
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md

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mOTU extender

Pre-requisites

Installation

Basic example

0. Test Data

1. mOTUs extender - prepare

2. mOTUs extender - membership

3. mOTUs extender - createdb

License

motu-tool/mOTUs-extender

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mOTU extender

Pre-requisites

Installation

Basic example

0. Test Data

1. mOTUs extender - prepare

2. mOTUs extender - membership

3. mOTUs extender - createdb