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@ -16,35 +16,35 @@
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- path: output/pirate/results/PIRATE.unique_alleles.tsv
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contains: ["allele_name"]
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- path: output/pirate/results/binary_presence_absence.fasta
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contains: ["GCF_000292685"]
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contains: ["test1"]
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- path: output/pirate/results/binary_presence_absence.nwk
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md5sum: 5b5d86bf97d97de37bb9db514abb7762
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md5sum: 1fcf7434911bbab39b74791259f1f989
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- path: output/pirate/results/cluster_alleles.tab
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contains: ["g0001"]
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- path: output/pirate/results/co-ords/GCF_000292685.co-ords.tab
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md5sum: d5ca0f06ca7ea1f5486683d5859bc9b8
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- path: output/pirate/results/co-ords/GCF_000298385.co-ords.tab
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md5sum: a24d6048b3074242bb558c7fa27a8b03
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- path: output/pirate/results/co-ords/GCF_002849995.co-ords.tab
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md5sum: 0c08228585f4fa95686e9b025e0fe9c1
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- path: output/pirate/results/co-ords/test1.co-ords.tab
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md5sum: f1e75c045b35bae260dadb1a2f000dfa
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- path: output/pirate/results/co-ords/test2.co-ords.tab
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md5sum: 953b0d2f1dfd4c3a6a6dd246c9174703
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- path: output/pirate/results/co-ords/test3.co-ords.tab
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md5sum: 61f2c52ef77dc9a97a200c57b89b7d69
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- path: output/pirate/results/genome2loci.tab
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md5sum: bbcea5bfcdcafe14a9aa7261c8e931b8
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md5sum: 2d9cdefd5b1a7f5e20b0a70a6e5fa588
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- path: output/pirate/results/genome_list.txt
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md5sum: 6534b1635c258ad92b829077addc1ff5
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md5sum: c19ac63da7949b15179f42093cbf95b8
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- path: output/pirate/results/link_clusters.log
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contains: ["parsing paralog file"]
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- path: output/pirate/results/loci_list.tab
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contains: ["GCF_000298385_00242"]
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contains: ["test1_00242"]
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- path: output/pirate/results/loci_paralog_categories.tab
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md5sum: 6404d2a32526a398f42d7da768a389bd
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- path: output/pirate/results/modified_gffs/GCF_000292685.gff
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md5sum: 2b73bda2f84dc634303dc90e641040ca
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- path: output/pirate/results/modified_gffs/GCF_000298385.gff
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md5sum: b1a9d6557d47e09249f08a7acdbbd618
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- path: output/pirate/results/modified_gffs/GCF_002849995.gff
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md5sum: 68532fc9bb639e6d83c731a069f60cf8
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md5sum: f8c3d31f445c3cb66bd95ba77be0a7b8
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- path: output/pirate/results/modified_gffs/test1.gff
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md5sum: 5dc220e472165c3b693e1017f38fc0e3
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- path: output/pirate/results/modified_gffs/test2.gff
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md5sum: 975f5c7fb363caf1be9c53e5e237bb5d
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- path: output/pirate/results/modified_gffs/test3.gff
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md5sum: a4735a5ac75ce82aadba8a3de6cabc2e
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- path: output/pirate/results/pan_sequences.fasta
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md5sum: ed835c77fdb20c36aa9d5208eb7ca0cb
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md5sum: 0492833706f0f969b49a3555c16ec40d
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- path: output/pirate/results/pangenome.connected_blocks.tsv
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contains: ["block_number"]
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- path: output/pirate/results/pangenome.edges
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@ -59,29 +59,29 @@
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contains: ["g0091"]
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- path: output/pirate/results/pangenome.temp
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- path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
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md5sum: 9da25d27684bfcc5488987ab2d1fd3a1
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md5sum: ffb3b5bf1ba24bf2bd0be677500139a2
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- path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
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contains: ["GCF_000298385_00081"]
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contains: ["test1_00081"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
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contains: ["GCF_000298385_00242"]
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contains: ["test1_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
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contains: ["chaos"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
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md5sum: 84668b6c65b57026a17a50b0edd02541
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md5sum: 6e483c773ed90bd50b33f2bd569343e4
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
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@ -95,4 +95,4 @@
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- path: output/pirate/results/representative_sequences.ffn
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contains: ["representative_genome"]
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- path: output/pirate/results/split_groups.log
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contains: ["g0213"]
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contains: ["g0"]
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