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Trinity
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Trinity
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#!/usr/bin/env perl
use strict;
use warnings;
use threads;
no strict qw(subs refs);
use FindBin;
use lib ("$FindBin::RealBin/PerlLib");
use File::Basename;
use Time::localtime;
use Cwd;
use Carp;
use COMMON;
use Getopt::Long qw(:config posix_default no_ignore_case pass_through gnu_compat no_auto_abbrev);
use Pipeliner;
use Fasta_reader;
use SAM_reader;
use SAM_entry;
use List::Util qw(min max);
use Data::Dumper;
my $VERSION = "Trinity-v2.12.0";
#my $VERSION = "__BLEEDING_EDGE__";
BEGIN {
$ENV{TRINITY_HOME} = "$FindBin::RealBin";
}
open (STDERR, ">&STDOUT"); ## capturing stderr and stdout in a single stdout stream
#directory defnintions
my $ROOTDIR = "$FindBin::RealBin";
my $UTILDIR = "$ROOTDIR/util";
my $MISCDIR = "$UTILDIR/misc";
my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/COLLECTL/collectl";
my $TRINITY_PLUGINS_DIR = "$ROOTDIR/trinity-plugins";
my $TRINITY_BIN_DIR = "$TRINITY_PLUGINS_DIR/BIN";
my $PARAFLY = "$TRINITY_BIN_DIR/ParaFly";
my $HTSLIB_DIR = "$ROOTDIR/trinity-plugins/htslib";
$ENV{LD_LIBRARY_PATH} .= ":${HTSLIB_DIR}";
if ($ENV{TRINITY_NO_RETRIES}) {
$PARAFLY .= " -max_retry 1 ";
}
my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
$ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
my $JAVA_VERSION_REQUIRED = 8;
# Site specific setup
my $USE_PERL_SCAFFOLDER = 1; # for testing purposes in chrysalis stage
my $KMER_SIZE = 25;
my $INCHWORM_CUSTOM_PARAMS = "";
# option list:
my ($seqType, @left_files, @right_files, @single_files, $SS_lib_type, $min_contig_length,
$group_pairs_distance, $jaccard_clip, $show_advanced_options,
$output_directory, $prep_only
);
# defaults:
$output_directory = &create_full_path("trinity_out_dir", 0);
#variable for bowtie2
my $bowtie2_path;
my $bowtie2_build_path;
# butterfly opts
$min_contig_length = 200;
$group_pairs_distance = 500;
my $path_reinforcement_distance;
my $PE_path_reinforcement_distance = 25;
my $SE_path_reinforcement_distance = 25;
my $bfly_opts = "";
my $bflyHeapSpaceMax = "10G";
my $bflyHeapSpaceInit = "1G";
my $BFLY_JAR = "";
my $JAVA_OPTS = "";
# butterfly path merging criteria
my $NO_PATH_MERGING = 0;
my $MIN_PER_ID_SAME_PATH; # leave these at the butterfy defaults
my $MAX_DIFFS_SAME_PATH;
my $MAX_INTERNAL_GAP_SAME_PATH;
my @BFLY_ALGORITHMS = ("ORIGINAL", "PASAFLY");
my $BFLY_ALGORITHM = "ORIGINAL"; # default
# misc opts
my $min_kmer_cov = 1;
my $meryl_opts = "";
my $inchworm_cpu = 6;
my $min_percent_read_iworm_kmers = -1; # experimental, off
my $CPU = 2;
my $np = 1;
my $mpiexec = "mpiexec";
my $bflyCPU;
my $bflyCalculateCPU = 0;
my $bflyGCThreads = 2;
my $long_reads = "";
my $LONG_READS_MODE = 0;
my $NO_SUPER_READS_FLAG = 0;
## ADVANCED OPTIONS:
## Chrysalis opts
my $min_glue = 2;
my $min_iso_ratio = 0.05;
my $glue_factor = 0.05;
my $max_reads_per_graph = 200000;
my $max_reads_per_loop = 50000000; #MW: Set default to 50M, still fits into main memory
my $min_pct_read_mapping = 10; # set to 50 for phase 2
my $chrysalis_output_dir = "chrysalis";
my $NO_RUN_CHRYSALIS_FLAG = 0;
my $NO_DISTRIBUTED_TRINITY_EXEC = 0;
my $IWORM_CDHIT;
my $help_flag;
my $advanced_help_flag;
my $SHOW_CITATION_FLAG = 0;
my $show_version_flag = 0;
## Kmer methods
my $kmer_method = "";
## Jellyfish
my $max_memory;
## Grid computing options:
my $grid_exec_toolname = "";
## Performance monitoring options
my $pm_logfile = "Trinity.timing";
my $pm_trinity_startstring="NA";
my $pm_trinity_endstring="NA";
my $pm_trinity_start="NA";
my $pm_trinity_end="NA";
my $pm_inchworm_start="NA";
my $pm_inchworm_end="NA";
my $pm_chrysalis_start="NA";
my $pm_chrysalis_end="NA";
my $pm_left_fa_size="NA";
my $pm_right_fa_size="NA";
my $pm_single_fa_size="NA";
my $pm_trinity_fa_size="NA";
my $pm_trinity_arguments="";
my $pm_inchworm_kmers=0;
my $pm_read_count="NA";
my $run_with_collectl = 0;
# flush each second, record procs+rest every 5 secs, use only process subsystem
my $collectl_output_directory = "collectl";
my $collectl_pid = 0;
my $collectl_out = "";
my $collectl_titlename = "";
my $start_dir = cwd();
my $COLLECTL_INTERVAL_SECONDS = 60;
## misc other opts, mostly for testing purposes
my $run_as_paired_flag = 0; ## in case we have paired reads in single fasta file, already oriented.
my $weldmer_size = 48;
my $FORCE_INCHWORM_KMER_METHOD = 0;
my $PARALLEL_IWORM_FLAG = 1;
my $NO_PARALLEL_IWORM = 0;
## Quality trimming params
my $RUN_TRIMMOMATIC_FLAG = 0;
my $trimmomatic_quality_trim_params = "ILLUMINACLIP:$TRIMMOMATIC_DIR/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25";
## Normalize reads
my $NORMALIZE_READS_FLAG = 0; ## now on by default, unless told not to via --no_normalize_reads! See below for logic.
my $NO_NORMALIZE_READS_FLAG = 0; ## set to turn off normalization (will be turned on if trinity_complete_flag and ! --normalize_reads set.
my $normalize_max_read_cov = 200; # better for polymorphic transcriptomes
my $normalize_max_CV = 10000; # effectively turn it off for this application.
my $NORMALIZE_BY_READ_SET = 0;
my $NO_PARALLEL_NORM_STATS = 0;
my $grid_node_CPU = 1;
my $grid_node_max_memory = "1G";
my $min_eff_read_cov = 2.0; # min effective read coverage (#reads * read_len / transcript_len)
my $FORCE_FLAG = 0;
# Note: For the Trinity logo below the backslashes are quoted in order to keep
# them from quoting the character than follows them. "\\" keeps "\ " from occuring.
my $INCLUDE_SUPERTRANSCRIPTS_FLAG = 0;
my $NO_SUPERTRANS_FLAG = 0; # for debugging
my $MAX_CHRYSALIS_CLUSTER_SIZE = 25; # might need to set higher for highly polymorphic transcriptomes.
my $JUST_NORMALIZE_READS_FLAG = 0;
my $NO_SEQTK = 0;
my $trinity_banner = qq^
______ ____ ____ ____ ____ ______ __ __
| || \\ | || \\ | || || | |
| || D ) | | | _ | | | | || | |
|_| |_|| / | | | | | | | |_| |_|| ~ |
| | | \\ | | | | | | | | | |___, |
| | | . \\ | | | | | | | | | | |
|__| |__|\\_||____||__|__||____| |__| |____/
$VERSION
^;
my $basic_usage = qq^
###############################################################################
#
$trinity_banner
#
#
# Required:
#
# --seqType <string> :type of reads: ('fa' or 'fq')
#
# --max_memory <string> :suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc)
# provided in Gb of RAM, ie. '--max_memory 10G'
#
# If paired reads:
# --left <string> :left reads, one or more file names (separated by commas, no spaces)
# --right <string> :right reads, one or more file names (separated by commas, no spaces)
#
# Or, if unpaired reads:
# --single <string> :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: --run_as_paired )
#
# Or,
# --samples_file <string> tab-delimited text file indicating biological replicate relationships.
# ex.
# cond_A cond_A_rep1 A_rep1_left.fq A_rep1_right.fq
# cond_A cond_A_rep2 A_rep2_left.fq A_rep2_right.fq
# cond_B cond_B_rep1 B_rep1_left.fq B_rep1_right.fq
# cond_B cond_B_rep2 B_rep2_left.fq B_rep2_right.fq
#
# # if single-end instead of paired-end, then leave the 4th column above empty.
#
####################################
## Misc: #########################
#
# --include_supertranscripts :yield supertranscripts fasta and gtf files as outputs.
#
# --SS_lib_type <string> :Strand-specific RNA-Seq read orientation.
# if paired: RF or FR,
# if single: F or R. (dUTP method = RF)
# See web documentation.
#
# --CPU <int> :number of CPUs to use, default: $CPU
# --min_contig_length <int> :minimum assembled contig length to report
# (def=$min_contig_length)
#
# --long_reads <string> :fasta file containing error-corrected or circular consensus (CCS) pac bio reads
# (** note: experimental parameter **, this functionality continues to be under development)
#
# --genome_guided_bam <string> :genome guided mode, provide path to coordinate-sorted bam file.
# (see genome-guided param section under --show_full_usage_info)
#
# --long_reads_bam <string> :long reads to include for genome-guided Trinity
# (bam file consists of error-corrected or circular consensus (CCS) pac bio read aligned to the genome)
#
# --jaccard_clip :option, set if you have paired reads and
# you expect high gene density with UTR
# overlap (use FASTQ input file format
# for reads).
# (note: jaccard_clip is an expensive
# operation, so avoid using it unless
# necessary due to finding excessive fusion
# transcripts w/o it.)
#
# --trimmomatic :run Trimmomatic to quality trim reads
# see '--quality_trimming_params' under full usage info for tailored settings.
#
# --output <string> :name of directory for output (will be
# created if it doesn't already exist)
# default( your current working directory: "$output_directory"
# note: must include 'trinity' in the name as a safety precaution! )
#
# --full_cleanup :only retain the Trinity fasta file, rename as \${output_dir}.Trinity.fasta
#
# --cite :show the Trinity literature citation
#
# --verbose :provide additional job status info during the run.
#
# --version :reports Trinity version ($VERSION) and exits.
#
# --show_full_usage_info :show the many many more options available for running Trinity (expert usage).
^;
my $full_usage = qq^
#
# --no_super_reads :turn off super-reads mode
#
# --prep :Only prepare files (high I/O usage) and stop before kmer counting.
#
# --no_cleanup :retain all intermediate input files.
#
# --no_version_check :dont run a network check to determine if software updates are available.
#
# --monitoring :use collectl to monitor all steps of Trinity
# --monitor_sec <int> : number of seconds for each interval of runtime monitoring (default: $COLLECTL_INTERVAL_SECONDS)
#
# --no_distributed_trinity_exec :do not run Trinity phase 2 (assembly of partitioned reads), and stop after generating command list.
#
# --workdir <string> :where Trinity phase-2 assembly computation takes place (defaults to --output setting).
# (can set this to a node-local drive or RAM disk)
#
####################################################
# Inchworm and K-mer counting-related options: #####
#
# --min_kmer_cov <int> :min count for K-mers to be assembled by
# Inchworm (default: $min_kmer_cov)
# --inchworm_cpu <int> :number of CPUs to use for Inchworm, default is min(6, --CPU option)
#
# --no_run_inchworm :stop after running jellyfish, before inchworm. (phase 1, read clustering only)
#
###################################
# Chrysalis-related options: ######
#
# --max_reads_per_graph <int> :maximum number of reads to anchor within
# a single graph (default: $max_reads_per_graph)
# --min_glue <int> :min number of reads needed to glue two inchworm contigs
# together. (default: $min_glue)
#
# --max_chrysalis_cluster_size <int> :max number of Inchworm contigs to be included in a single Chrysalis cluster. (default: $MAX_CHRYSALIS_CLUSTER_SIZE)
#
# --no_bowtie :dont run bowtie to use pair info in chrysalis clustering.
#
# --no_run_chrysalis :stop after running inchworm, before chrysalis. (phase 1, read clustering only)
#
#####################################
### Butterfly-related options: ####
#
# --bfly_algorithm <string> : assembly algorithm to use. Options: @BFLY_ALGORITHMS
#
# --bfly_opts <string> :additional parameters to pass through to butterfly
# (see butterfly options: java -jar Butterfly.jar ).
# (note: only for expert or experimental use. Commonly used parameters are exposed through this Trinity menu here).
#
#
# Butterfly read-pair grouping settings (used to define 'pair paths'):
#
# --group_pairs_distance <int> :maximum length expected between fragment pairs (default: $group_pairs_distance)
# (reads outside this distance are treated as single-end)
#
# ///////////////////////////////////////////////
# Butterfly default reconstruction mode settings.
#
# --path_reinforcement_distance <int> :minimum overlap of reads with growing transcript
# path (default: PE: $PE_path_reinforcement_distance, SE: $SE_path_reinforcement_distance)
# Set to 1 for the most lenient path extension requirements.
#
#
# /////////////////////////////////////////
# Butterfly transcript reduction settings:
#
# --no_path_merging : all final transcript candidates are output (including SNP variations, however, some SNPs may be unphased)
#
# By default, alternative transcript candidates are merged (in reality, discarded) if they are found to be too similar, according to the following logic:
#
# (identity=(numberOfMatches/shorterLen) > 98.0% or if we have <= 2 mismatches) and if we have internal gap lengths <= 10
#
# with parameters as:
#
# --min_per_id_same_path <int> default: 98 min percent identity for two paths to be merged into single paths
# --max_diffs_same_path <int> default: 2 max allowed differences encountered between path sequences to combine them
# --max_internal_gap_same_path <int> default: 10 maximum number of internal consecutive gap characters allowed for paths to be merged into single paths.
#
# If, in a comparison between two alternative transcripts, they are found too similar, the transcript with the greatest cumulative
# compatible read (pair-path) support is retained, and the other is discarded.
#
#
# //////////////////////////////////////////////
# Butterfly Java and parallel execution settings.
#
# --bflyHeapSpaceMax <string> :java max heap space setting for butterfly
# (default: $bflyHeapSpaceMax) => yields command
# 'java -Xmx$bflyHeapSpaceMax -jar Butterfly.jar ... \$bfly_opts'
# --bflyHeapSpaceInit <string> :java initial heap space settings for
# butterfly (default: $bflyHeapSpaceInit) => yields command
# 'java -Xms$bflyHeapSpaceInit -jar Butterfly.jar ... \$bfly_opts'
# --bflyGCThreads <int> :threads for garbage collection
# (default: $bflyGCThreads))
# --bflyCPU <int> :CPUs to use (default will be normal
# number of CPUs; e.g., $CPU)
# --bflyCalculateCPU :Calculate CPUs based on 80% of max_memory
# divided by maxbflyHeapSpaceMax
#
# --bfly_jar <string> : /path/to/Butterfly.jar, otherwise default
# Trinity-installed version is used.
#
#
################################################################################
#### Quality Trimming Options ####
#
# --quality_trimming_params <string> defaults to: "$trimmomatic_quality_trim_params"
#
################################################################################
#### In silico Read Normalization Options ###
#
# --normalize_max_read_cov <int> defaults to $normalize_max_read_cov
# --normalize_by_read_set run normalization separate for each pair of fastq files,
# then one final normalization that combines the individual normalized reads.
# Consider using this if RAM limitations are a consideration.
#
# --just_normalize_reads stop after performing read normalization
#
# --no_normalize_reads :Do *not* run in silico normalization of reads. Defaults to max. read coverage of $normalize_max_read_cov.
# see '--normalize_max_read_cov' under full usage info for tailored settings.
# (Note, as of Sept 21, 2016, normalization is on by default)
# (*Turning off normalization is not recommended for most applications)
#
# --no_parallel_norm_stats :Do not try to run the high-mem normalization stats generator in parallel for paired-end fastqs.
#
###############################################################################
#### Genome-guided de novo assembly
#
# * required:
#
# --genome_guided_max_intron <int> :maximum allowed intron length (also maximum fragment span on genome)
#
# * optional:
#
# --genome_guided_min_coverage <int> :minimum read coverage for identifying and expressed region of the genome. (default: 1)
#
# --genome_guided_min_reads_per_partition <int> :default min of 10 reads per partition
#
#
#######################################################################
# Trinity phase 2 (parallel assembly of read clusters) Options: #######
#
# --grid_exec <string> :your command-line utility for submitting jobs to the grid.
# This should be a command line tool that accepts a single parameter:
# \${your_submission_tool} /path/to/file/containing/commands.txt
# and this submission tool should exit(0) upon successful
# completion of all commands.
#
# --grid_node_CPU <int> number of threads for each parallel process to leverage. (default: $grid_node_CPU)
#
# --grid_node_max_memory <string> max memory targeted for each grid node. (default: $grid_node_max_memory)
#
# The --grid_node_CPU and --grid_node_max_memory are applied as
# the --CPU and --max_memory parameters for the Trinity jobs run in
# Trinity Phase 2 (assembly of read clusters)
#
# --FORCE ignore failed commands from earlier run, continue on.
# (Note, this should only be used after you've
# already dealt with these failed commands directly as needed)
#
^;
my $usage_synopsis = qq^#
#
###############################################################################
#
# *Note, a typical Trinity command might be:
#
# Trinity --seqType fq --max_memory 50G --left reads_1.fq --right reads_2.fq --CPU 6
#
# (if you have multiple samples, use --samples_file ... see above for details)
#
# and for Genome-guided Trinity, provide a coordinate-sorted bam:
#
# Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
# --genome_guided_max_intron 10000 --CPU 6
#
# see: $FindBin::RealBin/sample_data/test_Trinity_Assembly/
# for sample data and 'runMe.sh' for example Trinity execution
#
# For more details, visit: http://trinityrnaseq.github.io
#
###############################################################################
^;
my $advanced_usage = <<_ADVANCEDUSAGE_;
###################################################################################
## Not intended for users, instead for experimentation by developers ##
###################################################################################
#
#
# Inchworm-related options:
#
# --INCHWORM_CUSTOM_PARAMS <string> :additional parameters to be passed on to Inchworm
# --FORCE_INCHWORM_KMER_METHOD :uses inchworm built-in kmer cataloger instead of jellyfish (not recommended)
# --NO_PARALLEL_IWORM : turn off parallel iworm assembly
# --iworm_opts <string> : options for inchworm
#
# --iworm_cdhit : perform iworm contig database reduction using cdhit
# --__KMER_SIZE <int> : default $KMER_SIZE (do not change unless for experimental usage)
#
#
# Chyrsalis-related options:
#
# --min_pcnt_read_iworm_kmers <int> :min percentage of a read sequence that must be composed of inchworm kmers to be pursued
# by chrysalis (default: $min_percent_read_iworm_kmers) note: off if < 0
#
# --min_iso_ratio <float> :min fraction of average kmer coverage between two iworm contigs
# required for gluing. (default: $min_iso_ratio)
# --glue_factor <float> :fraction of max (iworm pair coverage) for read glue support (default: $glue_factor)
#
# --max_reads_per_loop <int> :maximum number of reads to read into
# memory at once (default: $max_reads_per_loop)
# --min_pct_read_mapping <int> :minimum percent of a reads kmers that must map to an
# inchworm bundle (aka. component) default: $min_pct_read_mapping
#
# --bowtie_components :use bowtie2 to generate readsToTranscripts mappings
#
#
# Other:
#
# --bypass_java_version_check : skip check for required java version 1.$JAVA_VERSION_REQUIRED
#
# --java_opts <string> : can include any additional custom options to the java command.
# ie. -Djava.io.tmpdir=/path/to/my/custom/tmpdir
# --no_salmon : remove salmon expression filtering
# --min_eff_read_cov <int> : minimum effective read coverage for reconstructed transcript (default: $min_eff_read_cov)
#
# --long_reads_mode : run in long reads mode (requires --single and the long reads integrated with LR$| accession prefixes.
#
# --no_check_coordsorted_bam : in genome-guided mode, won't test the bam file for coordinate-sortedness#
#
# --stomp_snps : stomp snps out of kmers before inchworm assembly
#
# --NO_SUPERTRANS : disable supertranscripts
#
# --NO_SEQTK :disable seqtk for fq->fa conversions, instead use slower perl code
#
_ADVANCEDUSAGE_
;
my $usage = $basic_usage . $usage_synopsis;
unless (@ARGV) {
die "$usage\n";
}
# Log command line parameters for performance monitoring
foreach (@ARGV) {
$pm_trinity_arguments = $pm_trinity_arguments . " " . $_;
};
my $NO_CLEANUP = 0;
my $FULL_CLEANUP = 0;
my $NO_BOWTIE = 0;
my $NO_RUN_INCHWORM_FLAG = 0;
my $JELLY_S;
#my $PASAFLY_MODE = 0;
#my $CUFFFLY_MODE = 0;
my $full_usage_info_flag;
my $NO_TRIPLET_LOCK;
## Genome-guided params:
my $genome_guided_max_intron;
my $genome_guided_bam;
my $genome_guided_min_coverage = 1;
my $genome_guided_min_reads_per_partition = 10;
my $genome_guided_just_prep_flag = 0;
my $long_reads_bam;
## trinity complete flag
my $TRINITY_COMPLETE_FLAG = 0;
my @ORIG_ARGS = @ARGV;
my $CHRYSALIS_DEBUG_WELD_ALL = 0;
my $iworm_opts = "";
my $bypass_java_version_check = 0;
my $VERBOSE = 0;
my $ANANAS_DIR = "";
my $NO_VERSION_CHECK = 0;
my $samples_file = "";
my $WORKDIR;
my $NO_CHECK_COORDSORTED_BAM = 0;
my $NO_SALMON = $ENV{TRINITY_NO_SALMON} || 0;
my $STOMP_SNPS = 0;
&GetOptions(
'h|help' => \$help_flag,
'advanced_help' => \$advanced_help_flag,
'show_full_usage_info' => \$full_usage_info_flag,
'verbose' => \$VERBOSE,
'verbose_level=i' => \$VERBOSE,
'no_version_check' => \$NO_VERSION_CHECK,
## general opts
"seqType=s" => \$seqType,
"left=s{,}" => \@left_files,
"right=s{,}" => \@right_files,
"single=s{,}" => \@single_files,
"samples_file=s" => \$samples_file,
"SS_lib_type=s" => \$SS_lib_type,
"long_reads=s" => \$long_reads,
"long_reads_mode" => \$LONG_READS_MODE,
"output=s" => \$output_directory,
"workdir=s" => \$WORKDIR,
"min_contig_length=i" => \$min_contig_length,
"jaccard_clip" => \$jaccard_clip,
"cite" => \$SHOW_CITATION_FLAG,
'CPU=i' => \$CPU,
'np=i' => \$np,
'mpiexec=s' => \$mpiexec,
'prep' => \$prep_only,
# Quality trimming:
'trimmomatic' => \$RUN_TRIMMOMATIC_FLAG,
'quality_trimming_params=s' => \$trimmomatic_quality_trim_params,
# In silico read normalization
'normalize_reads' => \$NORMALIZE_READS_FLAG, ## left here for backwards compatibility, set to 1 by default so a noop on setting.
'no_normalize_reads' => \$NO_NORMALIZE_READS_FLAG, ## new setting to turn it off.
'normalize_max_read_cov=i' => \$normalize_max_read_cov,
'normalize_by_read_set' => \$NORMALIZE_BY_READ_SET,
'just_normalize_reads' => \$JUST_NORMALIZE_READS_FLAG,
'no_parallel_norm_stats' => \$NO_PARALLEL_NORM_STATS,
# Butterfly opts
"bfly_algorithm=s" => \$BFLY_ALGORITHM,
"group_pairs_distance=i" => \$group_pairs_distance,
'bfly_opts=s' => \$bfly_opts,
'bflyHeapSpaceMax=s' => \$bflyHeapSpaceMax,
'bflyHeapSpaceInit=s' => \$bflyHeapSpaceInit,
'bflyGCThreads=i' => \$bflyGCThreads,
'bflyCPU=i' => \$bflyCPU,
'bflyCalculateCPU' => \$bflyCalculateCPU,
'bfly_jar=s' => \$BFLY_JAR,
'java_opts=s' => \$JAVA_OPTS,
'path_reinforcement_distance=i' => \$path_reinforcement_distance,
'no_path_merging' => \$NO_PATH_MERGING,
'min_per_id_same_path=i' => \$MIN_PER_ID_SAME_PATH,
'max_diffs_same_path=i' => \$MAX_DIFFS_SAME_PATH,
'max_internal_gap_same_path=i' => \$MAX_INTERNAL_GAP_SAME_PATH,
'no_salmon' => \$NO_SALMON,
'min_eff_read_cov=f' => \$min_eff_read_cov,
#'PasaFly' => \$PASAFLY_MODE,
#'CuffFly' => \$CUFFFLY_MODE,
# Inchworm & kmer catalog opts
'min_kmer_cov=i' => \$min_kmer_cov,
'inchworm_cpu=i' => \$inchworm_cpu,
'FORCE_INCHWORM_KMER_METHOD' => \$FORCE_INCHWORM_KMER_METHOD,
'INCHWORM_CUSTOM_PARAMS=s' => \$INCHWORM_CUSTOM_PARAMS,
'no_run_inchworm' => \$NO_RUN_INCHWORM_FLAG,
'iworm_opts=s' => \$iworm_opts,
'stomp_snps' => \$STOMP_SNPS,
'max_memory|M=s' => \$max_memory, # in GB
'iworm_cdhit' => \$IWORM_CDHIT,
# Chrysalis -related opts
'min_glue=i' => \$min_glue,
'glue_factor=f' => \$glue_factor,
'min_iso_ratio=f' => \$min_iso_ratio,
'min_pcnt_read_iworm_kmers=i' => \$min_percent_read_iworm_kmers,
'max_reads_per_graph=i' => \$max_reads_per_graph,
'max_reads_per_loop=i' => \$max_reads_per_loop,
'min_pct_read_mapping=i' => \$min_pct_read_mapping,
'weldmer_size=i' => \$weldmer_size,
"no_bowtie" => \$NO_BOWTIE,
"no_run_chrysalis" => \$NO_RUN_CHRYSALIS_FLAG,
"max_chrysalis_cluster_size=i" => \$MAX_CHRYSALIS_CLUSTER_SIZE,
"show_advanced_options" => \$show_advanced_options,
# Grid computing options
'grid_exec=s' => \$grid_exec_toolname,
"grid_node_CPU=i" => \$grid_node_CPU,
"grid_node_max_memory=s" => \$grid_node_max_memory,
# misc
'run_as_paired' => \$run_as_paired_flag,
'no_cleanup' => \$NO_CLEANUP,
'full_cleanup' => \$FULL_CLEANUP,
'version' => \$show_version_flag,
'monitoring' => \$run_with_collectl,
'monitor_sec=i' => \$COLLECTL_INTERVAL_SECONDS,
'no_distributed_trinity_exec' => \$NO_DISTRIBUTED_TRINITY_EXEC,
'include_supertranscripts' => \$INCLUDE_SUPERTRANSCRIPTS_FLAG,
# hidden (don't look here! ;)
'jelly_s=i' => \$JELLY_S,
'NO_PARALLEL_IWORM' => \$NO_PARALLEL_IWORM,
'chrysalis_debug_weld_all' => \$CHRYSALIS_DEBUG_WELD_ALL,
# genome guided
"genome_guided_bam=s" => \$genome_guided_bam,
"genome_guided_max_intron=i" => \$genome_guided_max_intron,
"long_reads_bam=s" => \$long_reads_bam,
"genome_guided_min_coverage=i" => \$genome_guided_min_coverage,
"genome_guided_min_reads_per_partition=i" => \$genome_guided_min_reads_per_partition,
"genome_guided_just_prep" => \$genome_guided_just_prep_flag,
"no_check_coordsorted_bam" => \$NO_CHECK_COORDSORTED_BAM,
"trinity_complete" => \$TRINITY_COMPLETE_FLAG,
"bypass_java_version_check" => \$bypass_java_version_check,
"ananas_dir=s" => \$ANANAS_DIR,
"FORCE" => \$FORCE_FLAG,
"NO_SUPERTRANS" => \$NO_SUPERTRANS_FLAG,
"NO_SEQTK" => \$NO_SEQTK,
"no_super_reads" => \$NO_SUPER_READS_FLAG,
"__KMER_SIZE=i" => \$KMER_SIZE,
);
my @__ALL_TRINITY_PARAMS = qw(
h
help
advanced_help
show_full_usage_info
verbose
no_version_check
seqType
left
right
single
SS_lib_type
long_reads
long_reads_mode
output
min_contig_length
jaccard_clip
cite
CPU
np
mpiexec
prep
trimmomatic
quality_trimming_params
normalize_reads
no_normalize_reads
just_normalize_reads
normalize_max_read_cov
normalize_by_read_set
group_pairs_distance
bfly_opts
bflyHeapSpaceMax
bflyHeapSpaceInit
bflyGCThreads
bflyCPU
bflyCalculateCPU
bfly_jar
path_reinforcement_distance
no_path_merging
min_per_id_same_path
max_diffs_same_path
max_internal_gap_same_path
min_kmer_cov
inchworm_cpu
FORCE_INCHWORM_KMER_METHOD
INCHWORM_CUSTOM_PARAMS
no_run_inchworm
iworm_opts
max_memory
M
min_glue
glue_factor
min_iso_ratio
min_pcnt_read_iworm_kmers
max_reads_per_graph
max_reads_per_loop
min_pct_read_mapping
weldmer_size
no_bowtie
bowtie_comp
no_run_chrysalis
grid_exec
show_advanced_options
run_as_paired
no_cleanup
full_cleanup
version
monitoring
no_distributed_trinity_exec
jelly_s
NO_PARALLEL_IWORM
chrysalis_debug_weld_all
genome_guided_bam
genome_guided_max_intron
genome_guided_min_coverage
genome_guided_min_reads_per_partition
genome_guided_just_prep
trinity_complete
bypass_java_version_check
ananas_dir
samples_file
workdir
stomp_snps
FORCE
include_supertranscripts
NO_SUPERTRANS
max_chrysalis_cluster_size
iworm_cdhit
bfly_algorithm
__KMER_SIZE
);
my %ACCEPTABLE_OPTS = map { + $_ => 1} @__ALL_TRINITY_PARAMS;
my $opts_not_recognized_flag = 0;
for my $opt (@ARGV) {
if ($opt =~ /^-+(\S+)/) {
my $opt_part = $1;
unless ($ACCEPTABLE_OPTS{$opt_part}) {
print STDERR "ERROR, don't recognize parameter: $opt\n";
$opts_not_recognized_flag = 1;
}
}
}
if ($opts_not_recognized_flag) {
die "Please review usage info for accepted parameters.\n";
}
if (! grep { $_ eq $BFLY_ALGORITHM } @BFLY_ALGORITHMS) {
die "Error, dont recognize bfly algorithm: $BFLY_ALGORITHM, choices are: @BFLY_ALGORITHMS";
}
if ($SHOW_CITATION_FLAG) {
&show_lit_citation();
exit(0);
}
my $sort_exec = &COMMON::get_sort_exec($CPU);
if ($full_usage_info_flag) {
$usage = $basic_usage . $full_usage . $usage_synopsis;
die "$usage\n";
}
if ($advanced_help_flag) {
die "$advanced_usage\n";
}
if ($help_flag) {
die "$usage\n";
}
if ($show_version_flag) {
&version_check();
exit(1);
}
## basic options check:
unless ($max_memory &&
($genome_guided_bam ||
($seqType && $seqType =~ /^(fq|fa)$/
&&
($samples_file || (@left_files && @right_files) || @single_files) )
)
) {
die "Must specify basic parameters: ex. Trinity --seqType fq --single reads.fq --max_memory 10G ";
}
## make sure properly installed
{
foreach my $trinity_tool ("ParaFly", "seqtk-trinity") {
my $loc = `which $trinity_tool`;
unless ($loc =~ /\w/) {
die "\n\n\tError, cannot locate Trinity-specific tool: $trinity_tool in the PATH setting: $ENV{PATH}, be sure to install Trinity by running 'make' in the base installation directory\n\n";
}
}
}
$output_directory = &create_full_path($output_directory, 0);
if ($WORKDIR) {
$WORKDIR = &create_full_path($WORKDIR, 0);
}
else {
$WORKDIR = $output_directory;
}
my $GRAPH_FROM_FASTA_CUSTOM_PARAMS = "";
my $GRAPH_FROM_FASTA_KK = 2*($KMER_SIZE-1);
if ($TRINITY_COMPLETE_FLAG) {
###############################################
## force some options for phase 2 read assembly
###############################################
## iworm opts
$inchworm_cpu = 1;
$NO_PARALLEL_IWORM = 1;
unless ($NORMALIZE_READS_FLAG) {
## do not normalize by default when in trinity-complete mode. Normalizion should have been done earlier.
$NO_NORMALIZE_READS_FLAG = 1;
}
if ($min_pct_read_mapping < 50) {
$min_pct_read_mapping = 50; # more stringent for phase2 chrysalis
}
}
else {
# Trinithy phase 1 (read clustering)
$INCHWORM_CUSTOM_PARAMS .= " --min_any_entropy 1.0 ";
}