From e1a53c00f2a38a9d573748559e26c558009b7450 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 5 Dec 2019 10:06:09 +0100
Subject: [PATCH] annotate is step 2. step 1 is prepare

---
 .../Genes/EXAM.1216.00002.gen                       |   0
 .../Genes/EXAM.1219.00001.gen                       |   0
 .../Genes/GEN2.1219.00001.gen                       |   0
 .../Genes/GEN4.1111.00001.gen                       |   0
 .../LSTINFO-list_genomes.lst                        |   0
 .../LSTINFO/EXAM.1216.00002.lst                     |   0
 .../LSTINFO/EXAM.1219.00001.lst                     |   0
 .../LSTINFO/GEN2.1219.00001.lst                     |   0
 .../LSTINFO/GEN4.1111.00001.lst                     |   0
 .../PanACoTA-annotate_list_genomes.log              |   0
 .../PanACoTA-annotate_list_genomes.log.details      |   0
 .../PanACoTA-annotate_list_genomes.log.err          |   0
 .../Proteins/EXAM.1216.00002.prt                    |   0
 .../Proteins/EXAM.1219.00001.prt                    |   0
 .../Proteins/GEN2.1219.00001.prt                    |   0
 .../Proteins/GEN4.1111.00001.prt                    |   0
 .../QC_L90-list_genomes.png                         | Bin
 .../QC_nb-contigs-list_genomes.png                  | Bin
 .../Replicons/EXAM.1216.00002.fna                   |   0
 .../Replicons/EXAM.1219.00001.fna                   |   0
 .../Replicons/GEN2.1219.00001.fna                   |   0
 .../Replicons/GEN4.1111.00001.fna                   |   0
 .../discarded-list_genomes.lst                      |   0
 .../gff3/EXAM.1216.00002.gff                        |   0
 .../gff3/EXAM.1219.00001.gff                        |   0
 .../gff3/GEN2.1219.00001.gff                        |   0
 .../gff3/GEN4.1111.00001.gff                        |   0
 .../tmp_files/genome1.fst_prodigal-split5N.fna      |   0
 .../genome1.fst_prodigal-split5N.fna-prodigal.log   |   0
 ...enome1.fst_prodigal-split5N.fna-prodigal.log.err |   0
 .../EXAM.1219.00001.faa                             |   0
 .../EXAM.1219.00001.ffn                             |   0
 .../EXAM.1219.00001.gff                             |   0
 .../tmp_files/genome2.fst_prodigal-split5N.fna      |   0
 .../genome2.fst_prodigal-split5N.fna-prodigal.log   |   0
 ...enome2.fst_prodigal-split5N.fna-prodigal.log.err |   0
 .../GEN2.1219.00001.faa                             |   0
 .../GEN2.1219.00001.ffn                             |   0
 .../GEN2.1219.00001.gff                             |   0
 .../tmp_files/genome3-chromo.fst-all.fna            |   0
 .../genome3-chromo.fst-all.fna_prodigal-split5N.fna |   0
 ...mo.fst-all.fna_prodigal-split5N.fna-prodigal.log |   0
 ...st-all.fna_prodigal-split5N.fna-prodigal.log.err |   0
 .../EXAM.1216.00002.faa                             |   0
 .../EXAM.1216.00002.ffn                             |   0
 .../EXAM.1216.00002.gff                             |   0
 .../tmp_files/genome4.fst_prodigal-split5N.fna      |   0
 .../genome4.fst_prodigal-split5N.fna-prodigal.log   |   0
 ...enome4.fst_prodigal-split5N.fna-prodigal.log.err |   0
 .../GEN4.1111.00001.faa                             |   0
 .../GEN4.1111.00001.ffn                             |   0
 .../GEN4.1111.00001.gff                             |   0
 52 files changed, 0 insertions(+), 0 deletions(-)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Genes/EXAM.1216.00002.gen (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Genes/EXAM.1219.00001.gen (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Genes/GEN2.1219.00001.gen (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Genes/GEN4.1111.00001.gen (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/LSTINFO-list_genomes.lst (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/LSTINFO/EXAM.1216.00002.lst (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/LSTINFO/EXAM.1219.00001.lst (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/LSTINFO/GEN2.1219.00001.lst (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/LSTINFO/GEN4.1111.00001.lst (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/PanACoTA-annotate_list_genomes.log (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/PanACoTA-annotate_list_genomes.log.details (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/PanACoTA-annotate_list_genomes.log.err (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Proteins/EXAM.1216.00002.prt (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Proteins/EXAM.1219.00001.prt (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Proteins/GEN2.1219.00001.prt (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Proteins/GEN4.1111.00001.prt (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/QC_L90-list_genomes.png (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/QC_nb-contigs-list_genomes.png (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Replicons/EXAM.1216.00002.fna (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Replicons/EXAM.1219.00001.fna (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Replicons/GEN2.1219.00001.fna (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/Replicons/GEN4.1111.00001.fna (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/discarded-list_genomes.lst (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/gff3/EXAM.1216.00002.gff (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/gff3/EXAM.1219.00001.gff (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/gff3/GEN2.1219.00001.gff (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/gff3/GEN4.1111.00001.gff (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome1.fst_prodigal-split5N.fna (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log.err (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.faa (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.ffn (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.gff (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome2.fst_prodigal-split5N.fna (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log.err (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.faa (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.ffn (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.gff (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome3-chromo.fst-all.fna (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log.err (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.faa (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.ffn (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.gff (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome4.fst_prodigal-split5N.fna (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log.err (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.faa (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.ffn (100%)
 rename Examples/{1-res-Annotate-prodigal => 2-res-Annotate-prodigal}/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.gff (100%)

diff --git a/Examples/1-res-Annotate-prodigal/Genes/EXAM.1216.00002.gen b/Examples/2-res-Annotate-prodigal/Genes/EXAM.1216.00002.gen
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/Genes/EXAM.1216.00002.gen
rename to Examples/2-res-Annotate-prodigal/Genes/EXAM.1216.00002.gen
diff --git a/Examples/1-res-Annotate-prodigal/Genes/EXAM.1219.00001.gen b/Examples/2-res-Annotate-prodigal/Genes/EXAM.1219.00001.gen
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/Genes/EXAM.1219.00001.gen
rename to Examples/2-res-Annotate-prodigal/Genes/EXAM.1219.00001.gen
diff --git a/Examples/1-res-Annotate-prodigal/Genes/GEN2.1219.00001.gen b/Examples/2-res-Annotate-prodigal/Genes/GEN2.1219.00001.gen
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/Genes/GEN2.1219.00001.gen
rename to Examples/2-res-Annotate-prodigal/Genes/GEN2.1219.00001.gen
diff --git a/Examples/1-res-Annotate-prodigal/Genes/GEN4.1111.00001.gen b/Examples/2-res-Annotate-prodigal/Genes/GEN4.1111.00001.gen
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/Genes/GEN4.1111.00001.gen
rename to Examples/2-res-Annotate-prodigal/Genes/GEN4.1111.00001.gen
diff --git a/Examples/1-res-Annotate-prodigal/LSTINFO-list_genomes.lst b/Examples/2-res-Annotate-prodigal/LSTINFO-list_genomes.lst
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/LSTINFO-list_genomes.lst
rename to Examples/2-res-Annotate-prodigal/LSTINFO-list_genomes.lst
diff --git a/Examples/1-res-Annotate-prodigal/LSTINFO/EXAM.1216.00002.lst b/Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1216.00002.lst
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/LSTINFO/EXAM.1216.00002.lst
rename to Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1216.00002.lst
diff --git a/Examples/1-res-Annotate-prodigal/LSTINFO/EXAM.1219.00001.lst b/Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1219.00001.lst
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/LSTINFO/EXAM.1219.00001.lst
rename to Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1219.00001.lst
diff --git a/Examples/1-res-Annotate-prodigal/LSTINFO/GEN2.1219.00001.lst b/Examples/2-res-Annotate-prodigal/LSTINFO/GEN2.1219.00001.lst
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/LSTINFO/GEN2.1219.00001.lst
rename to Examples/2-res-Annotate-prodigal/LSTINFO/GEN2.1219.00001.lst
diff --git a/Examples/1-res-Annotate-prodigal/LSTINFO/GEN4.1111.00001.lst b/Examples/2-res-Annotate-prodigal/LSTINFO/GEN4.1111.00001.lst
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/LSTINFO/GEN4.1111.00001.lst
rename to Examples/2-res-Annotate-prodigal/LSTINFO/GEN4.1111.00001.lst
diff --git a/Examples/1-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log b/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log
rename to Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log
diff --git a/Examples/1-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.details b/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.details
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rename from Examples/1-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.details
rename to Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.details
diff --git a/Examples/1-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.err b/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.err
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rename from Examples/1-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.err
rename to Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.err
diff --git a/Examples/1-res-Annotate-prodigal/Proteins/EXAM.1216.00002.prt b/Examples/2-res-Annotate-prodigal/Proteins/EXAM.1216.00002.prt
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rename from Examples/1-res-Annotate-prodigal/Proteins/EXAM.1216.00002.prt
rename to Examples/2-res-Annotate-prodigal/Proteins/EXAM.1216.00002.prt
diff --git a/Examples/1-res-Annotate-prodigal/Proteins/EXAM.1219.00001.prt b/Examples/2-res-Annotate-prodigal/Proteins/EXAM.1219.00001.prt
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rename from Examples/1-res-Annotate-prodigal/Proteins/EXAM.1219.00001.prt
rename to Examples/2-res-Annotate-prodigal/Proteins/EXAM.1219.00001.prt
diff --git a/Examples/1-res-Annotate-prodigal/Proteins/GEN2.1219.00001.prt b/Examples/2-res-Annotate-prodigal/Proteins/GEN2.1219.00001.prt
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rename from Examples/1-res-Annotate-prodigal/Proteins/GEN2.1219.00001.prt
rename to Examples/2-res-Annotate-prodigal/Proteins/GEN2.1219.00001.prt
diff --git a/Examples/1-res-Annotate-prodigal/Proteins/GEN4.1111.00001.prt b/Examples/2-res-Annotate-prodigal/Proteins/GEN4.1111.00001.prt
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rename from Examples/1-res-Annotate-prodigal/Proteins/GEN4.1111.00001.prt
rename to Examples/2-res-Annotate-prodigal/Proteins/GEN4.1111.00001.prt
diff --git a/Examples/1-res-Annotate-prodigal/QC_L90-list_genomes.png b/Examples/2-res-Annotate-prodigal/QC_L90-list_genomes.png
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diff --git a/Examples/1-res-Annotate-prodigal/QC_nb-contigs-list_genomes.png b/Examples/2-res-Annotate-prodigal/QC_nb-contigs-list_genomes.png
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rename from Examples/1-res-Annotate-prodigal/QC_nb-contigs-list_genomes.png
rename to Examples/2-res-Annotate-prodigal/QC_nb-contigs-list_genomes.png
diff --git a/Examples/1-res-Annotate-prodigal/Replicons/EXAM.1216.00002.fna b/Examples/2-res-Annotate-prodigal/Replicons/EXAM.1216.00002.fna
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rename from Examples/1-res-Annotate-prodigal/Replicons/EXAM.1216.00002.fna
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diff --git a/Examples/1-res-Annotate-prodigal/Replicons/EXAM.1219.00001.fna b/Examples/2-res-Annotate-prodigal/Replicons/EXAM.1219.00001.fna
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rename from Examples/1-res-Annotate-prodigal/Replicons/EXAM.1219.00001.fna
rename to Examples/2-res-Annotate-prodigal/Replicons/EXAM.1219.00001.fna
diff --git a/Examples/1-res-Annotate-prodigal/Replicons/GEN2.1219.00001.fna b/Examples/2-res-Annotate-prodigal/Replicons/GEN2.1219.00001.fna
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rename from Examples/1-res-Annotate-prodigal/Replicons/GEN2.1219.00001.fna
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diff --git a/Examples/1-res-Annotate-prodigal/Replicons/GEN4.1111.00001.fna b/Examples/2-res-Annotate-prodigal/Replicons/GEN4.1111.00001.fna
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rename from Examples/1-res-Annotate-prodigal/Replicons/GEN4.1111.00001.fna
rename to Examples/2-res-Annotate-prodigal/Replicons/GEN4.1111.00001.fna
diff --git a/Examples/1-res-Annotate-prodigal/discarded-list_genomes.lst b/Examples/2-res-Annotate-prodigal/discarded-list_genomes.lst
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diff --git a/Examples/1-res-Annotate-prodigal/gff3/EXAM.1216.00002.gff b/Examples/2-res-Annotate-prodigal/gff3/EXAM.1216.00002.gff
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diff --git a/Examples/1-res-Annotate-prodigal/gff3/EXAM.1219.00001.gff b/Examples/2-res-Annotate-prodigal/gff3/EXAM.1219.00001.gff
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diff --git a/Examples/1-res-Annotate-prodigal/gff3/GEN2.1219.00001.gff b/Examples/2-res-Annotate-prodigal/gff3/GEN2.1219.00001.gff
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diff --git a/Examples/1-res-Annotate-prodigal/gff3/GEN4.1111.00001.gff b/Examples/2-res-Annotate-prodigal/gff3/GEN4.1111.00001.gff
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rename from Examples/1-res-Annotate-prodigal/gff3/GEN4.1111.00001.gff
rename to Examples/2-res-Annotate-prodigal/gff3/GEN4.1111.00001.gff
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna
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rename from Examples/1-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log.err b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log.err
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log.err
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.faa b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.faa
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.faa
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.ffn b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.ffn
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.ffn
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.gff b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.gff
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.gff
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna
similarity index 100%
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log
similarity index 100%
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log.err b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log.err
similarity index 100%
rename from Examples/1-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log.err
rename to Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log.err
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.faa b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.faa
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.faa
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.ffn b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.ffn
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.ffn
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.gff b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.gff
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.gff
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna
similarity index 100%
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna
similarity index 100%
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log
similarity index 100%
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log.err b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log.err
similarity index 100%
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.faa b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.faa
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.faa
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.ffn b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.ffn
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.ffn
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.gff b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.gff
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.gff
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna
similarity index 100%
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log
similarity index 100%
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log.err b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log.err
similarity index 100%
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.faa b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.faa
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diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.ffn b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.ffn
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.ffn
diff --git a/Examples/1-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.gff b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.gff
similarity index 100%
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rename to Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.gff
-- 
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