added a bunch of annotation and maker codes and edited filter script …

…a little bit. changes since Dec 2021

MAKER.sh

@@ -0,0 +1,174 @@
+#!/bin/bash
+
+#SBATCH --mem 50G
+#SBATCH --job-name maker
+#SBATCH --mail-user [email protected] ## CHANGE THIS TO YOUR EMAIL
+#SBATCH --mail-type ALL
+#SBATCH -n 24
+#SBATCH -N 1
+#SBATCH -A h3abionet
+#SBATCH -o /home/groups/h3abionet/RefGraph/results/NeginV_Test_Summer2021/slurm_output/slurm-%j.out
+
+
+
+# HPCBio UIUC Gene Annotation pipeline (MAKER + EVidenceModeler); Created by Negin Valizadegan Jan 18, 2022; [email protected]
+
+##############################################################################
+##																		                                    	##
+##			           GENERAL WRAPPER RELATED SCRIPTS	                        ##
+##																			                                    ##	
+##############################################################################
+
+# Set fancy fonts for the help message ------
+NORM=`tput sgr0`
+BOLD=`tput bold`
+REV=`tput smso`
+
+# Help ------
+function HELP {
+  echo ""
+  echo "${BOLD}Help Documentation for the HPCBio UIUC Annotation (Filtering) Pipeline${NORM}"
+  echo ""
+  echo "The Following Options Must Be Specified:"
+  echo "${REV}-d${NORM}   The full path to the main results directory${NORM} (Required)"
+  echo "${REV}-s${NORM}   The name of the input sequence (Required)"
+  echo "${REV}-h${NORM}   Displays this help message without complaints (Optional)"
+  echo ""
+  echo "[ ${NORM}${BOLD}Example:${NORM} sbatch MAKER.sh -d /home/groups/h3abionet/RefGraph/results/NeginV_Test_Summer2021/results/ -s clustered_GRCH38_p0.fasta ]"
+  echo ""
+  exit 1
+}
+
+
+# Check the number of arguments. If none are passed, print message and exit ------
+NUMARGS=$#
+if [ $NUMARGS -eq 0 ]; then
+  echo ""
+  echo "You Did Not Pass Any Arguments. Please Specify the Arguments Below:" 
+  echo ""
+  HELP
+fi
+
+
+# Parse the inputs
+while getopts :d:s:h FLAG; do
+  case $FLAG in
+    d)  #set option "d"
+      OPT_d=$OPTARG
+      ;;
+    s)  #set option "s"
+      OPT_s=$OPTARG
+      ;;
+     h)  #set option "h"
+      OPT_h=$OPTARG
+      HELP
+      ;;
+    \?) #unrecognized option - show help
+      echo "Option -${BOLD}$OPTARG${NORM} not allowed."
+      exit 1
+      ;;
+  esac
+done
+
+
+# Exit if necessary options are not passed ------
+if [[ -z "$OPT_d" ]]; then
+        echo "No project directory specified, aborting script"
+        exit 1
+fi
+
+if [[ -z "$OPT_s" ]]; then
+        echo "No input sequence name is specified, aborting script"
+        exit 1
+fi
+
+##############################################################################
+##																			                                    ##
+##				                   STEP 0: LOAD MODULES                           ##
+##																			                                    ##	
+##############################################################################
+
+setup ()
+{
+
+# Load modules ------
+module load MAKER/3.01.03-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
+
+# Create 3 control files needed for maker ----- (do not run if present; control files should be edited manually)
+# cd ${OPT_d}/../HPCBio-Refgraph_pipeline/
+# maker -CITL
+
+echo "Control ctl files are created if not already exist. They are usually needed to be manually modified."
+
+}
+
+
+##############################################################################
+##																			                                    ##
+##				                    STEP 1: RUN MAKER                             ##
+##																			                                    ##	
+##############################################################################
+
+maker ()
+{
+
+# Set working directory -----
+cd ${OPT_d}/annotation
+
+# Create output directory
+mkdir -p MAKER
+cd MAKER
+
+echo "Working directory is set to" | tr '\n' ' ' && pwd
+
+# Create a temp directory ------
+mkdir -p /scratch/valizad2/maker # change valizad2 to your username
+
+start=`date +%s` # capture start time 
+echo "Start of maker annotation"
+
+#export AUGUSTUS_CONFIG_PATH=/home/n-z/valizad2/NeginV_Test_Summer2021/augustus/3.2.3-IGB-gcc-4.9.4/config export PATH=$PATH:=/home/n-z/valizad2/NeginV_Test_Summer2021/augustus/3.2.3-IGB-gcc-4.9.4/bin
+
+# Run maker -----
+mpiexec -n $SLURM_NPROCS maker \
+${OPT_d}/../HPCBio-Refgraph_pipeline/maker_opts.ctl \
+${OPT_d}/../HPCBio-Refgraph_pipeline/maker_bopts.ctl \
+${OPT_d}/../HPCBio-Refgraph_pipeline/maker_exe.ctl \
+-genome ${OPT_d}/annotation/Cluster_CDHIT/masurca/${OPT_s} \
+-fix_nucleotides # This will change Ys to Ns
+
+echo "Maker gene prediction is completed for ${OPT_s}"
+
+end=`date +%s`
+runtime=$((end-start))
+runtime=$( echo "scale=2;$((end-start)) / 60" | bc )
+echo "It took $runtime minutes to run maker on ${OPT_s}"
+
+}
+
+
+##############################################################################
+##																			                                    ##
+##						                      MAIN                                    ##
+##																		                                      ##
+##############################################################################
+
+# Main function runs each step/function of the pipeline separately so that
+# user can choose to run steps one at a time.
+
+main ()
+{
+	# Determine whether running full pipeline or single step
+	#runtype="PARTIAL"
+  runtype="FULL"
+  echo ""
+	echo "*** RUNNING ${runtype} ANNOTATION PIPELINE ***"
+
+  setup
+  maker
+
+  }
+
+
+# Run main function
+main

_Inline/config-x86_64-linux-5.026001

@@ -0,0 +1,14 @@
+version : 0.80
+languages : %
+    C : C
+    Foo : Foo
+    foo : Foo
+types : %
+    C : compiled
+    Foo : interpreted
+modules : %
+    C : Inline::C
+    Foo : Inline::Foo
+suffixes : %
+    C : so
+    Foo : foo

_Inline/lib/auto/Bio/DB/IndexedBase_168b/IndexedBase_168b.inl

@@ -0,0 +1,22 @@
+md5 : 168b5562b2d3d613c6ee4dee4c45c915
+name : Bio::DB::IndexedBase_168b
+version : ""
+language : C
+language_id : C
+installed : 0
+date_compiled : Wed Jan 19 11:50:34 2022
+inline_version : 0.80
+ILSM : %
+    module : Inline::C
+    suffix : so
+    type : compiled
+Config : %
+    apiversion : ?
+    archname : x86_64-linux
+    cc : gcc
+    ccflags : -O2 -march=x86-64 -mtune=generic -fPIC -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2
+    ld : gcc
+    osname : linux
+    osvers : 3.10.0-514.21.1.el7.x86_64
+    so : so
+    version : 5.26.1

annotation-config.conf

@@ -8,7 +8,10 @@ params {
     genome1 = "./GRCh38/GRCh38_full_analysis_set_plus_decoy_hla.fa"
     genome2 = "./GRCh38.p0/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
     genome3 = "./CHM13.v1.1_GRCh38.p13.chrY/CHM13.v1.1_GRCh38.p13.chrY.fna"
-    samplePath = "./results/filter/Final-Filtered/masurca/*_filter.final.fasta"
+    samplePath = "./results/filter/Final-Filtered/masurca/test/*_filter.final.fasta"
+    samplePath1 = "./results/filter/Final-Filtered/masurca/test/*_GRCH38_decoys_hla_filter.final.fasta"
+    samplePath2 = "./results/filter/Final-Filtered/masurca/test/*_GRCH38_p0_filter.final.fasta"
+    samplePath3 = "./results/filter/Final-Filtered/masurca/test/*_CHM13_filter.final.fasta"
     myQueue = "normal"
     clusterAcct = " -A h3abionet "
 }

annotation-run.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+#SBATCH --mem 18G
+#SBATCH --job-name annotation
+#SBATCH --mail-user [email protected] ## CHANGE THIS TO YOUR EMAIL
+#SBATCH --mail-type ALL
+#SBATCH -n 2
+#SBATCH -N 1
+#SBATCH -A h3abionet
+#SBATCH -o /home/groups/h3abionet/RefGraph/results/NeginV_Test_Summer2021/slurm_output/slurm-%A.out
+
+### This Runs Nextflow Annotation UIUC pipeline 
+## Date File Created: Dec 5, 2021
+
+
+# Set working directory -------
+cd /home/groups/h3abionet/RefGraph/results/NeginV_Test_Summer2021
+
+# Load nextflow ------
+module load nextflow/21.04.1-Java-1.8.0_152
+
+# Run nextflow UIUC workflow -----
+nextflow run HPCBio-Refgraph_pipeline/annotation.nf \
+-c HPCBio-Refgraph_pipeline/annotation-config.conf \
+-qs 3 -resume \
+-with-report nextflow_reports/nf_report.html \
+-with-timeline nextflow_reports/nf_timeline.html \
+-with-trace nextflow_reports/nf_trace.txt
+
+# -log custom.log  #add this for log not hidden
+# -q  # Disable the printing of information to the terminal.
+
+# -with-report nf_exec_report_annotation.html \
+# -with-timeline nf_timeline_annotation.html \
+# -with-trace > nf_trace_annotation.txt \ # this is the same as slurm output, if you use this, slurm output will be empty
+# -with-dag nf_flowchart_annotation.pdf
+
+#if [ echo "wc -l ${keep}" == echo "grep -E ">" ${id}_kn_filtered.fasta | wc -l" ]
+ #   then 
+  #      echo "The filtering has not been done correctly. Please check your blastncontam script"
+   # fi
+
+
+