diff --git a/HybPhyloMaker0a_preparedata.sh b/HybPhyloMaker0a_preparedata.sh index 5e2fd4c..2d21c3e 100644 --- a/HybPhyloMaker0a_preparedata.sh +++ b/HybPhyloMaker0a_preparedata.sh @@ -19,7 +19,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 0a - Download & prepare data * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker0b_preparereference.sh b/HybPhyloMaker0b_preparereference.sh index 69b1e1a..94c498b 100644 --- a/HybPhyloMaker0b_preparereference.sh +++ b/HybPhyloMaker0b_preparereference.sh @@ -18,7 +18,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 0b - Prepare pseudoreference * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker0c_Rsetup_MetaCentrum.sh b/HybPhyloMaker0c_Rsetup_MetaCentrum.sh index 0615b55..ff7bcfc 100644 --- a/HybPhyloMaker0c_Rsetup_MetaCentrum.sh +++ b/HybPhyloMaker0c_Rsetup_MetaCentrum.sh @@ -9,7 +9,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 0c - Setup R packages on Metacentrum * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker1_rawprocess.sh b/HybPhyloMaker1_rawprocess.sh index e9d6263..da3e9e3 100644 --- a/HybPhyloMaker1_rawprocess.sh +++ b/HybPhyloMaker1_rawprocess.sh @@ -18,7 +18,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 01 - Raw data processing * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042* @@ -179,12 +179,12 @@ do #Adapter and general quality trimming echo "Adapter removal & quality trimming..." if [[ $location == "1" ]]; then - java -jar /software/trimmomatic-0.32/dist/jar/trimmomatic-0.32.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../NEBNext-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1 + java -jar /software/trimmomatic-0.32/dist/jar/trimmomatic-0.32.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../${adapterfile}:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1 #trimmomatic PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../NEBNext-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1 elif [[ $location == "2" ]]; then - java -d64 -server -XX:MaxHeapSize=10g -jar ../trimmomatic-0.33.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../NEBNext-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1 + java -d64 -server -XX:MaxHeapSize=10g -jar ../trimmomatic-0.33.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../${adapterfile}:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1 else - java -jar ../trimmomatic-0.33.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../NEBNext-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1 + java -jar ../trimmomatic-0.33.jar PE -phred33 $file-noPhiX_1.fq.gz $file-noPhiX_2.fq.gz $file-1P $file-1U $file-2P $file-2U ILLUMINACLIP:../${adapterfile}:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:5:20 MINLEN:36 >Trimmomatic.log 2>&1 fi #Copy trimmed reads to home if [[ $location == "1" ]]; then diff --git a/HybPhyloMaker3_generatepslx.sh b/HybPhyloMaker3_generatepslx.sh index a0cad43..b3c2810 100644 --- a/HybPhyloMaker3_generatepslx.sh +++ b/HybPhyloMaker3_generatepslx.sh @@ -18,7 +18,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 03 - Process consensus after mapping, make pslx files * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042* diff --git a/HybPhyloMaker4_processpslx.sh b/HybPhyloMaker4_processpslx.sh index 149fc14..e7a675a 100644 --- a/HybPhyloMaker4_processpslx.sh +++ b/HybPhyloMaker4_processpslx.sh @@ -20,7 +20,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 04 - Process pslx files * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # * based on Weitemier et al. (2014), Applications in Plant Science 2(9): 1400042* diff --git a/HybPhyloMaker4b_correctframe_translate.sh b/HybPhyloMaker4b_correctframe_translate.sh index 6134303..018cfc0 100644 --- a/HybPhyloMaker4b_correctframe_translate.sh +++ b/HybPhyloMaker4b_correctframe_translate.sh @@ -8,7 +8,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 04b - Put exons to correct reading frame and translate * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker5_missingdataremoval.sh b/HybPhyloMaker5_missingdataremoval.sh index 29f8e4c..2036dbd 100644 --- a/HybPhyloMaker5_missingdataremoval.sh +++ b/HybPhyloMaker5_missingdataremoval.sh @@ -19,7 +19,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 05 - Missing data handling * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** @@ -243,7 +243,7 @@ do #Calculate percentage of missing data as integer (for evaluation in bash) percentage=$(echo -e "scale=0;($count * 100) / $y" | bc) echo -e "$header\t$percentageprint" >> ${file}_${MISSINGPERCENT}percN.fas - if [ "$percentage" -lt "$MISSINGPERCENT" ]; then + if [ "$percentage" -le "$MISSINGPERCENT" ]; then echo "$line" >> ${file}_modif${MISSINGPERCENT}.fas else echo -e "Deleting $header with $percentageprint of missing data" diff --git a/HybPhyloMaker6a2_RAxML_trees_summary.sh b/HybPhyloMaker6a2_RAxML_trees_summary.sh index 9bba7b8..e536a2f 100644 --- a/HybPhyloMaker6a2_RAxML_trees_summary.sh +++ b/HybPhyloMaker6a2_RAxML_trees_summary.sh @@ -19,7 +19,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 06a2 - summary of RAxML gene trees * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker6a_RAxML_for_selected.sh b/HybPhyloMaker6a_RAxML_for_selected.sh index 0e9f31b..ae33d6e 100644 --- a/HybPhyloMaker6a_RAxML_for_selected.sh +++ b/HybPhyloMaker6a_RAxML_for_selected.sh @@ -17,7 +17,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 06a - RAxML gene tree building * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker6b_FastTree_for_selected.sh b/HybPhyloMaker6b_FastTree_for_selected.sh index b070bb8..79e9dc1 100644 --- a/HybPhyloMaker6b_FastTree_for_selected.sh +++ b/HybPhyloMaker6b_FastTree_for_selected.sh @@ -18,7 +18,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 06b - FastTree gene tree building * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker7_roottrees.sh b/HybPhyloMaker7_roottrees.sh index f124037..21bf39b 100644 --- a/HybPhyloMaker7_roottrees.sh +++ b/HybPhyloMaker7_roottrees.sh @@ -17,7 +17,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 07 - Root gene trees * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker8a_astral.sh b/HybPhyloMaker8a_astral.sh index 1176e6a..b249358 100644 --- a/HybPhyloMaker8a_astral.sh +++ b/HybPhyloMaker8a_astral.sh @@ -18,7 +18,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 08a - Astral species tree * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker8b_astrid.sh b/HybPhyloMaker8b_astrid.sh index b76dfa4..ae597fa 100644 --- a/HybPhyloMaker8b_astrid.sh +++ b/HybPhyloMaker8b_astrid.sh @@ -19,7 +19,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 08b - Astrid species tree * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker8c_mrl.sh b/HybPhyloMaker8c_mrl.sh index d526fa9..459b640 100644 --- a/HybPhyloMaker8c_mrl.sh +++ b/HybPhyloMaker8c_mrl.sh @@ -18,7 +18,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 08c - MRL species tree * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker8e_concatenatedFastTree.sh b/HybPhyloMaker8e_concatenatedFastTree.sh index 1179761..48ac5e8 100644 --- a/HybPhyloMaker8e_concatenatedFastTree.sh +++ b/HybPhyloMaker8e_concatenatedFastTree.sh @@ -18,7 +18,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 08e - concatenated species tree * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker8f_concatenatedExaML.sh b/HybPhyloMaker8f_concatenatedExaML.sh index 3ab49a7..48b4d11 100644 --- a/HybPhyloMaker8f_concatenatedExaML.sh +++ b/HybPhyloMaker8f_concatenatedExaML.sh @@ -8,7 +8,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 08f - ExaML concatenated tree * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/HybPhyloMaker9_update_trees.sh b/HybPhyloMaker9_update_trees.sh index f3cd007..6c66c2c 100644 --- a/HybPhyloMaker9_update_trees.sh +++ b/HybPhyloMaker9_update_trees.sh @@ -18,7 +18,7 @@ # ******************************************************************************** # * HybPhyloMaker - Pipeline for Hyb-Seq data processing and tree building * # * Script 09 - Update trees * -# * v.1.4.1 * +# * v.1.4.2 * # * Tomas Fer, Dept. of Botany, Charles University, Prague, Czech Republic, 2017 * # * tomas.fer@natur.cuni.cz * # ******************************************************************************** diff --git a/install_software.sh b/install_software.sh index 20abce1..30b6040 100644 --- a/install_software.sh +++ b/install_software.sh @@ -8,7 +8,7 @@ # Tomas Fer, 2017 # # tomas.fer@natur.cuni.cz # # https://github.com/tomas-fer/HybPhyloMaker # -# v.1.4.0 # +# v.1.4.2 # ########################################################################################################################## #Carefully set your distribution