SPECIMENS := Escherichia_coli--K-12_MG1655 Escherichia_coli--EDL933 Salmonella_enterica--LT2 Escherichia_coli--CFT073 Bacillus_subtilis--168 Salmonella_enterica--P125109 Shouchella_clausii--KSM-K16 Escherichia_coli--K-12_W3110 Klebsiella_pneumoniae--MGH_78578 Opitutus_terrae--PB90-1 Saccharolobus_islandicus--M.16.4 Acidobacterium_capsulatum--ATCC_51196 Salmonella_enterica--AKU_12601 Proteus_mirabilis--HI4320 Salmonella_enterica--CT18 Klebsiella_pneumoniae--HS11286 Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1 Klebsiella_pneumoniae--ATCC_13883 Yersinia_ruckeri--YRB Candidozyma_auris--GCF_003013715.1_ASM301371v2
SPECIES   := Escherichia_coli Salmonella_enterica Bacillus_subtilis Shouchella_clausii Klebsiella_pneumoniae Opitutus_terrae Saccharolobus_islandicus Acidobacterium_capsulatum Proteus_mirabilis Wolbachia_endosymbiont Yersinia_ruckeri Candidozyma_auris

# Escherichia_coli--K-12_MG1655
run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: run/genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
run/reference_index/Escherichia_coli--K-12_MG1655.npz: run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
run/specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done run/stats/indexing_presence/Escherichia_coli--K-12_MG1655.stats: run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
run/specimen_index_count/Escherichia_coli--K-12_MG1655/index.done run/stats/indexing_count/Escherichia_coli--K-12_MG1655.stats: run/simulated_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz
run/stats/verify_presence/Escherichia_coli--K-12_MG1655.stats: run/reference_index/Escherichia_coli--K-12_MG1655.npz run/specimen_index_presence/Escherichia_coli--K-12_MG1655/index.done
run/stats/verify_count/Escherichia_coli--K-12_MG1655.stats: run/reference_index/Escherichia_coli--K-12_MG1655.npz run/specimen_index_count/Escherichia_coli--K-12_MG1655/index.done

# Escherichia_coli--EDL933
run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz: run/genomes/GCF_000006665.1_ASM666v1_genomic.fna.gz
run/reference_index/Escherichia_coli--EDL933.npz: run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
run/specimen_index_presence/Escherichia_coli--EDL933/index.done run/stats/indexing_presence/Escherichia_coli--EDL933.stats: run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
run/specimen_index_count/Escherichia_coli--EDL933/index.done run/stats/indexing_count/Escherichia_coli--EDL933.stats: run/simulated_data/Escherichia_coli/EDL933/reads_R1.fastq.gz
run/stats/verify_presence/Escherichia_coli--EDL933.stats: run/reference_index/Escherichia_coli--EDL933.npz run/specimen_index_presence/Escherichia_coli--EDL933/index.done
run/stats/verify_count/Escherichia_coli--EDL933.stats: run/reference_index/Escherichia_coli--EDL933.npz run/specimen_index_count/Escherichia_coli--EDL933/index.done

# Salmonella_enterica--LT2
run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz: run/genomes/GCF_000006945.2_ASM694v2_genomic.fna.gz
run/reference_index/Salmonella_enterica--LT2.npz: run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
run/specimen_index_presence/Salmonella_enterica--LT2/index.done run/stats/indexing_presence/Salmonella_enterica--LT2.stats: run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
run/specimen_index_count/Salmonella_enterica--LT2/index.done run/stats/indexing_count/Salmonella_enterica--LT2.stats: run/simulated_data/Salmonella_enterica/LT2/reads_R1.fastq.gz
run/stats/verify_presence/Salmonella_enterica--LT2.stats: run/reference_index/Salmonella_enterica--LT2.npz run/specimen_index_presence/Salmonella_enterica--LT2/index.done
run/stats/verify_count/Salmonella_enterica--LT2.stats: run/reference_index/Salmonella_enterica--LT2.npz run/specimen_index_count/Salmonella_enterica--LT2/index.done

# Escherichia_coli--CFT073
run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz: run/genomes/GCF_000007445.1_ASM744v1_genomic.fna.gz
run/reference_index/Escherichia_coli--CFT073.npz: run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
run/specimen_index_presence/Escherichia_coli--CFT073/index.done run/stats/indexing_presence/Escherichia_coli--CFT073.stats: run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
run/specimen_index_count/Escherichia_coli--CFT073/index.done run/stats/indexing_count/Escherichia_coli--CFT073.stats: run/simulated_data/Escherichia_coli/CFT073/reads_R1.fastq.gz
run/stats/verify_presence/Escherichia_coli--CFT073.stats: run/reference_index/Escherichia_coli--CFT073.npz run/specimen_index_presence/Escherichia_coli--CFT073/index.done
run/stats/verify_count/Escherichia_coli--CFT073.stats: run/reference_index/Escherichia_coli--CFT073.npz run/specimen_index_count/Escherichia_coli--CFT073/index.done

# Bacillus_subtilis--168
run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz: run/genomes/GCF_000009045.1_ASM904v1_genomic.fna.gz
run/reference_index/Bacillus_subtilis--168.npz: run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
run/specimen_index_presence/Bacillus_subtilis--168/index.done run/stats/indexing_presence/Bacillus_subtilis--168.stats: run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
run/specimen_index_count/Bacillus_subtilis--168/index.done run/stats/indexing_count/Bacillus_subtilis--168.stats: run/simulated_data/Bacillus_subtilis/168/reads_R1.fastq.gz
run/stats/verify_presence/Bacillus_subtilis--168.stats: run/reference_index/Bacillus_subtilis--168.npz run/specimen_index_presence/Bacillus_subtilis--168/index.done
run/stats/verify_count/Bacillus_subtilis--168.stats: run/reference_index/Bacillus_subtilis--168.npz run/specimen_index_count/Bacillus_subtilis--168/index.done

# Salmonella_enterica--P125109
run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz: run/genomes/GCF_000009505.1_ASM950v1_genomic.fna.gz
run/reference_index/Salmonella_enterica--P125109.npz: run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
run/specimen_index_presence/Salmonella_enterica--P125109/index.done run/stats/indexing_presence/Salmonella_enterica--P125109.stats: run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
run/specimen_index_count/Salmonella_enterica--P125109/index.done run/stats/indexing_count/Salmonella_enterica--P125109.stats: run/simulated_data/Salmonella_enterica/P125109/reads_R1.fastq.gz
run/stats/verify_presence/Salmonella_enterica--P125109.stats: run/reference_index/Salmonella_enterica--P125109.npz run/specimen_index_presence/Salmonella_enterica--P125109/index.done
run/stats/verify_count/Salmonella_enterica--P125109.stats: run/reference_index/Salmonella_enterica--P125109.npz run/specimen_index_count/Salmonella_enterica--P125109/index.done

# Shouchella_clausii--KSM-K16
run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz: run/genomes/GCF_000009825.1_ASM982v1_genomic.fna.gz
run/reference_index/Shouchella_clausii--KSM-K16.npz: run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
run/specimen_index_presence/Shouchella_clausii--KSM-K16/index.done run/stats/indexing_presence/Shouchella_clausii--KSM-K16.stats: run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
run/specimen_index_count/Shouchella_clausii--KSM-K16/index.done run/stats/indexing_count/Shouchella_clausii--KSM-K16.stats: run/simulated_data/Shouchella_clausii/KSM-K16/reads_R1.fastq.gz
run/stats/verify_presence/Shouchella_clausii--KSM-K16.stats: run/reference_index/Shouchella_clausii--KSM-K16.npz run/specimen_index_presence/Shouchella_clausii--KSM-K16/index.done
run/stats/verify_count/Shouchella_clausii--KSM-K16.stats: run/reference_index/Shouchella_clausii--KSM-K16.npz run/specimen_index_count/Shouchella_clausii--KSM-K16/index.done

# Escherichia_coli--K-12_W3110
run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz: run/genomes/GCF_000010245.2_ASM1024v1_genomic.fna.gz
run/reference_index/Escherichia_coli--K-12_W3110.npz: run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
run/specimen_index_presence/Escherichia_coli--K-12_W3110/index.done run/stats/indexing_presence/Escherichia_coli--K-12_W3110.stats: run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
run/specimen_index_count/Escherichia_coli--K-12_W3110/index.done run/stats/indexing_count/Escherichia_coli--K-12_W3110.stats: run/simulated_data/Escherichia_coli/K-12_W3110/reads_R1.fastq.gz
run/stats/verify_presence/Escherichia_coli--K-12_W3110.stats: run/reference_index/Escherichia_coli--K-12_W3110.npz run/specimen_index_presence/Escherichia_coli--K-12_W3110/index.done
run/stats/verify_count/Escherichia_coli--K-12_W3110.stats: run/reference_index/Escherichia_coli--K-12_W3110.npz run/specimen_index_count/Escherichia_coli--K-12_W3110/index.done

# Klebsiella_pneumoniae--MGH_78578
run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz: run/genomes/GCF_000016305.1_ASM1630v1_genomic.fna.gz
run/reference_index/Klebsiella_pneumoniae--MGH_78578.npz: run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
run/specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done run/stats/indexing_presence/Klebsiella_pneumoniae--MGH_78578.stats: run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
run/specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done run/stats/indexing_count/Klebsiella_pneumoniae--MGH_78578.stats: run/simulated_data/Klebsiella_pneumoniae/MGH_78578/reads_R1.fastq.gz
run/stats/verify_presence/Klebsiella_pneumoniae--MGH_78578.stats: run/reference_index/Klebsiella_pneumoniae--MGH_78578.npz run/specimen_index_presence/Klebsiella_pneumoniae--MGH_78578/index.done
run/stats/verify_count/Klebsiella_pneumoniae--MGH_78578.stats: run/reference_index/Klebsiella_pneumoniae--MGH_78578.npz run/specimen_index_count/Klebsiella_pneumoniae--MGH_78578/index.done

# Opitutus_terrae--PB90-1
run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz: run/genomes/GCF_000019965.1_ASM1996v1_genomic.fna.gz
run/reference_index/Opitutus_terrae--PB90-1.npz: run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
run/specimen_index_presence/Opitutus_terrae--PB90-1/index.done run/stats/indexing_presence/Opitutus_terrae--PB90-1.stats: run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
run/specimen_index_count/Opitutus_terrae--PB90-1/index.done run/stats/indexing_count/Opitutus_terrae--PB90-1.stats: run/simulated_data/Opitutus_terrae/PB90-1/reads_R1.fastq.gz
run/stats/verify_presence/Opitutus_terrae--PB90-1.stats: run/reference_index/Opitutus_terrae--PB90-1.npz run/specimen_index_presence/Opitutus_terrae--PB90-1/index.done
run/stats/verify_count/Opitutus_terrae--PB90-1.stats: run/reference_index/Opitutus_terrae--PB90-1.npz run/specimen_index_count/Opitutus_terrae--PB90-1/index.done

# Saccharolobus_islandicus--M.16.4
run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: run/genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
run/reference_index/Saccharolobus_islandicus--M.16.4.npz: run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
run/specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done run/stats/indexing_presence/Saccharolobus_islandicus--M.16.4.stats: run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
run/specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done run/stats/indexing_count/Saccharolobus_islandicus--M.16.4.stats: run/simulated_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz
run/stats/verify_presence/Saccharolobus_islandicus--M.16.4.stats: run/reference_index/Saccharolobus_islandicus--M.16.4.npz run/specimen_index_presence/Saccharolobus_islandicus--M.16.4/index.done
run/stats/verify_count/Saccharolobus_islandicus--M.16.4.stats: run/reference_index/Saccharolobus_islandicus--M.16.4.npz run/specimen_index_count/Saccharolobus_islandicus--M.16.4/index.done

# Acidobacterium_capsulatum--ATCC_51196
run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz: run/genomes/GCF_000022565.1_ASM2256v1_genomic.fna.gz
run/reference_index/Acidobacterium_capsulatum--ATCC_51196.npz: run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
run/specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done run/stats/indexing_presence/Acidobacterium_capsulatum--ATCC_51196.stats: run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
run/specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done run/stats/indexing_count/Acidobacterium_capsulatum--ATCC_51196.stats: run/simulated_data/Acidobacterium_capsulatum/ATCC_51196/reads_R1.fastq.gz
run/stats/verify_presence/Acidobacterium_capsulatum--ATCC_51196.stats: run/reference_index/Acidobacterium_capsulatum--ATCC_51196.npz run/specimen_index_presence/Acidobacterium_capsulatum--ATCC_51196/index.done
run/stats/verify_count/Acidobacterium_capsulatum--ATCC_51196.stats: run/reference_index/Acidobacterium_capsulatum--ATCC_51196.npz run/specimen_index_count/Acidobacterium_capsulatum--ATCC_51196/index.done

# Salmonella_enterica--AKU_12601
run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz: run/genomes/GCF_000026565.1_ASM2656v1_genomic.fna.gz
run/reference_index/Salmonella_enterica--AKU_12601.npz: run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
run/specimen_index_presence/Salmonella_enterica--AKU_12601/index.done run/stats/indexing_presence/Salmonella_enterica--AKU_12601.stats: run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
run/specimen_index_count/Salmonella_enterica--AKU_12601/index.done run/stats/indexing_count/Salmonella_enterica--AKU_12601.stats: run/simulated_data/Salmonella_enterica/AKU_12601/reads_R1.fastq.gz
run/stats/verify_presence/Salmonella_enterica--AKU_12601.stats: run/reference_index/Salmonella_enterica--AKU_12601.npz run/specimen_index_presence/Salmonella_enterica--AKU_12601/index.done
run/stats/verify_count/Salmonella_enterica--AKU_12601.stats: run/reference_index/Salmonella_enterica--AKU_12601.npz run/specimen_index_count/Salmonella_enterica--AKU_12601/index.done

# Proteus_mirabilis--HI4320
run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz: run/genomes/GCF_000069965.1_ASM6996v1_genomic.fna.gz
run/reference_index/Proteus_mirabilis--HI4320.npz: run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
run/specimen_index_presence/Proteus_mirabilis--HI4320/index.done run/stats/indexing_presence/Proteus_mirabilis--HI4320.stats: run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
run/specimen_index_count/Proteus_mirabilis--HI4320/index.done run/stats/indexing_count/Proteus_mirabilis--HI4320.stats: run/simulated_data/Proteus_mirabilis/HI4320/reads_R1.fastq.gz
run/stats/verify_presence/Proteus_mirabilis--HI4320.stats: run/reference_index/Proteus_mirabilis--HI4320.npz run/specimen_index_presence/Proteus_mirabilis--HI4320/index.done
run/stats/verify_count/Proteus_mirabilis--HI4320.stats: run/reference_index/Proteus_mirabilis--HI4320.npz run/specimen_index_count/Proteus_mirabilis--HI4320/index.done

# Salmonella_enterica--CT18
run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz: run/genomes/GCF_000195995.1_ASM19599v1_genomic.fna.gz
run/reference_index/Salmonella_enterica--CT18.npz: run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
run/specimen_index_presence/Salmonella_enterica--CT18/index.done run/stats/indexing_presence/Salmonella_enterica--CT18.stats: run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
run/specimen_index_count/Salmonella_enterica--CT18/index.done run/stats/indexing_count/Salmonella_enterica--CT18.stats: run/simulated_data/Salmonella_enterica/CT18/reads_R1.fastq.gz
run/stats/verify_presence/Salmonella_enterica--CT18.stats: run/reference_index/Salmonella_enterica--CT18.npz run/specimen_index_presence/Salmonella_enterica--CT18/index.done
run/stats/verify_count/Salmonella_enterica--CT18.stats: run/reference_index/Salmonella_enterica--CT18.npz run/specimen_index_count/Salmonella_enterica--CT18/index.done

# Klebsiella_pneumoniae--HS11286
run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz: run/genomes/GCF_000240185.1_ASM24018v2_genomic.fna.gz
run/reference_index/Klebsiella_pneumoniae--HS11286.npz: run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
run/specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done run/stats/indexing_presence/Klebsiella_pneumoniae--HS11286.stats: run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
run/specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done run/stats/indexing_count/Klebsiella_pneumoniae--HS11286.stats: run/simulated_data/Klebsiella_pneumoniae/HS11286/reads_R1.fastq.gz
run/stats/verify_presence/Klebsiella_pneumoniae--HS11286.stats: run/reference_index/Klebsiella_pneumoniae--HS11286.npz run/specimen_index_presence/Klebsiella_pneumoniae--HS11286/index.done
run/stats/verify_count/Klebsiella_pneumoniae--HS11286.stats: run/reference_index/Klebsiella_pneumoniae--HS11286.npz run/specimen_index_count/Klebsiella_pneumoniae--HS11286/index.done

# Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1
run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz: run/genomes/GCF_000306885.1_ASM30688v1_genomic.fna.gz
run/reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz: run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
run/specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done run/stats/indexing_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
run/specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done run/stats/indexing_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/simulated_data/Wolbachia_endosymbiont/GCF_000306885.1_ASM30688v1/reads_R1.fastq.gz
run/stats/verify_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz run/specimen_index_presence/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done
run/stats/verify_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.stats: run/reference_index/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1.npz run/specimen_index_count/Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1/index.done

# Klebsiella_pneumoniae--ATCC_13883
run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz: run/genomes/GCF_000742135.1_ASM74213v1_genomic.fna.gz
run/reference_index/Klebsiella_pneumoniae--ATCC_13883.npz: run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
run/specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done run/stats/indexing_presence/Klebsiella_pneumoniae--ATCC_13883.stats: run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
run/specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done run/stats/indexing_count/Klebsiella_pneumoniae--ATCC_13883.stats: run/simulated_data/Klebsiella_pneumoniae/ATCC_13883/reads_R1.fastq.gz
run/stats/verify_presence/Klebsiella_pneumoniae--ATCC_13883.stats: run/reference_index/Klebsiella_pneumoniae--ATCC_13883.npz run/specimen_index_presence/Klebsiella_pneumoniae--ATCC_13883/index.done
run/stats/verify_count/Klebsiella_pneumoniae--ATCC_13883.stats: run/reference_index/Klebsiella_pneumoniae--ATCC_13883.npz run/specimen_index_count/Klebsiella_pneumoniae--ATCC_13883/index.done

# Yersinia_ruckeri--YRB
run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz: run/genomes/GCF_000834255.1_ASM83425v1_genomic.fna.gz
run/reference_index/Yersinia_ruckeri--YRB.npz: run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
run/specimen_index_presence/Yersinia_ruckeri--YRB/index.done run/stats/indexing_presence/Yersinia_ruckeri--YRB.stats: run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
run/specimen_index_count/Yersinia_ruckeri--YRB/index.done run/stats/indexing_count/Yersinia_ruckeri--YRB.stats: run/simulated_data/Yersinia_ruckeri/YRB/reads_R1.fastq.gz
run/stats/verify_presence/Yersinia_ruckeri--YRB.stats: run/reference_index/Yersinia_ruckeri--YRB.npz run/specimen_index_presence/Yersinia_ruckeri--YRB/index.done
run/stats/verify_count/Yersinia_ruckeri--YRB.stats: run/reference_index/Yersinia_ruckeri--YRB.npz run/specimen_index_count/Yersinia_ruckeri--YRB/index.done

# Candidozyma_auris--GCF_003013715.1_ASM301371v2
run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz: run/genomes/GCF_003013715.1_ASM301371v2_genomic.fna.gz
run/reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz: run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
run/specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done run/stats/indexing_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
run/specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done run/stats/indexing_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/simulated_data/Candidozyma_auris/GCF_003013715.1_ASM301371v2/reads_R1.fastq.gz
run/stats/verify_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz run/specimen_index_presence/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done
run/stats/verify_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2.stats: run/reference_index/Candidozyma_auris--GCF_003013715.1_ASM301371v2.npz run/specimen_index_count/Candidozyma_auris--GCF_003013715.1_ASM301371v2/index.done

# Escherichia_coli
run/specific_index_presence/Escherichia_coli/index.done run/stats/specific_kmer_presence/Escherichia_coli.stats: run/global_index_presence/index.done
run/specific_index_count/Escherichia_coli/index.done run/stats/specific_kmer_count/Escherichia_coli.stats: run/global_index_count/index.done
# Salmonella_enterica
run/specific_index_presence/Salmonella_enterica/index.done run/stats/specific_kmer_presence/Salmonella_enterica.stats: run/global_index_presence/index.done
run/specific_index_count/Salmonella_enterica/index.done run/stats/specific_kmer_count/Salmonella_enterica.stats: run/global_index_count/index.done
# Bacillus_subtilis
run/specific_index_presence/Bacillus_subtilis/index.done run/stats/specific_kmer_presence/Bacillus_subtilis.stats: run/global_index_presence/index.done
run/specific_index_count/Bacillus_subtilis/index.done run/stats/specific_kmer_count/Bacillus_subtilis.stats: run/global_index_count/index.done
# Shouchella_clausii
run/specific_index_presence/Shouchella_clausii/index.done run/stats/specific_kmer_presence/Shouchella_clausii.stats: run/global_index_presence/index.done
run/specific_index_count/Shouchella_clausii/index.done run/stats/specific_kmer_count/Shouchella_clausii.stats: run/global_index_count/index.done
# Klebsiella_pneumoniae
run/specific_index_presence/Klebsiella_pneumoniae/index.done run/stats/specific_kmer_presence/Klebsiella_pneumoniae.stats: run/global_index_presence/index.done
run/specific_index_count/Klebsiella_pneumoniae/index.done run/stats/specific_kmer_count/Klebsiella_pneumoniae.stats: run/global_index_count/index.done
# Opitutus_terrae
run/specific_index_presence/Opitutus_terrae/index.done run/stats/specific_kmer_presence/Opitutus_terrae.stats: run/global_index_presence/index.done
run/specific_index_count/Opitutus_terrae/index.done run/stats/specific_kmer_count/Opitutus_terrae.stats: run/global_index_count/index.done
# Saccharolobus_islandicus
run/specific_index_presence/Saccharolobus_islandicus/index.done run/stats/specific_kmer_presence/Saccharolobus_islandicus.stats: run/global_index_presence/index.done
run/specific_index_count/Saccharolobus_islandicus/index.done run/stats/specific_kmer_count/Saccharolobus_islandicus.stats: run/global_index_count/index.done
# Acidobacterium_capsulatum
run/specific_index_presence/Acidobacterium_capsulatum/index.done run/stats/specific_kmer_presence/Acidobacterium_capsulatum.stats: run/global_index_presence/index.done
run/specific_index_count/Acidobacterium_capsulatum/index.done run/stats/specific_kmer_count/Acidobacterium_capsulatum.stats: run/global_index_count/index.done
# Proteus_mirabilis
run/specific_index_presence/Proteus_mirabilis/index.done run/stats/specific_kmer_presence/Proteus_mirabilis.stats: run/global_index_presence/index.done
run/specific_index_count/Proteus_mirabilis/index.done run/stats/specific_kmer_count/Proteus_mirabilis.stats: run/global_index_count/index.done
# Wolbachia_endosymbiont
run/specific_index_presence/Wolbachia_endosymbiont/index.done run/stats/specific_kmer_presence/Wolbachia_endosymbiont.stats: run/global_index_presence/index.done
run/specific_index_count/Wolbachia_endosymbiont/index.done run/stats/specific_kmer_count/Wolbachia_endosymbiont.stats: run/global_index_count/index.done
# Yersinia_ruckeri
run/specific_index_presence/Yersinia_ruckeri/index.done run/stats/specific_kmer_presence/Yersinia_ruckeri.stats: run/global_index_presence/index.done
run/specific_index_count/Yersinia_ruckeri/index.done run/stats/specific_kmer_count/Yersinia_ruckeri.stats: run/global_index_count/index.done
# Candidozyma_auris
run/specific_index_presence/Candidozyma_auris/index.done run/stats/specific_kmer_presence/Candidozyma_auris.stats: run/global_index_presence/index.done
run/specific_index_count/Candidozyma_auris/index.done run/stats/specific_kmer_count/Candidozyma_auris.stats: run/global_index_count/index.done

QUERY_SPECIMENS := Escherichia_coli--K-12_MG1655 Saccharolobus_islandicus--M.16.4

# query: Escherichia_coli--K-12_MG1655
run/query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz: run/genomes/GCF_000005845.2_ASM584v2_genomic.fna.gz
run/query_presence_dense/Escherichia_coli--K-12_MG1655.fasta.gz run/stats/query_presence_dense/Escherichia_coli--K-12_MG1655.stats: run/query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz run/global_index_presence_dense/index.done
run/query_presence_sparse/Escherichia_coli--K-12_MG1655.fasta.gz run/stats/query_presence_sparse/Escherichia_coli--K-12_MG1655.stats: run/query_data/Escherichia_coli/K-12_MG1655/reads_R1.fastq.gz run/global_index_presence/index.done
run/stats/verify_query/Escherichia_coli--K-12_MG1655.stats: run/query_presence_dense/Escherichia_coli--K-12_MG1655.fasta.gz run/query_presence_sparse/Escherichia_coli--K-12_MG1655.fasta.gz

# query: Saccharolobus_islandicus--M.16.4
run/query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz: run/genomes/GCF_000022445.1_ASM2244v1_genomic.fna.gz
run/query_presence_dense/Saccharolobus_islandicus--M.16.4.fasta.gz run/stats/query_presence_dense/Saccharolobus_islandicus--M.16.4.stats: run/query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz run/global_index_presence_dense/index.done
run/query_presence_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz run/stats/query_presence_sparse/Saccharolobus_islandicus--M.16.4.stats: run/query_data/Saccharolobus_islandicus/M.16.4/reads_R1.fastq.gz run/global_index_presence/index.done
run/stats/verify_query/Saccharolobus_islandicus--M.16.4.stats: run/query_presence_dense/Saccharolobus_islandicus--M.16.4.fasta.gz run/query_presence_sparse/Saccharolobus_islandicus--M.16.4.fasta.gz