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ParkinsonLab / MetaPro

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MetaPro: Meta-analysis pipeline for Transcriptomics + Genomics

The MetaPro Meta Transcriptomics/Genomics Pipeline is a software tool that will perform Transcriptomics and Genomic analysis on Paired and Single Reads of FASTQ data. This readme is for getting started with setting up and using MetaPro.

We have prepared a tutorial demonstrating bioinformatics concepts through the use of MetaPro. It can be found here: https://github.com/ParkinsonLab/MetaPro_tutorial

How to get the pipeline

This package is meant to work in conjunction with Docker/Singularity. All of the prerequisite tools, including the pipeline code is delivered via the Docker Hub. https://hub.docker.com/r/parkinsonlab/metapro/ Alternatively, individual parts of the pipeline are avaiable from this Github repository.

Therefore, to use this pipeline, Docker (https://www.docker.com/) or Singularity (https://www.sylabs.io/guides/2.6/user-guide/) is needed. This also means there is nothing to install (tools and code) besides Docker/Docker CE/Singularity

How to install MetaPro

There is no installation for the pipeline. MetaPro is a script, bundled into a docker image. However, in order to use MetaPro, there are a few steps to perform:

Database files

We recommend using the Databases and libraries we have created for We have created a convenient downloader/extractor program for you to use, bundled with the software

singularity exec <singularity image.sif> python3 /pipeline/lib_downloader.py <your destination>

This script will download, and unpack the libraries we host to your desired location. The details of the libraries can be found further down this document, under the configurations section.

MetaGeneMark license

MetaPro uses MetaGeneMark in its workflow. To use this software, the user must obtain a free license for the 64-bit version here:

http://exon.gatech.edu/license_download.cgi

The resulting license file (.gm_key) must be placed in the home directory of the docker/singularity environment

/home/<your username>

How to use MetaPro

Since the pipeline is a script, the commands require the user to have a basic understanding of how to invoke a python script. This pipeline comes with a config.ini file. The user is meant to modify the file to point to the location of local files and Databases. Our config file is written with Python's ConfigParser, using the basic interpretation.
The docker invocation command should look like:

docker run python3 /pipeline/MetaPro.py -c <your config.ini> -1 <your forward read.fastq> -2 <your reverse read.fastq> -o <your output directory>

If you are running MetaPro with singletons, the command would change to:

docker run python3 /pipeline/MetaPro.py -c <your config.ini> -s <your singletons.fastq> -o <your output directory>

if you are invoking the pipeline using Singularity:

singularity exec <your singularity image.sif> python3 /pipeline/MetaPro.py -c <your config file> -1 <your forward read.fastq> -2 <your reverse read.fastq> -o <your output directory>

If you are running MetaPro with singletons, the command would change to:

singularity exec <your singularity image.sif> python3 /pipeline/MetaPro.py -c <your config file> -s <your     singletons.fastq> -o <your output directory>

MetaPro is built with runtime arguments and options:

--help: call a menu displaying the runtime functions
-o | --output: sets the output path where all files will be generated
-c | --config: sets the path to the configuration file
-1 | --pair1: expects the absolute path for the forward reads of a paired-end dataset
-2 | --pair2: expects the absolute path for the reverse reads of a paired-end dataset
-s | --single: expects the absolute path for single-end data (singletons).  Note: If the path to singletons are set, the data is assumed to be single-end, even if -1 and -2 are set. 
-con | --contig: (for tutorial use only) This argument expects contig segments
--nhost | --no-host: option to set MetaPro to bypass host filtering
--tutorial: calls MetaPro in tutorial mode.  This mode lets users run one step at a time. It requires specific keywords to invoke, which are explained below

Tutorial mode lets users call MetaPro to run only 1 specific stage at a time. To use this mode, the user must set the paths to the input data and call MetaPro with the tutorial arguemnt, and a keyword. The input data is entered through the arguments -1, -2, -s, and -con The keywords are:

How to schedule on a job scheduler

MetaPro is a python script. To schedule MetaPro on a job scheduler, the user should call on singularity to call on python, to call on the MetaPro.py script. An example would be:

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=40
#SBATCH --time=24:00:00
#SBATCH --job-name mpro_501_cqy
#SBATCH --output=/scratch/j/jparkin/billyc59/kneaddata_run/run_logs/mpro_501_cqy_out.txt
#SBATCH --error=/scratch/j/jparkin/billyc59/kneaddata_run/run_logs/mpro_501_cqy_err.txt
image='/home/j/jparkin/billyc59/metapro_develop.sif'
read1='/scratch/j/jparkin/billyc59/kneaddata_run/NOD501CecQY_r1_new.fastq'
read2='/scratch/j/jparkin/billyc59/kneaddata_run/NOD501CecQY_r3_new.fastq'
config='/scratch/j/jparkin/billyc59/kneaddata_run/config_mouse.ini'
output='/scratch/j/jparkin/billyc59/kneaddata_run/mpro/501_cqy'
singularity exec -B /home -B /project -B /scratch $image python3 /pipeline/MetaPro.py -c $config -1 $read1 -2 $read2 --verbose_mode leave -o $output

Configuration file

MetaPro relies on a configuration file to set program operation directives, paths, and various filter limits. To get the most out of MetaPro, we recommend becoming familiar with the following:

Databases

The libraries MetaPro uses are critically important for the user to use the pipeline properly.

We intentionally did not include any database files in the Docker/Singularity image due to size constraints. We also want to highlight the fact that users can use their own databases for MetaPro based on their own needs.

However, many of these databases require indexing, so we are curating ready-to-go versions these databases on our webserver:

https://compsysbio.org/metapro_libs/

There is also a library downloader script embedded in MetaPro, located at:

python3 /pipeline/lib_downloader.py <your destination folder> <optional keyword to download selective elements>

This downloader script is built automate the downloading and extraction of MetaPro's databases from our webserver. However, it also comes with the ability to download and extract individual portions. The optional keywords are:

all: downloads + extacts everything, default for leaving the option blank is <all>
detect: detect2's libraries
ec_pathway: EC-to-pathway map <needed for reporting>
priam: PRIAM libraries
rfam: rfam libraries
wevote: wevote names and nodes
accession2taxid: accession -> taxid map for TA
centrifuge: centrifuge libraries
chocophlan: This option downloads + extracts all 3 copies of our taxa-grouped ChocoPhlAn
choco_genus: downloads + extracts only the genus-grouped ChocoPhlAn
choco_family: downloads + extracts only the family-grouped ChocoPhlAn
choco_order: downloads + extracts only the order-grouped ChocoPhlAn
kraken2: kraken2 libraries. k2_standard_20230314
nr: NR from October 10, 2021 
path_to_superpath: pathway-to-superpathway map
swissprot: june 10, 2020
trimmomatic: for version 0.36
univec: july 05, 2018

Below is a description of each of the database fields we used. 

Database_path
Univec_Core
Adapter
Host
Rfam
source_taxa_db
DNA_DB
Prot_DB
Prot_DB_reads
accession2taxid
nodes
names
kraken2_db
Centrifuge_db
SWISS_PROT
SWISS_PROT_map
PriamDB
DetectDB
WEVOTEDB
EC_pathway
path_to_superpath
MetaGeneMark_model
taxid_tree

Tools

MetaPro uses this section of the configuration to control what version of which tool is called. All of the default tools are installed onto the docker/singularity container.

Python: python3 
Java: java -jar (For running jarfiles)
cdhit_dup: version 4.6.8-2017-1208
adapterremoval: version 2.1.7 
vsearch: version 2,7.1
BWA: version 0.7.17
SAMTOOLS: verison 1.8
BLAT: pBLAT version 2.0
DIAMOND: version 0.9.19 
BlastP: version 2.7.1+
Barrnap: version 0.8
Needle: A tool within emboss (using version 6.6.0)
Infernal: version 1.1.2-linux
Kaiju: version 1.6.2
Centrifuge: latest version
PRIAM: We host this one ourselves, due to there being intermittent downtimes on the site
DETECT: Using a modified copy of DETECTv2, built for parallel execution (Detect 2.2.9)
BLAST_dir: prerequisite for PRIAM 
WEVOTE: latest version
Spades: version 3.15.2
MetaGeneMark: There is only 1 version

If the user wants to change the tool version, they are free to, but the pipeline is not gauranteed to work if there are significant formatting changes to the input, or output

Settings

The 3rd section of MetaPro's configuration file controls the various runtime resource settings.

AdapterRemoval_minlength
Show_unclassified
bypass_log_name
debug_stop_flat
num_threads
taxa_exist_cutoff
DNA_DB_mode
filter_stringency

The mem threshold settings control the amount of remaining RAM that must exist for additional instances of each tool to be launched (available RAM is measured during the initial launch)

BWA_mem_threshold: default 50(%)
BLAT_mem_threshold: default 50(%)
DIAMOND_mem_threshold: default 50(%)
BWA_pp_mem_threshold: default 50(%)
BLAT_pp_mem_threshold: default 50(%)
DIAMOND_pp_mem_threshold: default 50(%)
DETECT_mem_threshold: default 50(%)
Infernal_mem_threshold: default 50(%)
Barrnap_mem_threshold: default 50(%)
TA_mem_threshold: default 50(%)

Job limits: controls the amount of concurrent jobs allowed to launch at any one time. This setting should be changed to fit the user's single-node thread-count

BWA_job_limit: default (80% of max CPUs on system)    
BLAT_job_limit: default (80% of max CPUs on system)
DIAMOND_job_limit: default (80% of max CPUs on system)
BWA_pp_job_limit: default (80% of max CPUs on system)
BLAT_pp_job_limit: default (80% of max CPUs on system)
DIAMOND_pp_job_limit: default (80% of max CPUs on system)
DETECT_job_limit: default (80% of max CPUs on system)
Infernal_job_limit: default (80% of max CPUs on system)
Barrnap_job_limit: default (80% of max CPUs on system)
TA_job_limit: default (80% of max CPUs on system)

The job delay settings control the amount of time the master controller waits until a new process is started. This is used in conjuction with the memory limit settings to avoid out-of-memory issues, and process-kill issues as the full RAM usage isn't realized until some of the programs get underway.

BWA_job_delay: default 5 (seconds)
BLAT_job_delay: default 5 (seconds)
DIAMOND_job_delay: default 5 (seconds)
BWA_pp_job_delay: default 5 (seconds)
BLAT_pp_job_delay: default 5 (seconds)
DIAMOND_pp_job_delay: default 5 (seconds)
TA_job_delay: default 5 (seconds)

Keep settings: controls whether the interim data is kept in MetaPro. 

keep_all | default: yes
keep_quality | default: no
keep_host | default: no
keep_vector | default: no
keep_rRNA | default: no
keep_repop | default: no
keep_assemble_contigs | default: no
keep_GA_BWA | default: no
keep_GA_BLAT | default: no
keep_GA_DIAMOND | default: no
keep_GA_final | default: no
keep_TA | default: no
keep_EC | default: no
keep_outputs | default: no

Labels

Labels are how MetaPro names each stage. In cases where users want to test different settings in GA/TA/EC, or to try a battery of trials using the same data, we now let users name their stages in customized ways:

quality_filter | default: quality_filter
host_filter | default: host_filter
vector_filter | default: vector_filter
rRNA_filter | default: rRNA_filter
repop | default: duplicate_repopulation
assemble_contigs | default: assemble_contigs
GA_pre_scan | default: GA_pre_scan
GA_split | default: GA_split
GA_BWA | default: GA_BWA
GA_BLAT | default: GA_BLAT
GA_DIAMOND | default: GA_DMD
GA_final_merge | default: GA_final_merge
ta | default: taxonomic_annotation
ec | default: enzyme_annotation
outputs | default: outputw

Important note for MetaGeneMark

MetaGeneMark is free to use, but requires a license. If your MetaGeneMark license is not valid, MetaPro will not proceed past the Contig Assembly stage. To acquire a valid MetaGeneMark license, please visit: http://exon.gatech.edu/GeneMark/license_download.cgi Select MetaGeneMark, along with the linux 64bit version, and fill in the required fields. Then download the 64bit key. Extract the key to obtain the .gm_key file. The expected location of the license file (.gm_key) is in the home folder of your singularity instance. Place your license in:

/home/

Important Features

This pipeline was built with a few key features that make it easier to use than other pipelines.

Verbose-mode

This pipeline will produce many interim files along the way. In an effort to maintain transparency, and allow for debugging and inspection of stages, the interim files have been saved, and compressed at each stage of the pipeline. If the user wishes to avoid compression (saving roughly 1/100th of the runtime), the compress flag argument should be set to "verbose". Otherwise, the default is to compress the interim files.

Auto-resume

The pipeline is capable of skipping any and all stages it has run before. If the user wishes to run a subset of stages, the user has to remove the stage folders, and any compressed files of the accompanying stage, and the pipeline will re-run the missing stages. Note: The removed stages do not have to be contiguous, but it is recommended that they are, to ensure the accuracy of the pipeline results. Eg: a pipeline runs A -> B -> C -> D -> E. If A, and D are removed, The pipeline will re-run A and D, leaving B, C, and E alone. However, if D depends on C, then the changes from A -> B -> C will not propagate downward. This feature also has the benefit of being able to resume running if the pipeline run was operating on a job-scheduler-controlled system, and inadequate time was allocated to the job. The pipeline will simply pick up where it left off until the job is complete.

Auto-death

In an effort to save computational resources, the pipeline will shut itself down if the dependencies of a stage are not met. This is to ensure that if a pipeline run is part of a batch-processing scheduler, the pipeline will not continue to waste resources on an erroneous job.

Increasing performance

Operating mode

MetaPro runs in a Singularity instance. As of writing (Sept 28, 2018), Singularity does not support multi-machine parallelism. This pipeline does not utilize MPI, but instead strives to use all the cores made available by the singularity machine through the Python Multiprocessing module. To increase the performance of the pipeline, more cores should be given to the host machine, and increasing the number of cores the pipeline is allowed to use.

Taxa population settings

Beginning from version 3.0.0, MetaPro can shrink the size of its native gene annotation database to speed up the BWA + BLAT portions of gene annotation.
By adjusting the

Guide to outputs

MetaPro produces many outputs for the user to use:

read count

The read count table (read_count.tsv) is the full accounting of the sequence reads as they progress through MetaPro The columns are:

Total reads: The number of unique raw sequence reads in the sample
High quality: The number of unique sequence reads after the low-quality filtering step
% high quality: High quality, as a percentage of total reads
host reads: the number of host sequence reads found by MetaPro
% host reads: host reads, as a percentage of total reads
vector reads: the number of vector reads found by MetaPro
% vector reads: vector reads, as a percentage of total reads
rRNA + tRNA reads: the number of rRNA and tRNA reads removed by MetaPro
% rRNA + tRNA reads: rRNA + tRNA reads, as a percentage of total reads
Putative reads: the number of mRNA reads that will be annotated by MetaPro
% Putative reads: putative reads, as a percentage of total reads
annotated mRNA reads: the number of putative reads that were assigned to a gene or protein
% annotated reads: annotated mRNA reads, as a percentage of putative reads
Unique transcripts: the number of unique genes and proteins found by MetaPro
High-Quality enzymes: The number of enzymes found by MetaPro (using the high-quality EC filter settings)
Low-Quality enzymes: the number of enzymes found by MetaPro (usiing the low-quality EC filter settings)

Contig stats

This file displays the N50 and L50 read lengths of the contigs assembled by rnaSPADes.

Gene map

The Gene map shows all of the genes and proteins that have been identified by either BWA, BLAT, or DIAMOND. The map shows every read that has been identified to those genes/proteins.

The columns in the Gene map are: 

Gene ID / Protein accession
Length of the gene / protein
Number of reads annotated to the gene/protein
The read IDs that annotated to the gene/protein

RPKM table

The RPKM table shows the abundance of each gene, expressed as RPKM of the reads annotated to the gene/protein. The columns are:

The ID of the gene/protein
The length of the gene/protein
The number of reads associated with each gene/protein
The ECs associated with each gene/protein (delineated with a "|" to show multiple ECs per gene/protein)
The RPKM of the gene/protein
The rest of the columns are taxa, representing at least 1% of the sample (on default), and the RPKM associated by taxa.

Enzyme superpathway heatmap

This table is not meant to be used externally. It is for generating the EC heatmap This table contains no new information from RPKM, and is a transformed table to flatten the data where there are multiple ECs per gene/protein Each row corresponds to each enzyme superpathway, while each column will be one of the major organisms (at least 1%) in the sample

Taxa Classifications

This table shows the taxa classification for every putative read that MetaPro processed. The columns are:

Classified/Unclassified.  C is classified, U is unclassified.  
The read ID
The full taxonomic tree of the read

Taxa Summary

This table is a tally of all unique taxa trees found in the sample The columns are:

taxa: the full taxonomic tree 
count: the number of times a sequence read annotated to this specific taxa tree