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set -o pipefail
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progname=${0##*/ } # run_get_phylomarkers_pipeline.sh
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- VERSION=' 2.8.0.1_2024 -04-14'
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+ VERSION=' 2.8.0.2_2024 -04-14'
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# Set GLOBALS
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# in Strict mode, need to explicitly set undefined variables to an empty string var=''
@@ -1605,7 +1605,7 @@ then
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# -h doesn't work with globs. Use a for loop
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# for i in $(find .. -maxdepth 1 -name "${id}"\* -printf "%f\n")
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- while read i; do
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+ while read -r i; do
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(( DEBUG > 0 )) && msg " > reading top_markers_tab:$top_markers_tab in top_markers_dir:$top_markers_dir ; running: ln -s ../${i} ." DEBUG NC
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if [ ! -h " $i " ]
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then
@@ -2087,11 +2087,13 @@ then
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# "${distrodir}"/remove_uninformative_sites_from_aln.pl < concat_cdnAlns.fna > concat_cdnAlns.fnainf
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# Generate the snp-matrix in FASTA format
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- " $bindir " /snp-sites -cm -o concat_cdnAlns_SNPs.fasta concat_cdnAlns.fna
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+ # "$bindir"/snp-sites -cm -o concat_cdnAlns_SNPs.fasta concat_cdnAlns.fna # activate only for statically-linked binary
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+ snp-sites -cm -o concat_cdnAlns_SNPs.fasta concat_cdnAlns.fna
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check_output concat_cdnAlns_SNPs.fasta " $parent_PID "
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# Generate the snp-matrix in VCF format
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- " $bindir " /snp-sites -cv -o concat_cdnAlns_SNPs.vcf concat_cdnAlns.fna
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+ # "$bindir"/snp-sites -cv -o concat_cdnAlns_SNPs.vcf concat_cdnAlns.fna # activate only for statically-linked binary
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+ snp-sites -cv -o concat_cdnAlns_SNPs.vcf concat_cdnAlns.fna
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check_output concat_cdnAlns_SNPs.vcf " $parent_PID "
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# compute phylogeny
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