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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -6,12 +6,12 @@ | |
| # | # | ||
| # # | ||
| # File: batchRunFolders.sh # | ||
| VERSION="v1.0.2" # | ||
| VERSION="v1.0.3" # | ||
| # Author: Justin C. Bagley # | ||
| # Date: Created by Justin Bagley on Sun, May 3 11:00:32 CDT 2020. # | ||
| # Last update: July 31, 2020 # | ||
| # Last update: December 16, 2020 # | ||
| # Copyright (c) 2020 Justin C. Bagley. All rights reserved. # | ||
| # Please report bugs to <[email protected]>. # | ||
| # Please report bugs to <[email protected]>. # | ||
| # # | ||
| # Description: # | ||
| # SHELL SCRIPT THAT AUTOMATES PREPPING RUNS BY ORGANIZING A SET OF INPUT FILES INTO # | ||
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@@ -137,7 +137,7 @@ batchRunFolders () { | |
| ########################################################################################## | ||
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| echo "INFO | $(date) |----------------------------------------------------------------" | ||
| echo "INFO | $(date) | batchRunFolders, v1.0.2 July 2020 " | ||
| echo "INFO | $(date) | batchRunFolders, v1.0.3 December 2020 " | ||
| echo "INFO | $(date) | Copyright (c) 2020 Justin C. Bagley. All rights reserved. " | ||
| echo "INFO | $(date) |----------------------------------------------------------------" | ||
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@@ -228,7 +228,7 @@ echo "INFO | $(date) | Step #2: Organize input files (and other files) into | |
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| echo "INFO | $(date) | Making batch list files using PIrANHA splitFile function... " | ||
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| MY_PIRANHA_PATH="$(echo ${SCRIPT_PATH}/../piranha | sed 's/bin\/\.\.\///g')"; | ||
| MY_PIRANHA_PATH="$(echo ${SCRIPT_PATH}/../piranha.sh | sed 's/bin\/\.\.\///g')"; | ||
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| #piranha -f splitFile -i "$MY_INPUT_LIST_FILE" -n "$MY_NUM_BATCHES" -o "$MY_BATCH_FILE_PREFIX" ; | ||
| echo "#!/bin/sh | ||
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@@ -279,7 +279,7 @@ $MY_PIRANHA_PATH -f splitFile -i $MY_INPUT_LIST_FILE -n $MY_NUM_BATCHES -o $MY_B | |
| #!/bin/bash | ||
| #\$ -N ${MY_BATCH_FILE_PREFIX}1_mafft | ||
| #\$ -pe smp 3 | ||
| #\$ -pe smp ${MY_NUM_THREADS} | ||
| #\$ -cwd | ||
| #\$ -V | ||
| #\$ -S /bin/bash | ||
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@@ -296,7 +296,7 @@ echo + NSLOTS = \$NSLOTS | |
| $(printf '\t')list=${MY_BATCH_FILE_PREFIX}1.txt | ||
| $(printf '\t')MY_BASENAME=\"\$(basename \"\$list\" '.txt')\"; | ||
| $(printf '\t')export MY_NUM_THREADS=3 | ||
| #$(printf '\t')export MY_NUM_THREADS=3 | ||
| ( | ||
| $(printf '\t')$(printf '\t')$(printf '\t')for i in ./*.{fasta,fas,FASTA,FAS} ; do | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')if [[ \"\$i\" != \"./*.fasta\" ]] && [[ \"\$i\" != \"./*.fas\" ]] && [[ \"\$i\" != \"./*.FASTA\" ]] && [[ \"\$i\" != \"./*.FAS\" ]]; then | ||
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@@ -375,7 +375,7 @@ fi | |
| #!/bin/bash | ||
| #\$ -N ${MY_BATCH_FILE_PREFIX}1_iqtree | ||
| #\$ -pe smp 3 | ||
| #\$ -pe smp ${MY_NUM_THREADS} | ||
| #\$ -cwd | ||
| #\$ -V | ||
| #\$ -S /bin/bash | ||
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@@ -390,6 +390,9 @@ echo + NSLOTS = \$NSLOTS | |
| ######################################## START ########################################### | ||
| $(printf '\t')MY_IQTREE_V1_CHECK=\"\$(iqtree --version | grep 'version\ 1' | wc -l | sed 's/\ //g')\"; | ||
| $(printf '\t')MY_IQTREE_V2_CHECK=\"\$(iqtree --version | grep 'version\ 2' | wc -l | sed 's/\ //g')\"; | ||
| $(printf '\t')list=${MY_BATCH_FILE_PREFIX}1.txt | ||
| $(printf '\t')MY_BASENAME=\"\$(basename \"\$list\" '.txt')\"; | ||
| ( | ||
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@@ -398,10 +401,13 @@ $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')MY_PHYLIP_BASENAME=\"\$( | |
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')echo \"\$i\" >> ./\"\$MY_BASENAME\"_PHYLIP_iqtree_fileOrder.list.txt | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')echo \"INFO | \$(date) | ###------ \$i ------### \" | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')echo \"INFO | \$(date) | \" | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')echo \"INFO | \$(date) | Performing model selection (ModelFinder), building ML gene tree phylogeny, and performing SH-aLRT test and 1000 ultrafast bootstraps with IQ-tree... \" | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')echo \"INFO | \$(date) | Performing model selection (ModelFinder), building ML gene tree phylogeny, and performing SH-aLRT test and 1000 ultrafast bootstraps \" | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')echo \"INFO | \$(date) | with IQ-tree with ${MY_NUM_THREADS} threads...\" | ||
| # | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')if [[ ! -s \"\$MY_PHYLIP_BASENAME\".phy.iqtree ]] && [[ ! -s \"\$MY_PHYLIP_BASENAME\".aln.phy.iqtree ]] && [[ ! -s \"\$MY_PHYLIP_BASENAME\".aln.phy.contree ]] && [[ ! -s \"\$MY_PHYLIP_BASENAME\".phy.contree ]]; then | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')iqtree -s \"\$i\" -alrt 1000 -bb 1000 -nt 3 ; | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')if [[ ! -s \"\$MY_PHYLIP_BASENAME\".phy.iqtree ]] && [[ ! -s \"\$MY_PHYLIP_BASENAME\".aln.phy.iqtree ]] && [[ ! -s \"\$MY_PHYLIP_BASENAME\".aln.phy.contree ]] && [[ ! -s \"\$MY_PHYLIP_BASENAME\".phy.contree ]] && [[ \"\$MY_IQTREE_V1_CHECK\" = \"1\" ]] && [[ \"\$MY_IQTREE_V2_CHECK\" = \"0\" ]]; then | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')iqtree -s \"\$i\" -alrt 1000 -bb 1000 -nt ${MY_NUM_THREADS} ; | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')elif [[ ! -s \"\$MY_PHYLIP_BASENAME\".phy.iqtree ]] && [[ ! -s \"\$MY_PHYLIP_BASENAME\".aln.phy.iqtree ]] && [[ ! -s \"\$MY_PHYLIP_BASENAME\".aln.phy.contree ]] && [[ ! -s \"\$MY_PHYLIP_BASENAME\".phy.contree ]] && [[ \"\$MY_IQTREE_V1_CHECK\" = \"0\" ]] && [[ \"\$MY_IQTREE_V2_CHECK\" = \"1\" ]]; then | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')iqtree -s \"\$i\" -alrt 1000 -B 1000 -T ${MY_NUM_THREADS} ; | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')fi | ||
| # | ||
| $(printf '\t')$(printf '\t')$(printf '\t')$(printf '\t')echo \"INFO | \$(date) | \" | ||
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@@ -530,6 +536,8 @@ USAGE="Usage: $(basename "$0") [OPTION]... | |
| -f, --filetype fileType (def: phylip; other: fasta, nexus) input file type | ||
| -s, --software targetSoftware (def: mafft; other: iqtree, raxml) target run software that | ||
| input files will be analyzed with | ||
| -t, --threads numThreads (def: 3) number of threads for each software run (currently only | ||
| accommodates multi-threading for mafft and iqtree) | ||
| -b, --batches batchNumber (def: 10) number of batches (parts) to split input files into | ||
| -p, --prefix batchPrefix (def: align) prefix for batch parts file and other dir/file names | ||
| -l, --logfile logFile (def: aligning_log.txt) log screen output to file in working dir | ||
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