/home/sam/programs/quast-5.0.2/metaquast.py --threads=20 --min-contig=100 --labels=MG1_ets,MG1_sjw,MG2_ets,MG2_sjw,MG3_ets,MG3_sjw,MG5_ets,MG5_sjw,MG6_ets,MG6_sjw,MG7_ets,MG7_sjw /home/sam/data/metagenomics/P_generosa/contigsMG1S3.fa /home/sam/data/metagenomics/P_generosa/MG1.contigs.fa /home/sam/data/metagenomics/P_generosa/contigsMG2S4.fa /home/sam/data/metagenomics/P_generosa/MG2.contigs.fa /home/sam/data/metagenomics/P_generosa/contigsM32S1.fa /home/sam/data/metagenomics/P_generosa/MG3.contigs.fa /home/sam/data/metagenomics/P_generosa/contigsM5S6.fa /home/sam/data/metagenomics/P_generosa/MG5.contigs.fa /home/sam/data/metagenomics/P_generosa/contigsM6S5.fa /home/sam/data/metagenomics/P_generosa/MG6.contigs.fa /home/sam/data/metagenomics/P_generosa/contigsM7S2.fa /home/sam/data/metagenomics/P_generosa/MG7.contigs.fa Version: 5.0.2 System information: OS: Linux-4.4.0-142-generic-x86_64-with-debian-stretch-sid (linux_64) Python version: 3.6.8 CPUs number: 24 Started: 2019-04-03 08:23:17 Logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/metaquast.log Contigs: Pre-processing... 1 /home/sam/data/metagenomics/P_generosa/contigsMG1S3.fa ==> MG1_ets 2 /home/sam/data/metagenomics/P_generosa/MG1.contigs.fa ==> MG1_sjw 3 /home/sam/data/metagenomics/P_generosa/contigsMG2S4.fa ==> MG2_ets 4 /home/sam/data/metagenomics/P_generosa/MG2.contigs.fa ==> MG2_sjw 5 /home/sam/data/metagenomics/P_generosa/contigsM32S1.fa ==> MG3_ets 6 /home/sam/data/metagenomics/P_generosa/MG3.contigs.fa ==> MG3_sjw 7 /home/sam/data/metagenomics/P_generosa/contigsM5S6.fa ==> MG5_ets 8 /home/sam/data/metagenomics/P_generosa/MG5.contigs.fa ==> MG5_sjw 9 /home/sam/data/metagenomics/P_generosa/contigsM6S5.fa ==> MG6_ets 10 /home/sam/data/metagenomics/P_generosa/MG6.contigs.fa ==> MG6_sjw 11 /home/sam/data/metagenomics/P_generosa/contigsM7S2.fa ==> MG7_ets 12 /home/sam/data/metagenomics/P_generosa/MG7.contigs.fa ==> MG7_sjw No references are provided, starting to search for reference genomes in SILVA 16S rRNA database and to download them from NCBI... 2019-04-03 08:24:16 Running BlastN.. processing MG1_ets processing MG1_sjw processing MG2_ets processing MG2_sjw processing MG3_ets /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/contigsMG1S3.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG1_ets \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/MG1.contigs.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG1_sjw \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err processing MG3_sjw /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/contigsMG2S4.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG2_ets \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err processing MG5_ets /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/MG2.contigs.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG2_sjw \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/contigsM32S1.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG3_ets \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/MG3.contigs.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG3_sjw \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/contigsM5S6.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG5_ets \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err processing MG5_sjw processing MG6_ets processing MG6_sjw processing MG7_ets processing MG7_sjw /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/MG5.contigs.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG5_sjw \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/contigsM6S5.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG6_ets \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/MG6.contigs.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG6_sjw \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/contigsM7S2.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG7_ets \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err /home/sam/programs/minicocnda3/bin/blastn -query /home/sam/data/metagenomics/P_generosa/MG7.contigs.fa \ -db /home/sam/programs/quast-5.0.2/quast_libs/silva/silva.123.db -outfmt 7 -num_threads \ 1 > quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG7_sjw \ 2>> quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.err BLAST results for MG5_ets are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG5_ets... BLAST results for MG6_ets are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG6_ets... BLAST results for MG7_ets are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG7_ets... BLAST results for MG2_ets are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG2_ets... BLAST results for MG1_ets are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG1_ets... BLAST results for MG3_ets are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG3_ets... BLAST results for MG5_sjw are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG5_sjw... BLAST results for MG6_sjw are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG6_sjw... BLAST results for MG3_sjw are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG3_sjw... BLAST results for MG7_sjw are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG7_sjw... BLAST results for MG2_sjw are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG2_sjw... BLAST results for MG1_sjw are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/blast.res_MG1_sjw... 2019-04-03 09:10:55 Trying to download found references from NCBI. Totally 294 organisms to try. unknown_marine_alpha_proteobacterium_JP66.1 | not found in the NCBI database unknown_marine_alpha_proteobacterium_JP66.1 was not found in NCBI database, trying to download the next best match alpha_proteobacterium_BH-4 | not found in the NCBI database alpha_proteobacterium_BH-4 was not found in NCBI database, trying to download the next best match Hoeflea_phototrophica_DFL-43 | successfully downloaded (total 1, 293 more to go) unidentified_proteobacterium | not found in the NCBI database unidentified_proteobacterium was not found in NCBI database, trying to download the next best match Gracilibacteria_bacterium_JGI_0000069-P22 | successfully downloaded (total 2, 292 more to go) unidentified_planctomycete | not found in the NCBI database unidentified_marine_eubacterium | not found in the NCBI database unidentified_marine_eubacterium was not found in NCBI database, trying to download the next best match bacterium_KD52 | successfully downloaded (total 3, 290 more to go) unidentified_marine_bacterioplankton | not found in the NCBI database unidentified_eubacterium_SCB49 | successfully downloaded (total 4, 288 more to go) unidentified_bacterium_wb1_D18 | not found in the NCBI database unidentified_bacterium_wb1_D18 was not found in NCBI database, trying to download the next best match Gimesia_maris | successfully downloaded (total 5, 287 more to go) unclassified_Pseudomonadales_(miscellaneous) | not found in the NCBI database unclassified_Pseudomonadales_(miscellaneous) was not found in NCBI database, trying to download the next best match Saccharophagus_degradans_2-40 | successfully downloaded (total 6, 286 more to go) sulfur-oxidizing_bacterium_NDII1.2 | not found in the NCBI database sulfur-oxidizing_bacterium_NDII1.2 was not found in NCBI database, trying to download the next best match bacterium_enrichment_culture_clone_41(2013) | not found in the NCBI database bacterium_enrichment_culture_clone_41(2013) was not found in NCBI database, trying to download the next best match Thiohalobacter_thiocyanaticus | successfully downloaded (total 7, 285 more to go) psychrophilic_sulfate-reducing_bacterium_LSv55 | not found in the NCBI database psychrophilic_marine_bacterium_PS32 | not found in the NCBI database mine_drainage_metagenome | successfully downloaded (total 8, 282 more to go) microbial mat metagenome has too fragmented reference genome! It will not be downloaded. microbial_mat_metagenome | not found in the NCBI database microbial_mat_metagenome was not found in NCBI database, trying to download the next best match Flammeovirgaceae_bacterium_EF2C-B566 | not found in the NCBI database marine metagenome has too fragmented reference genome! It will not be downloaded. marine_metagenome | not found in the NCBI database marine_metagenome was not found in NCBI database, trying to download the next best match bacterium_symbiont_of_Pliocardia_sp._SKG-2011 | not found in the NCBI database marine_gamma_proteobacterium_HTCC2188 | not found in the NCBI database marine_gamma_proteobacterium_HTCC2080 | successfully downloaded (total 9, 278 more to go) marine_bacterium_NAMAF003 | not found in the NCBI database marine_bacterium_NAMAF003 was not found in NCBI database, trying to download the next best match Cryomorphaceae_bacterium_JNU-L074 | not found in the NCBI database marine_bacterium_K9-13 | not found in the NCBI database marine_bacterium_K9-13 was not found in NCBI database, trying to download the next best match Kordia_algicida_OT-1 | successfully downloaded (total 10, 276 more to go) magnetic_proteobacterium_strain_rj12 | not found in the NCBI database magnetic_proteobacterium_strain_rj12 was not found in NCBI database, trying to download the next best match Magnetofaba_australis_IT-1 | successfully downloaded (total 11, 275 more to go) magnetic_coccus_MP17 | not found in the NCBI database magnetic_coccus_MP17 was not found in NCBI database, trying to download the next best match Nitrosococcus_halophilus_Nc_4 | successfully downloaded (total 12, 274 more to go) gamma_proteobacterium_SCGC_AB-629-P17 | successfully downloaded (total 13, 273 more to go) freshwater_sediment_metagenome | not found in the NCBI database freshwater_sediment_metagenome was not found in NCBI database, trying to download the next best match Ferritrophicum_radicicola | not found in the NCBI database Ferritrophicum_radicicola was not found in NCBI database, trying to download the next best match Gallionella_sp._enrichment_culture_clone_MWE_N34 | not found in the NCBI database Gallionella_sp._enrichment_culture_clone_MWE_N34 was not found in NCBI database, trying to download the next best match denitrifying_bacterium_72Chol | not found in the NCBI database filamentous_cyanobacterium_LLi71 | not found in the NCBI database filamentous_cyanobacterium_LLi71 was not found in NCBI database, trying to download the next best match Leptolyngbya_sp._LEGE_07075 | not found in the NCBI database Leptolyngbya_sp._LEGE_07075 was not found in NCBI database, trying to download the next best match filamentous_cyanobacterium_FLK9 | not found in the NCBI database filamentous_cyanobacterium_FLK9 was not found in NCBI database, trying to download the next best match Leptolyngbya_sp._ANT.L52.1 | not found in the NCBI database endosymbiont_of_Ridgeia_piscesae | successfully downloaded (total 14, 270 more to go) endosymbiont_of_Oligobrachia_haakonmosbiensis | not found in the NCBI database endosymbiont_of_Oligobrachia_haakonmosbiensis was not found in NCBI database, trying to download the next best match Alteromonas_sp._KU27F1 | not found in the NCBI database Alteromonas_sp._KU27F1 was not found in NCBI database, trying to download the next best match bacterium_K2-7 | not found in the NCBI database delta_proteobacterium_JS_SRB50Lac | not found in the NCBI database delta_proteobacterium_JS_SRB50Lac was not found in NCBI database, trying to download the next best match Acidobacteria_bacterium_DG1540 | not found in the NCBI database Acidobacteria_bacterium_DG1540 was not found in NCBI database, trying to download the next best match Desulfobacula_sp._TS | successfully downloaded (total 15, 268 more to go) carbazole-degrading_bacterium_OC9 | not found in the NCBI database carbazole-degrading_bacterium_OC9 was not found in NCBI database, trying to download the next best match carbazole-degrading_bacterium_OC13S | not found in the NCBI database carbazole-degrading_bacterium_OC6S | not found in the NCBI database carbazole-degrading_bacterium_OC6S was not found in NCBI database, trying to download the next best match carbazole-degrading_bacterium_OC13S | not found in the NCBI database carbazole-degrading_bacterium_OC13S was not found in NCBI database, trying to download the next best match alpha_proteobacterium_enrichment_culture_clone_DH-1602 | not found in the NCBI database bioreactor metagenome has too fragmented reference genome! It will not be downloaded. bioreactor_metagenome | not found in the NCBI database bioreactor_metagenome was not found in NCBI database, trying to download the next best match Gracilibacteria_bacterium_JGI_0000069-P22 | was downloaded previously (total 16, 265 more to go) bacterium_symbiont_of_Idas_sp | not found in the NCBI database bacterium_symbiont_of_Idas_sp was not found in NCBI database, trying to download the next best match gamma_proteobacterium_enrichment_culture_clone_TT-294 | not found in the NCBI database gamma_proteobacterium_enrichment_culture_clone_TT-294 was not found in NCBI database, trying to download the next best match gamma_proteobacterium_enrichment_culture_clone_TT-1456 | not found in the NCBI database bacterium_symbiont_of_Christineconcha_regab | not found in the NCBI database bacterium_symbiont_of_Christineconcha_regab was not found in NCBI database, trying to download the next best match Vesicomya_stearnsii_symbiont | not found in the NCBI database bacterium_enrichment_culture_clone_heteroA15_4W | not found in the NCBI database bacterium_enrichment_culture_clone_heteroA15_4W was not found in NCBI database, trying to download the next best match Methylocystis_sp._m1511 | not found in the NCBI database Methylocystis_sp._m1511 was not found in NCBI database, trying to download the next best match Agrobacterium_sp._enrichment_culture_clone_ECC2-23 | not found in the NCBI database Agrobacterium_sp._enrichment_culture_clone_ECC2-23 was not found in NCBI database, trying to download the next best match Nisaea_sp._MOLA_138 | not found in the NCBI database bacterium_enrichment_culture_clone_SRAO_14 | not found in the NCBI database bacterium_enrichment_culture_clone_SRAO_14 was not found in NCBI database, trying to download the next best match Nitrosomonas_sp._Nm86 | successfully downloaded (total 17, 261 more to go) bacterium_enrichment_culture_clone_NCAAH_30A7 | not found in the NCBI database bacterium_enrichment_culture_clone_NCAAH_30A7 was not found in NCBI database, trying to download the next best match Formosa_sp._AK20 | successfully downloaded (total 18, 260 more to go) bacterium_enrichment_culture_clone_B30(2011) | not found in the NCBI database bacterium_enrichment_culture_clone_B30(2011) was not found in NCBI database, trying to download the next best match Syntrophaceae_bacterium_enrichment_culture_clone_BM_12 | not found in the NCBI database Syntrophaceae_bacterium_enrichment_culture_clone_BM_12 was not found in NCBI database, trying to download the next best match Arctic_bacterium_NP27 | not found in the NCBI database Arctic_bacterium_NP27 was not found in NCBI database, trying to download the next best match Devosia_sp._Asd_M4A1 | not found in the NCBI database bacterium_enrichment_culture_clone_69(2013) | not found in the NCBI database bacterium_enrichment_culture_clone_69(2013) was not found in NCBI database, trying to download the next best match Magnetovibrio_blakemorei | successfully downloaded (total 19, 258 more to go) bacterium_endosymbiont_of_Osedax_mucofloris | not found in the NCBI database bacterium_endosymbiont_of_Osedax_mucofloris was not found in NCBI database, trying to download the next best match alpha_proteobacterium_enrichment_culture_clone_DH-1602 | not found in the NCBI database alpha_proteobacterium_enrichment_culture_clone_DH-1602 was not found in NCBI database, trying to download the next best match carbazole-degrading_bacterium_OC13S | not found in the NCBI database bacterium_endosymbiont_of_Abyssogena_southwardae | not found in the NCBI database bacterium_endosymbiont_of_Abyssogena_southwardae was not found in NCBI database, trying to download the next best match Calyptogena_fausta_symbiont | not found in the NCBI database bacterium_WHC4-5 | not found in the NCBI database bacterium_WHC4-5 was not found in NCBI database, trying to download the next best match gamma_proteobacterium_IMCC2136 | not found in the NCBI database gamma_proteobacterium_IMCC2136 was not found in NCBI database, trying to download the next best match Gilvimarinus_chinensis_DSM_19667 | successfully downloaded (total 20, 255 more to go) bacterium_SH4-10 | not found in the NCBI database bacterium_SH4-10 was not found in NCBI database, trying to download the next best match Parcubacteria_bacterium_SCGC_AAA011-A08 | successfully downloaded (total 21, 254 more to go) bacterium_SH1-3 | not found in the NCBI database bacterium_SH1-3 was not found in NCBI database, trying to download the next best match Fluviicola_taffensis_DSM_16823 | successfully downloaded (total 22, 253 more to go) bacterium_RFB_D08 | not found in the NCBI database bacterium_RFB_D08 was not found in NCBI database, trying to download the next best match Gracilibacteria_bacterium_canine_oral_taxon_323 | not found in the NCBI database bacterium_RCC_1908 | not found in the NCBI database bacterium_RCC_1908 was not found in NCBI database, trying to download the next best match bacterium_RCC_1925 | not found in the NCBI database bacterium_RCC_1925 was not found in NCBI database, trying to download the next best match bacterium_DG949 | not found in the NCBI database bacterium_DG949 was not found in NCBI database, trying to download the next best match Ahrensia_kielensis_DSM_5890 | successfully downloaded (total 23, 251 more to go) bacterium_RC21 | not found in the NCBI database bacterium_RC21 was not found in NCBI database, trying to download the next best match Rhodovibrio_salinarum | successfully downloaded (total 24, 250 more to go) bacterium_EMS | not found in the NCBI database bacterium_EMS was not found in NCBI database, trying to download the next best match Methylobacillus_glycogenes | successfully downloaded (total 25, 249 more to go) bacterium_DY22613 | successfully downloaded (total 26, 248 more to go) bacterium_DG890 | not found in the NCBI database bacterium_DG890 was not found in NCBI database, trying to download the next best match iron-reducing_bacterium_enrichment_culture_clone_HN105 | not found in the NCBI database iron-reducing_bacterium_enrichment_culture_clone_HN105 was not found in NCBI database, trying to download the next best match wastewater metagenome has too fragmented reference genome! It will not be downloaded. wastewater_metagenome | not found in the NCBI database wastewater_metagenome was not found in NCBI database, trying to download the next best match bacterium_enrichment_culture_clone_AOM-SR-B3 | not found in the NCBI database bacterium_DG873 | not found in the NCBI database bacterium_DG873 was not found in NCBI database, trying to download the next best match Flammeovirgaceae_bacterium_EF2C-B566 | not found in the NCBI database bacterium_DG1026 | not found in the NCBI database bacterium_DG1026 was not found in NCBI database, trying to download the next best match Dichotomicrobium_thermohalophilum | successfully downloaded (total 27, 245 more to go) bacterium_DG1021 | not found in the NCBI database bacterium_DG1021 was not found in NCBI database, trying to download the next best match Lishizhenia_tianjinensis | successfully downloaded (total 28, 244 more to go) bacterium_D78 | not found in the NCBI database bacterium_D78 was not found in NCBI database, trying to download the next best match Oceanibaculum_pacificum | successfully downloaded (total 29, 243 more to go) archaeon_enrichment_culture_clone_AOM-Clone-D10 | not found in the NCBI database archaeon_enrichment_culture_clone_AOM-Clone-D10 was not found in NCBI database, trying to download the next best match archaeon_enrichment_culture_clone_AOM-SR-A22 | not found in the NCBI database archaeon_enrichment_culture_clone_AOM-SR-A22 was not found in NCBI database, trying to download the next best match Methanosaeta_sp | successfully downloaded (total 30, 242 more to go) alpha_proteobacterium_dMB-MAT35 | not found in the NCBI database alpha_proteobacterium_dMB-MAT35 was not found in NCBI database, trying to download the next best match carbazole-degrading_bacterium_OC13S | not found in the NCBI database alpha_proteobacterium_SCGC_AAA076-C03 | successfully downloaded (total 31, 240 more to go) actinobacterium_R-36733 | not found in the NCBI database actinobacterium_R-36733 was not found in NCBI database, trying to download the next best match actinobacterium_CH20i | not found in the NCBI database actinobacterium_CH20i was not found in NCBI database, trying to download the next best match Leifsonia_antarctica | not found in the NCBI database Leifsonia_antarctica was not found in NCBI database, trying to download the next best match Microbacterium_dextranolyticum | not found in the NCBI database actinobacterium_BGR_127 | not found in the NCBI database Zooshikella_sp._JE-34 | not found in the NCBI database Zooshikella_sp._JE-34 was not found in NCBI database, trying to download the next best match Zooshikella_ganghwensis_DSM_15267 | successfully downloaded (total 32, 237 more to go) Zoogloea_ramigera | not found in the NCBI database Zoogloea_ramigera was not found in NCBI database, trying to download the next best match Oxalobacter_sp._HI-D2 | not found in the NCBI database Oxalobacter_sp._HI-D2 was not found in NCBI database, trying to download the next best match beta_proteobacterium_Gu1-7 | not found in the NCBI database Zhouia_amylolytica_AD3 | successfully downloaded (total 33, 235 more to go) Zea_mays | successfully downloaded (total 34, 234 more to go) Xenococcus_sp._PCC_7305 | successfully downloaded (total 35, 233 more to go) Xanthomonas_axonopodis_pv._aurantifolii | not found in the NCBI database Xanthomonas_axonopodis_pv._aurantifolii was not found in NCBI database, trying to download the next best match Xanthomonas_translucens_pv._graminis | successfully downloaded (total 36, 232 more to go) Xanthobacter_autotrophicus_Py2 | successfully downloaded (total 37, 231 more to go) Xanthobacillum_maris | not found in the NCBI database Xanthobacillum_maris was not found in NCBI database, trying to download the next best match Dokdonia_donghaensis_DSW-1 | successfully downloaded (total 38, 230 more to go) Winogradskyella_sp._K7-7 | not found in the NCBI database Winogradskyella_sp._K7-7 was not found in NCBI database, trying to download the next best match Bizionia_echini | successfully downloaded (total 39, 229 more to go) Wandonia_haliotis | not found in the NCBI database Wandonia_haliotis was not found in NCBI database, trying to download the next best match Lishizhenia_caseinilytica | not found in the NCBI database Lishizhenia_caseinilytica was not found in NCBI database, trying to download the next best match Crocinitomix_catalasitica | successfully downloaded (total 40, 228 more to go) Waddlia_sp._G817 | not found in the NCBI database Waddlia_sp._G817 was not found in NCBI database, trying to download the next best match Parachlamydia_acanthamoebae_UV-7 | successfully downloaded (total 41, 227 more to go) Vitreoscilla_stercoraria_DSM_513 | successfully downloaded (total 42, 226 more to go) Vitellibacter_sp._HC6-5 | not found in the NCBI database Vitellibacter_sp._HC6-5 was not found in NCBI database, trying to download the next best match Muricauda_sp._H15 | not found in the NCBI database Muricauda_sp._H15 was not found in NCBI database, trying to download the next best match Muricauda_sp._DH111 | not found in the NCBI database Muricauda_sp._DH111 was not found in NCBI database, trying to download the next best match Muricauda_ruestringensis_DSM_13258 | successfully downloaded (total 43, 225 more to go) Vibrio_lentus | successfully downloaded (total 44, 224 more to go) Vesicomya_sp._mt-II_symbiont | not found in the NCBI database Vesicomya_sp._mt-II_symbiont was not found in NCBI database, trying to download the next best match Calyptogena_sp._Florida_gill_symbiont | not found in the NCBI database Calyptogena_sp._Florida_gill_symbiont was not found in NCBI database, trying to download the next best match bacterium_symbiont_of_Laubiericoncha_chuni | not found in the NCBI database Verrucomicrobia bacterium SCGC AAA164-O14 has too fragmented reference genome! It will not be downloaded. Verrucomicrobia_bacterium_SCGC_AAA164-O14 | not found in the NCBI database Verrucomicrobia_bacterium_SCGC_AAA164-O14 was not found in NCBI database, trying to download the next best match Persicirhabdus_sediminis | not found in the NCBI database Persicirhabdus_sediminis was not found in NCBI database, trying to download the next best match Roseibacillus_ishigakijimensis | not found in the NCBI database Roseibacillus_ishigakijimensis was not found in NCBI database, trying to download the next best match Akkermansia_muciniphila | successfully downloaded (total 45, 222 more to go) Uncultured_Pseudospirillum_sp | not found in the NCBI database Umboniibacter_marinipuniceus | successfully downloaded (total 46, 220 more to go) Tolypothrix_campylonemoides_VB511288 | successfully downloaded (total 47, 219 more to go) Tistrella_mobilis | successfully downloaded (total 48, 218 more to go) Tistrella_bauzanensis | not found in the NCBI database Tistrella_bauzanensis was not found in NCBI database, trying to download the next best match Tistrella_mobilis_KA081020-065 | successfully downloaded (total 49, 217 more to go) Thiorhodococcus_sp._AK35 | successfully downloaded (total 50, 216 more to go) Thiorhodococcus_drewsii_AZ1 | successfully downloaded (total 51, 215 more to go) Thiogranum_longum | successfully downloaded (total 52, 214 more to go) Thiocystis_violacea | not found in the NCBI database Thiocystis_violacea was not found in NCBI database, trying to download the next best match Thiococcus_pfennigii | not found in the NCBI database Thiococcus_pfennigii was not found in NCBI database, trying to download the next best match Thioflavicoccus_mobilis | successfully downloaded (total 53, 213 more to go) Thiobacillus_sp._ISA11 | not found in the NCBI database Thiobacillus_sp._ISA11 was not found in NCBI database, trying to download the next best match Thiobacillus_sp | not found in the NCBI database Thiobacillus_sp was not found in NCBI database, trying to download the next best match Globicatella_sp._canine_oral_taxon_218 | not found in the NCBI database Globicatella_sp._canine_oral_taxon_218 was not found in NCBI database, trying to download the next best match Olavius_algarvensis_associated_proteobacterium_Delta_3 | not found in the NCBI database Thioalkalivibrio_sulfidiphilus_HL-EbGr7 | successfully downloaded (total 54, 211 more to go) Thermoplasmatales_archaeon_E-plasma | successfully downloaded (total 55, 210 more to go) Thermoplasma_acidophilum | successfully downloaded (total 56, 209 more to go) Thalassospira_xiamenensis_M-5_=_DSM_17429 | successfully downloaded (total 57, 208 more to go) Thalassospira_profundimaris | successfully downloaded (total 58, 207 more to go) Thalassolituus_sp._U1368-101106-SW100 | not found in the NCBI database Thalassolituus_sp._U1368-101106-SW100 was not found in NCBI database, trying to download the next best match Gilvimarinus_sp._YN3 | successfully downloaded (total 59, 206 more to go) Thalassobaculum_salexigens_DSM_19539 | successfully downloaded (total 60, 205 more to go) Tetraselmis_sp._GSL018 | not found in the NCBI database Tenacibaculum_sp._KYW_576 | not found in the NCBI database Tenacibaculum_sp._KYW_576 was not found in NCBI database, trying to download the next best match Cytophaga_sp._IAJ12 | not found in the NCBI database Cytophaga_sp._IAJ12 was not found in NCBI database, trying to download the next best match Tenacibaculum_sp._MOLA_395 | not found in the NCBI database Tenacibaculum_sp._C28 | not found in the NCBI database Tenacibaculum_sp._C28 was not found in NCBI database, trying to download the next best match Cytophaga_sp._IAJ12 | not found in the NCBI database Cytophaga_sp._IAJ12 was not found in NCBI database, trying to download the next best match Tenacibaculum_sp._MOLA_395 | not found in the NCBI database Tenacibaculum_sp._MOLA_395 was not found in NCBI database, trying to download the next best match Tenacibaculum_skagerrakense | successfully downloaded (total 61, 202 more to go) Tenacibaculum_maritimum_NBRC_15946 | not found in the NCBI database Tenacibaculum_maritimum_NBRC_15946 was not found in NCBI database, trying to download the next best match Tenacibaculum_maritimum | successfully downloaded (total 62, 201 more to go) Tenacibaculum_gallaicum | successfully downloaded (total 63, 200 more to go) Symploca_sp._VP642b | not found in the NCBI database Symploca_sp._VP642b was not found in NCBI database, trying to download the next best match Aphanothece_sacrum | successfully downloaded (total 64, 199 more to go) Symploca_sp._VP642a | not found in the NCBI database Symploca_sp._VP642a was not found in NCBI database, trying to download the next best match Aphanothece_sacrum | was downloaded previously (total 65, 198 more to go) Sulfitobacter_sp._NAS-14.1 | successfully downloaded (total 66, 197 more to go) Sulfitobacter_sp._EE-36 | successfully downloaded (total 67, 196 more to go) Subsaxibacter_broadyi | not found in the NCBI database Subsaxibacter_broadyi was not found in NCBI database, trying to download the next best match Bizionia_hallyeonensis | not found in the NCBI database Bizionia_hallyeonensis was not found in NCBI database, trying to download the next best match Bizionia_sp._KJF12-2 | not found in the NCBI database Streptomyces_sp._2H51-1 | not found in the NCBI database Streptomyces_sp._2H51-1 was not found in NCBI database, trying to download the next best match Streptomyces_indicus | successfully downloaded (total 68, 194 more to go) Streptomyces niveiscabiei has too fragmented reference genome! It will not be downloaded. Streptomyces_niveiscabiei | not found in the NCBI database Streptomyces_niveiscabiei was not found in NCBI database, trying to download the next best match Streptomyces_indicus | was downloaded previously (total 69, 193 more to go) Streptomyces_mobaraensis_NBRC_13819_=_DSM_40847 | successfully downloaded (total 70, 192 more to go) Streptomyces_longispororuber | not found in the NCBI database Streptomyces_longispororuber was not found in NCBI database, trying to download the next best match Streptomyces_albulus | successfully downloaded (total 71, 191 more to go) Streptococcus_sanguinis_SK115 | successfully downloaded (total 72, 190 more to go) Streptococcus_agalactiae_SS1219 | successfully downloaded (total 73, 189 more to go) Stigonema_ocellatum_SAMA_35 | not found in the NCBI database Stigonema_ocellatum_SAMA_35 was not found in NCBI database, trying to download the next best match Stigonema_ocellatum_SAG_48.90 | not found in the NCBI database Stigonema_ocellatum_SAG_48.90 was not found in NCBI database, trying to download the next best match Cyanothece_sp._PCC_7425 | successfully downloaded (total 74, 188 more to go) Stenotrophomonas_sp._RIT309 | successfully downloaded (total 75, 187 more to go) Stenotrophomonas_maltophilia_JV3 | successfully downloaded (total 76, 186 more to go) Stanieria_cyanosphaera_PCC_7437 | successfully downloaded (total 77, 185 more to go) Sporosarcina_sp._Con12 | not found in the NCBI database Sporosarcina_sp._Con12 was not found in NCBI database, trying to download the next best match Olavius_algarvensis_Delta_4_endosymbiont | successfully downloaded (total 78, 184 more to go) Spongiispira_norvegica | not found in the NCBI database Spongiispira_norvegica was not found in NCBI database, trying to download the next best match gamma_proteobacterium_Yb007 | not found in the NCBI database gamma_proteobacterium_Yb007 was not found in NCBI database, trying to download the next best match Oceaniserpentilla_haliotis | not found in the NCBI database Oceaniserpentilla_haliotis was not found in NCBI database, trying to download the next best match Bermanella_marisrubri | successfully downloaded (total 79, 183 more to go) Spongiibacter_tropicus | successfully downloaded (total 80, 182 more to go) Spongiibacter_sp._JYr4 | not found in the NCBI database Spongiibacter_sp._JYr4 was not found in NCBI database, trying to download the next best match Microbulbifer_sp._C4-8 | not found in the NCBI database Microbulbifer_sp._C4-8 was not found in NCBI database, trying to download the next best match Microbulbifer_variabilis | successfully downloaded (total 81, 181 more to go) Sphingosinicella_sp._BS11 | not found in the NCBI database Sphingosinicella_sp._BS11 was not found in NCBI database, trying to download the next best match Sphingorhabdus_planktonica | not found in the NCBI database Sphingorhabdus_planktonica was not found in NCBI database, trying to download the next best match Sphingopyxis_sp._NMC18 | not found in the NCBI database Sphingopyxis_sp._NMC18 was not found in NCBI database, trying to download the next best match alpha_proteobacterium_WY6 | not found in the NCBI database Sphingopyxis_sp._PR52-21 | not found in the NCBI database Sphingopyxis_sp._PR52-21 was not found in NCBI database, trying to download the next best match Pelagibacterium_halotolerans_B2 | successfully downloaded (total 82, 179 more to go) Sphingomonas_taxi | successfully downloaded (total 83, 178 more to go) Sphingomonas_sp._WSCII | not found in the NCBI database Sphingomonas_sp._WSCII was not found in NCBI database, trying to download the next best match Novosphingobium_sp._MN38 | not found in the NCBI database Sphingomonas_sp._ROi43 | not found in the NCBI database Sphingomonas_sp._ROi43 was not found in NCBI database, trying to download the next best match Sphingopyxis_sp._MC1 | successfully downloaded (total 84, 176 more to go) Sphingomonas_sp._NBRC_101718 | not found in the NCBI database Sphingomonas_sp._NBRC_101718 was not found in NCBI database, trying to download the next best match Rhodospira_trueperi | successfully downloaded (total 85, 175 more to go) Sphingomonas_sp._B6.09-105 | not found in the NCBI database Sphingomonas_sp._B6.09-105 was not found in NCBI database, trying to download the next best match Sphingomonas_alpina | not found in the NCBI database Sphingomonas_alpina was not found in NCBI database, trying to download the next best match Blastomonas_sp._AMV5 | not found in the NCBI database Blastomonas_sp._AMV5 was not found in NCBI database, trying to download the next best match Sphingomonas_sp._ERG5 | successfully downloaded (total 86, 174 more to go) Sphingomonas_sanxanigenens_DSM_19645_=_NX02 | successfully downloaded (total 87, 173 more to go) Sphingobium_sp._SYK-6 | successfully downloaded (total 88, 172 more to go) Sphingobium_sp._GR1 | not found in the NCBI database Sphingobium_sp._GR1 was not found in NCBI database, trying to download the next best match Sphingobium_sp._FL24 | not found in the NCBI database Sphingobium_sp._FL24 was not found in NCBI database, trying to download the next best match Sphingomonas_sp._A1XXyl1-5 | not found in the NCBI database Sphingomonas_sp._A1XXyl1-5 was not found in NCBI database, trying to download the next best match Sphingobium_czechense_LL01 | successfully downloaded (total 89, 171 more to go) Solemya_velum_gill_symbiont | successfully downloaded (total 90, 170 more to go) Solemya_reidi_gill_symbiont | not found in the NCBI database Solemya_reidi_gill_symbiont was not found in NCBI database, trying to download the next best match bacterium_enrichment_culture_clone_41(2013) | not found in the NCBI database Sneathiella_glossodoripedis_JCM_23214 | successfully downloaded (total 91, 168 more to go) Smithella sp. SC K08D17 has too fragmented reference genome! It will not be downloaded. Smithella_sp._SC_K08D17 | not found in the NCBI database Simiduia_agarivorans_SA1_=_DSM_21679 | successfully downloaded (total 92, 166 more to go) Silicibacter_sp._LS103 | not found in the NCBI database Silicibacter_sp._LS103 was not found in NCBI database, trying to download the next best match Rhodoligotrophos_sp._BUT-3 | not found in the NCBI database Rhodoligotrophos_sp._BUT-3 was not found in NCBI database, trying to download the next best match carbazole-degrading_bacterium_OC13S | not found in the NCBI database Shewanella_woodyi_ATCC_51908 | successfully downloaded (total 93, 164 more to go) Shewanella_putrefaciens | successfully downloaded (total 94, 163 more to go) Shewanella_glacialipiscicola | not found in the NCBI database Shewanella_glacialipiscicola was not found in NCBI database, trying to download the next best match Shewanella_morhuae | successfully downloaded (total 95, 162 more to go) Serratia_symbiotica | successfully downloaded (total 96, 161 more to go) Sediminitomix_flava | successfully downloaded (total 97, 160 more to go) Seculamonas_ecuadoriensis | not found in the NCBI database Seculamonas_ecuadoriensis was not found in NCBI database, trying to download the next best match Reclinomonas_americana | not found in the NCBI database Reclinomonas_americana was not found in NCBI database, trying to download the next best match Reclinomonas_americana_ATCC_50283 | not found in the NCBI database Scytonema_millei_VB511283 | successfully downloaded (total 98, 158 more to go) Sanguibacter_keddieii_DSM_10542 | successfully downloaded (total 99, 157 more to go) Salinirepens_amamiensis | not found in the NCBI database Salinirepens_amamiensis was not found in NCBI database, trying to download the next best match Brumimicrobium_sp._P99 | not found in the NCBI database Saccharicrinis_fermentans_DSM_9555_=_JCM_21142 | successfully downloaded (total 100, 155 more to go) Ruegeria_sp._JZ08IS47 | not found in the NCBI database Ruegeria_sp._JZ08IS47 was not found in NCBI database, trying to download the next best match Ruegeria_sp._JZ08IS40 | not found in the NCBI database Ruegeria_sp._JZ08IS40 was not found in NCBI database, trying to download the next best match Rhodobacter_sphaeroides | successfully downloaded (total 101, 154 more to go) Rothia_dentocariosa | successfully downloaded (total 102, 153 more to go) Roseobacter_sp._SK209-2-6 | successfully downloaded (total 103, 152 more to go) Roseivirga_sp._F8 | not found in the NCBI database Roseivirga_sp._F8 was not found in NCBI database, trying to download the next best match Marinoscillum_luteum | not found in the NCBI database Marinoscillum_luteum was not found in NCBI database, trying to download the next best match Bacteroidetes_bacterium_O-014 | not found in the NCBI database Roseinatronobacter_sp._MOL1.10 | not found in the NCBI database Roseinatronobacter_sp._MOL1.10 was not found in NCBI database, trying to download the next best match Roseinatronobacter_sp._3.5P10 | not found in the NCBI database Roseinatronobacter_sp._3.5P10 was not found in NCBI database, trying to download the next best match Rhodovulum_kholense | successfully downloaded (total 104, 150 more to go) Riemerella_anatipestifer | successfully downloaded (total 105, 149 more to go) Rickettsia_prowazekii_str._Breinl | successfully downloaded (total 106, 148 more to go) Rickettsia_parkeri_str._Portsmouth | successfully downloaded (total 107, 147 more to go) Rickettsia_montanensis_str._OSU_85-930 | successfully downloaded (total 108, 146 more to go) Richelia_intracellularis | successfully downloaded (total 109, 145 more to go) Rhodovibrio_sp._K12-12B | not found in the NCBI database Rhodovibrio_sp._K12-12B was not found in NCBI database, trying to download the next best match Rhodovibrio_sp._K12-11A | not found in the NCBI database Rhodovibrio_sp._K12-11A was not found in NCBI database, trying to download the next best match Rhodovibrio_sp._2Mb1 | not found in the NCBI database Rhodovibrio_salinarum_DSM_9154 | successfully downloaded (total 110, 143 more to go) Rhodospirillaceae_bacterium_MOLA_82 | not found in the NCBI database Rhodospirillaceae_bacterium_MOLA_82 was not found in NCBI database, trying to download the next best match Thalassospira_sp._p67 | not found in the NCBI database Thalassospira_sp._p67 was not found in NCBI database, trying to download the next best match Thalassospira_sp._DG1258 | not found in the NCBI database Thalassospira_sp._DG1258 was not found in NCBI database, trying to download the next best match marine_bacterium_SCRIPPS_94 | not found in the NCBI database Rhodobacterales_bacterium_HTCC2255 | successfully downloaded (total 111, 141 more to go) Rhodobacteraceae_bacterium_B8-2 | not found in the NCBI database Rhodobacteraceae_bacterium_B8-2 was not found in NCBI database, trying to download the next best match Rhodobacteraceae_bacterium_B7-4 | not found in the NCBI database Rhodobacteraceae_bacterium_B7-4 was not found in NCBI database, trying to download the next best match Roseinatronobacter_sp._3.5P10 | not found in the NCBI database Rhizobacter_sp._DS48-6-7 | not found in the NCBI database Rhizobacter_sp._DS48-6-7 was not found in NCBI database, trying to download the next best match Rhizobacter_sp._DS48-6-5 | not found in the NCBI database Rhizobacter_sp._DS48-6-5 was not found in NCBI database, trying to download the next best match Rhizobacter_fulvus | not found in the NCBI database Rhizobacter_fulvus was not found in NCBI database, trying to download the next best match Chaetosphaeridium_globosum | not found in the NCBI database Rheinheimera_sp._JL1145 | not found in the NCBI database Rheinheimera_sp._JL1145 was not found in NCBI database, trying to download the next best match Rheinheimera_baltica_DSM_14885 | successfully downloaded (total 112, 138 more to go) Rheinheimera_aquimaris | successfully downloaded (total 113, 137 more to go) Reclinomonas_americana_ATCC_50284 | not found in the NCBI database Reclinomonas_americana_ATCC_50284 was not found in NCBI database, trying to download the next best match Reclinomonas_americana_ATCC_50283 | not found in the NCBI database Reclinomonas_americana_ATCC_50283 was not found in NCBI database, trying to download the next best match Reclinomonas_americana | not found in the NCBI database Ralstonia_sp._enrichment_culture_clone_Van98 | not found in the NCBI database Ralstonia_sp._enrichment_culture_clone_Van98 was not found in NCBI database, trying to download the next best match Gallionella_capsiferriformans_ES-2 | successfully downloaded (total 114, 135 more to go) Puniceicoccus_vermicola | not found in the NCBI database Puniceicoccus_vermicola was not found in NCBI database, trying to download the next best match Cerasicoccus_arenae | not found in the NCBI database Cerasicoccus_arenae was not found in NCBI database, trying to download the next best match Lentimonas_marisflavi | not found in the NCBI database Lentimonas_marisflavi was not found in NCBI database, trying to download the next best match Coraliomargarita_sp._IMCC15062 | not found in the NCBI database Psychroserpens_sp._PAMC_27130 | successfully downloaded (total 115, 133 more to go) Psychroserpens_mesophilus | successfully downloaded (total 116, 132 more to go) Psychroserpens_damuponensis | successfully downloaded (total 117, 131 more to go) Psychroserpens_burtonensis | successfully downloaded (total 118, 130 more to go) Pseudomonas_sp._f1(2011) | not found in the NCBI database Pseudomonas_sp._f1(2011) was not found in NCBI database, trying to download the next best match Pseudomonas_sp._DA2(2012) | not found in the NCBI database Pseudomonas_sp._DA2(2012) was not found in NCBI database, trying to download the next best match Pseudomonas_mendocina | successfully downloaded (total 119, 129 more to go) Pseudomonas_sp._S9 | successfully downloaded (total 120, 128 more to go) Pseudomonas_sp._G-R2A7 | not found in the NCBI database Pseudomonas_sp._G-R2A7 was not found in NCBI database, trying to download the next best match Pseudomonas_sp._G-R2A19 | not found in the NCBI database Pseudomonas_sp._G-R2A19 was not found in NCBI database, trying to download the next best match Legionella_longbeachae_NSW150 | successfully downloaded (total 121, 127 more to go) Pseudomonas_sp._BE07 | not found in the NCBI database Pseudomonas_sp._BE07 was not found in NCBI database, trying to download the next best match Teleogryllus_commodus | not found in the NCBI database Teleogryllus_commodus was not found in NCBI database, trying to download the next best match Pseudomonas_psychrophila_HA-4 | successfully downloaded (total 122, 126 more to go) Pseudomonas_sp._Asd_M6-6 | not found in the NCBI database Pseudomonas_sp._Asd_M6-6 was not found in NCBI database, trying to download the next best match Pseudomonas_sp._FSGSY10 | not found in the NCBI database Pseudomonas_sp._FSGSY10 was not found in NCBI database, trying to download the next best match Pseudomonas_parafulva | successfully downloaded (total 123, 125 more to go) Pseudomonas_rhizosphaerae | successfully downloaded (total 124, 124 more to go) Pseudomonas_putida | successfully downloaded (total 125, 123 more to go) Pseudomonas_marincola | successfully downloaded (total 126, 122 more to go) Pseudomonas_graminis | successfully downloaded (total 127, 121 more to go) Pseudomonas_fluorescens | successfully downloaded (total 128, 120 more to go) Pseudomonas_filiscindens | not found in the NCBI database Pseudohongiella_spirulinae | successfully downloaded (total 129, 118 more to go) Pseudanabaena_limnetica_CHAB792 | not found in the NCBI database Pseudanabaena_limnetica_CHAB792 was not found in NCBI database, trying to download the next best match Chroococcus_sp._2T05h | not found in the NCBI database Chroococcus_sp._2T05h was not found in NCBI database, trying to download the next best match Chroococcus_sp._VP2-02 | not found in the NCBI database Chroococcus_sp._VP2-02 was not found in NCBI database, trying to download the next best match Dermocarpella_sp._PCC_7326 | not found in the NCBI database Propionibacterium_sp._434-HC2 | successfully downloaded (total 130, 116 more to go) Porticoccus_litoralis | not found in the NCBI database Porticoccus_litoralis was not found in NCBI database, trying to download the next best match Spongiibacter_sp._CC-AMW-B | not found in the NCBI database Spongiibacter_sp._CC-AMW-B was not found in NCBI database, trying to download the next best match Porticoccus_hydrocarbonoclasticus | successfully downloaded (total 131, 115 more to go) Porticoccus_hydrocarbonoclasticus_MCTG13d | successfully downloaded (total 132, 114 more to go) Polycyclovorans_algicola_TG408 | successfully downloaded (total 133, 113 more to go) Polaribacter_sp._R-2-R-3-1 | not found in the NCBI database Polaribacter_sp._R-2-R-3-1 was not found in NCBI database, trying to download the next best match Lutibacter_sp._Hel1_33_84 | not found in the NCBI database Lutibacter_sp._Hel1_33_84 was not found in NCBI database, trying to download the next best match Kordia_algicida | successfully downloaded (total 134, 112 more to go) Polaribacter_sp._Hel1_85 | successfully downloaded (total 135, 111 more to go) Polaribacter_irgensii_23-P | successfully downloaded (total 136, 110 more to go) Polaribacter_dokdonensis | successfully downloaded (total 137, 109 more to go) Pleurocapsa_sp._HA4302 | not found in the NCBI database Pleurocapsa_sp._HA4302 was not found in NCBI database, trying to download the next best match Pseudophormidium_sp._ANT.LPE.3 | not found in the NCBI database Pseudophormidium_sp._ANT.LPE.3 was not found in NCBI database, trying to download the next best match Leptolyngbya_sp._ANT.L52.1 | not found in the NCBI database Pleionea_mediterranea | successfully downloaded (total 138, 107 more to go) Planktothrix_agardhii_NIVA-CYA_15 | successfully downloaded (total 139, 106 more to go) Planktomarina_temperata_RCA23 | successfully downloaded (total 140, 105 more to go) Planctomyces_maris_DSM_8797 | successfully downloaded (total 141, 104 more to go) Phormidium_sp._DVL1003c | not found in the NCBI database Phaeospirillum_sp._P-57 | not found in the NCBI database Phaeospirillum_sp._P-57 was not found in NCBI database, trying to download the next best match Oceanibaculum_pacificum | was downloaded previously (total 142, 102 more to go) Phaeospirillum_molischianum_DSM_120 | successfully downloaded (total 143, 101 more to go) Phaeospirillum_molischianum | successfully downloaded (total 144, 100 more to go) Phaeodactylum_tricornutum | successfully downloaded (total 145, 99 more to go) Phaeocystidibacter_sp._G18 | not found in the NCBI database Phaeocystidibacter_sp._G18 was not found in NCBI database, trying to download the next best match Phaeocystidibacter_luteus | not found in the NCBI database Pedobacter_westerhofensis | not found in the NCBI database Pedobacter_westerhofensis was not found in NCBI database, trying to download the next best match Pedobacter_sp._BG5 | not found in the NCBI database Pedobacter_sp._BG5 was not found in NCBI database, trying to download the next best match Pedobacter_sp._MaI11-5 | not found in the NCBI database Pedobacter_sp._MaI11-5 was not found in NCBI database, trying to download the next best match Sphingobacterium_antarcticus_4BY | successfully downloaded (total 146, 97 more to go) Parcubacteria_bacterium_SCGC_AAA011-N16 | successfully downloaded (total 147, 96 more to go) Parcubacteria_bacterium_RAAC4_OD1_1 | successfully downloaded (total 148, 95 more to go) Parachlamydiaceae_bacterium_HS-T3 | successfully downloaded (total 149, 94 more to go) Paenisporosarcina_macmurdoensis | not found in the NCBI database Paenisporosarcina_macmurdoensis was not found in NCBI database, trying to download the next best match Desulfuromonas_svalbardensis | not found in the NCBI database Desulfuromonas_svalbardensis was not found in NCBI database, trying to download the next best match bacterium_REGD8 | not found in the NCBI database Oxalobacter_vibrioformis | not found in the NCBI database Oxalobacter_vibrioformis was not found in NCBI database, trying to download the next best match Dechloromonas_sp._R-28400 | not found in the NCBI database Dechloromonas_sp._R-28400 was not found in NCBI database, trying to download the next best match Rhodocyclus_tenuis | not found in the NCBI database Rhodocyclus_tenuis was not found in NCBI database, trying to download the next best match Dechloromonas_sp._EMB_269 | not found in the NCBI database Owenweeksia_sp._MEBiC09403 | not found in the NCBI database Owenweeksia_sp._MEBiC09403 was not found in NCBI database, trying to download the next best match Owenweeksia_hongkongensis | successfully downloaded (total 150, 91 more to go) Owenweeksia_hongkongensis_DSM_17368 | successfully downloaded (total 151, 90 more to go) Osedax_symbiont_Rs2 | successfully downloaded (total 152, 89 more to go) Oscillatoria_lutea_SAG_1459-3 | not found in the NCBI database Oscillatoria_lutea_SAG_1459-3 was not found in NCBI database, trying to download the next best match Kamptonema_animale_SAG_1459-6 | not found in the NCBI database Kamptonema_animale_SAG_1459-6 was not found in NCBI database, trying to download the next best match Chamaesiphon_polonicus_SAG_32.87 | not found in the NCBI database Chamaesiphon_polonicus_SAG_32.87 was not found in NCBI database, trying to download the next best match Cyanothece_aeruginosa_SAG_87.79 | not found in the NCBI database Olleya_sp._VCSA23 | successfully downloaded (total 153, 87 more to go) Olleya_marilimosa_CAM030 | successfully downloaded (total 154, 86 more to go) Oleispira_antarctica_RB-8 | successfully downloaded (total 155, 85 more to go) Oleibacter_marinus | successfully downloaded (total 156, 84 more to go) Ochrobactrum_sp._s163 | not found in the NCBI database Ochrobactrum_sp._s163 was not found in NCBI database, trying to download the next best match Azospirillum_palatum | not found in the NCBI database Azospirillum_palatum was not found in NCBI database, trying to download the next best match Azospirillum_sp._CA6 | not found in the NCBI database Azospirillum_sp._CA6 was not found in NCBI database, trying to download the next best match Pannonibacter_sp._ODC-40 | not found in the NCBI database Oceanicola_granulosus_HTCC2516 | successfully downloaded (total 157, 82 more to go) Oceanibaculum_indicum_P24 | successfully downloaded (total 158, 81 more to go) Nocardioides_terrae | successfully downloaded (total 159, 80 more to go) Nitrospina_gracilis_3 | not found in the NCBI database Nitrospina_gracilis_3 was not found in NCBI database, trying to download the next best match Nitrospina_gracilis | successfully downloaded (total 160, 79 more to go) Nitrosospira_sp._NpAV | successfully downloaded (total 161, 78 more to go) Nitrosomonas_cryotolerans_ATCC_49181 | successfully downloaded (total 162, 77 more to go) Nisaea_nitritireducens | not found in the NCBI database Nisaea_nitritireducens was not found in NCBI database, trying to download the next best match Oceanibaculum_indicum | successfully downloaded (total 163, 76 more to go) Neptunomonas_japonica | successfully downloaded (total 164, 75 more to go) Neisseria_sp._CSL_7565 | not found in the NCBI database Neisseria_mucosa_ATCC_25996 | successfully downloaded (total 165, 73 more to go) Neisseria_macacae_ATCC_33926 | successfully downloaded (total 166, 72 more to go) Nannochloropsis oculata has too fragmented reference genome! It will not be downloaded. Nannochloropsis_oculata | not found in the NCBI database Nannochloropsis_oculata was not found in NCBI database, trying to download the next best match Nannochloropsis granulata has too fragmented reference genome! It will not be downloaded. Nannochloropsis_granulata | not found in the NCBI database Nannochloropsis_granulata was not found in NCBI database, trying to download the next best match Nannochloropsis_oceanica | successfully downloaded (total 167, 71 more to go) Mycobacterium_simulans | not found in the NCBI database Moritella_sp._PE36 | successfully downloaded (total 168, 69 more to go) Microscilla_sp._DG946 | not found in the NCBI database Microscilla_sp._DG946 was not found in NCBI database, trying to download the next best match Marinoscillum_furvescens | successfully downloaded (total 169, 68 more to go) Micromonospora_sp._NEAU-NH7 | not found in the NCBI database Micromonospora_sp._NEAU-NH7 was not found in NCBI database, trying to download the next best match Verrucosispora_maris_AB-18-032 | successfully downloaded (total 170, 67 more to go) Microbulbifer_agarilyticus_S89 | successfully downloaded (total 171, 66 more to go) Methylotenera_sp._SMs12 | not found in the NCBI database Methylotenera_sp._SMs12 was not found in NCBI database, trying to download the next best match Methylophilus_methylotrophus | successfully downloaded (total 172, 65 more to go) Methylotenera_sp._73s | successfully downloaded (total 173, 64 more to go) Methylotenera_mobilis_13 | successfully downloaded (total 174, 63 more to go) Methylophilus_sp._OH31 | successfully downloaded (total 175, 62 more to go) Methylophilaceae_bacterium_MMS-10A-187 | not found in the NCBI database Methylophilaceae_bacterium_MMS-10A-187 was not found in NCBI database, trying to download the next best match Methylophilaceae_bacterium_MMS-10A-34 | not found in the NCBI database Methylophilaceae_bacterium_MMS-10A-34 was not found in NCBI database, trying to download the next best match Methylophilaceae_bacterium_MMS-10A-77 | not found in the NCBI database Methylophilaceae_bacterium_B1 | not found in the NCBI database Methylophilaceae_bacterium_B1 was not found in NCBI database, trying to download the next best match Methylotenera_versatilis_79 | successfully downloaded (total 176, 60 more to go) Methylophaga_marina | not found in the NCBI database Methylophaga_marina was not found in NCBI database, trying to download the next best match bacterium_SH6-1 | not found in the NCBI database Methylomonas_clara | successfully downloaded (total 177, 58 more to go) Methanothermococcus_okinawensis_IH1 | successfully downloaded (total 178, 57 more to go) Methanolobus_taylorii | not found in the NCBI database Methanolobus_taylorii was not found in NCBI database, trying to download the next best match Methanolobus_psychrophilus | successfully downloaded (total 179, 56 more to go) Methanolobus_profundi | successfully downloaded (total 180, 55 more to go) Methanocaldococcus_sp._JH146 | successfully downloaded (total 181, 54 more to go) Methanobrevibacter_sp._HW1 | not found in the NCBI database Methanobrevibacter_sp._HW1 was not found in NCBI database, trying to download the next best match Methanobrevibacter_sp._RsW3 | not found in the NCBI database Marivirga_tractuosa_DSM_4126 | successfully downloaded (total 182, 52 more to go) Marinoscillum_pacificum | not found in the NCBI database Marinoscillum_pacificum was not found in NCBI database, trying to download the next best match Algoriphagus_sp._p1(2011) | not found in the NCBI database Algoriphagus_sp._p1(2011) was not found in NCBI database, trying to download the next best match Sporocytophaga_sp._JL-01 | not found in the NCBI database Marinobacter_sp._BSs20002 | not found in the NCBI database Marinobacter_sp._BSs20002 was not found in NCBI database, trying to download the next best match Marinobacter_psychrophilus | successfully downloaded (total 183, 50 more to go) Lyngbya_confervoides_BDU141951 | successfully downloaded (total 184, 49 more to go) Luminiphilus_syltensis_NOR5-1B | successfully downloaded (total 185, 48 more to go) Limnothrix_cf._redekei_AH21 | not found in the NCBI database Limnothrix_cf._redekei_AH21 was not found in NCBI database, trying to download the next best match Aphanothece_cf._sacrum_SAG_2412 | not found in the NCBI database Aphanothece_cf._sacrum_SAG_2412 was not found in NCBI database, trying to download the next best match Pseudanabaena_biceps_PCC_7429 | successfully downloaded (total 186, 47 more to go) Leptolyngbya_sp._PCC_6406 | successfully downloaded (total 187, 46 more to go) Leptolyngbya_scottii_EcFYyyy_00 | not found in the NCBI database Leptolyngbya_scottii_EcFYyyy_00 was not found in NCBI database, trying to download the next best match Calothrix_sp._HA4186-MV5 | not found in the NCBI database Calothrix_sp._HA4186-MV5 was not found in NCBI database, trying to download the next best match Calothrix_sp._PCC_7103 | successfully downloaded (total 188, 45 more to go) Lentisphaera_araneosa_HTCC2155 | successfully downloaded (total 189, 44 more to go) Legionella_santicrucis | successfully downloaded (total 190, 43 more to go) Lacibacterium_sp._UR7-11 | not found in the NCBI database Lacibacterium_sp._UR7-11 was not found in NCBI database, trying to download the next best match Dichotomicrobium_thermohalophilum | was downloaded previously (total 191, 42 more to go) Halorhodospira_halophila_SL1 | successfully downloaded (total 192, 41 more to go) Halioglobus_japonicus | successfully downloaded (total 193, 40 more to go) Gloeothece_sp._SK40 | not found in the NCBI database Gloeothece_sp._SK40 was not found in NCBI database, trying to download the next best match Cyanothece_sp._ATCC_51472 | successfully downloaded (total 194, 39 more to go) Geothermobacter_ehrlichii | not found in the NCBI database Geobacter_sp._GSS01 | successfully downloaded (total 195, 37 more to go) Geitlerinema_sp._PCC_7407 | successfully downloaded (total 196, 36 more to go) Geitlerinema_sp._PCC_7105 | successfully downloaded (total 197, 35 more to go) Gangjinia_marincola | not found in the NCBI database Gangjinia_marincola was not found in NCBI database, trying to download the next best match Flavobacterium_psychrophilum | successfully downloaded (total 198, 34 more to go) Formosa_sp._Sl14 | not found in the NCBI database Formosa_sp._Sl14 was not found in NCBI database, trying to download the next best match Formosa_undariae | not found in the NCBI database Formosa_undariae was not found in NCBI database, trying to download the next best match Zobellia_sp._SS10.15 | not found in the NCBI database Zobellia_sp._SS10.15 was not found in NCBI database, trying to download the next best match Maribacter_sp._BSw21917 | not found in the NCBI database Formosa_sp._SS15.5 | not found in the NCBI database Formosa_sp._SS15.5 was not found in NCBI database, trying to download the next best match Aquibacter_zeaxanthinifaciens | not found in the NCBI database Aquibacter_zeaxanthinifaciens was not found in NCBI database, trying to download the next best match Flavobacteriaceae_bacterium_SW325 | not found in the NCBI database Flexithrix_dorotheae | successfully downloaded (total 199, 31 more to go) Flexibacteraceae_bacterium_MOLA_120 | not found in the NCBI database Flexibacteraceae_bacterium_MOLA_120 was not found in NCBI database, trying to download the next best match Marinoscillum_furvescens | was downloaded previously (total 200, 30 more to go) Flavobacterium_sp._SCGC_AAA160-P02 | successfully downloaded (total 201, 29 more to go) Flavobacterium_psychrophilum_FPG3 | successfully downloaded (total 202, 28 more to go) Flavobacteriaceae_bacterium_scsio713 | not found in the NCBI database Flavobacteriaceae_bacterium_scsio713 was not found in NCBI database, trying to download the next best match Olleya_sp._2EP4 | not found in the NCBI database Olleya_sp._2EP4 was not found in NCBI database, trying to download the next best match Olleya_aquimaris | successfully downloaded (total 203, 27 more to go) Firmicutes_bacterium_LX-D | not found in the NCBI database Fabibacter_sp._NBRC_110216 | successfully downloaded (total 204, 25 more to go) Euzebya_tangerina | successfully downloaded (total 205, 24 more to go) Ensifer_mexicanus | not found in the NCBI database Ensifer_mexicanus was not found in NCBI database, trying to download the next best match Ensifer_terangae | not found in the NCBI database Ensifer_terangae was not found in NCBI database, trying to download the next best match alpha_proteobacterium_MBIC3923 | not found in the NCBI database alpha_proteobacterium_MBIC3923 was not found in NCBI database, trying to download the next best match Ensifer_sp._JNVU_CM6 | not found in the NCBI database Endozoicomonas_montiporae | successfully downloaded (total 206, 22 more to go) Dokdonia_sp._HMF2319 | not found in the NCBI database Dokdonia_sp._HMF2319 was not found in NCBI database, trying to download the next best match Lutibacter_agarilyticus | successfully downloaded (total 207, 21 more to go) Devosia_sp._NH131 | not found in the NCBI database Devosia_sp._NH131 was not found in NCBI database, trying to download the next best match Kordiimonas_aestuarii | not found in the NCBI database Kordiimonas_aestuarii was not found in NCBI database, trying to download the next best match sediment_bacterium_22-39 | not found in the NCBI database sediment_bacterium_22-39 was not found in NCBI database, trying to download the next best match Pelagibacterium_luteolum | successfully downloaded (total 208, 20 more to go) Desulfotomaculum_sp._Lac-2 | not found in the NCBI database Desulfotomaculum_sp._Lac-2 was not found in NCBI database, trying to download the next best match Desulfotomaculum_alkaliphilum_DSM_12257 | successfully downloaded (total 209, 19 more to go) Cytophaga_sp | not found in the NCBI database Cytophaga_sp was not found in NCBI database, trying to download the next best match Kordia_algicida_OT-1 | was downloaded previously (total 210, 18 more to go) Cryobacterium_sp._TP-Snow-C59 | not found in the NCBI database Cryobacterium_sp._TP-Snow-C59 was not found in NCBI database, trying to download the next best match Cryobacterium_sp._Lc30-4 | not found in the NCBI database Cryobacterium_sp._Lc30-4 was not found in NCBI database, trying to download the next best match Alpinimonas_psychrophila | not found in the NCBI database Alpinimonas_psychrophila was not found in NCBI database, trying to download the next best match Cryobacterium_psychrophilum | successfully downloaded (total 211, 17 more to go) Corynebacterium_durum | successfully downloaded (total 212, 16 more to go) Coccinistipes_vermicola | not found in the NCBI database Coccinistipes_vermicola was not found in NCBI database, trying to download the next best match Phaeocystidibacter_luteus | not found in the NCBI database Burkholderia_rhizoxinica_HKI_454 | successfully downloaded (total 213, 14 more to go) Brassica_napus_(rape) | not found in the NCBI database Brassica_napus_(rape) was not found in NCBI database, trying to download the next best match Gloeocapsopsis_sp._AAB1 | successfully downloaded (total 214, 13 more to go) Bdellovibrionales_bacterium_RKEM611 | successfully downloaded (total 215, 12 more to go) Bacteriovorax_sp._NA7 | not found in the NCBI database Bacteriovorax_sp._NA7 was not found in NCBI database, trying to download the next best match Bacteriovorax_sp._RH1B4-S | not found in the NCBI database Bacteriovorax_sp._RH1B4-S was not found in NCBI database, trying to download the next best match Bacteriovorax_sp._RH3S1-S | not found in the NCBI database Bacteriovorax_sp._RH3S1-S was not found in NCBI database, trying to download the next best match Bacteriovorax_sp._RM2B3-S | not found in the NCBI database Bacteriovorax_sp._GSL371 | not found in the NCBI database Bacteriovorax_sp._GSL371 was not found in NCBI database, trying to download the next best match bacterium_enrichment_culture_clone_SBIa19 | not found in the NCBI database bacterium_enrichment_culture_clone_SBIa19 was not found in NCBI database, trying to download the next best match bacterium_enrichment_culture_clone_SBIa16 | not found in the NCBI database bacterium_enrichment_culture_clone_SBIa16 was not found in NCBI database, trying to download the next best match bacterium_enrichment_culture_clone_SBIa32 | not found in the NCBI database Bacillus_licheniformis_9945A | successfully downloaded (total 216, 9 more to go) Azospirillum_zeae | not found in the NCBI database Azospirillum_zeae was not found in NCBI database, trying to download the next best match Azospirillum_brasilense | successfully downloaded (total 217, 8 more to go) Aureimarina_marisflavi | not found in the NCBI database Aureimarina_marisflavi was not found in NCBI database, trying to download the next best match Cellulophaga_sp._NBRC_101309 | not found in the NCBI database Cellulophaga_sp._NBRC_101309 was not found in NCBI database, trying to download the next best match Maribacter_sp._BSw21908 | not found in the NCBI database Maribacter_sp._BSw21908 was not found in NCBI database, trying to download the next best match Cellulophaga_tyrosinoxydans | successfully downloaded (total 218, 7 more to go) Arachis ipaensis has too fragmented reference genome! It will not be downloaded. Arachis_ipaensis | not found in the NCBI database Arachis_ipaensis was not found in NCBI database, trying to download the next best match beta_proteobacterium_Nit1 | not found in the NCBI database beta_proteobacterium_Nit1 was not found in NCBI database, trying to download the next best match Azoarcus_sp._JMC-UBL_43 | not found in the NCBI database Azoarcus_sp._JMC-UBL_43 was not found in NCBI database, trying to download the next best match Hydrogenophaga_intermedia | successfully downloaded (total 219, 6 more to go) Aquaspirillum_sp._feline_oral_taxon_082 | not found in the NCBI database Aquaspirillum_sp._feline_oral_taxon_082 was not found in NCBI database, trying to download the next best match Rhodospirillaceae_bacterium_CAU1121 | not found in the NCBI database Rhodospirillaceae_bacterium_CAU1121 was not found in NCBI database, trying to download the next best match Bacillus_sp._DY17 | not found in the NCBI database Bacillus_sp._DY17 was not found in NCBI database, trying to download the next best match Bacillus_licheniformis | successfully downloaded (total 220, 5 more to go) Altibacter_lentus | successfully downloaded (total 221, 4 more to go) Actinomyces_sp._oral_taxon_175_str._F0384 | successfully downloaded (total 222, 3 more to go) Acinetobacter_sp._151 | not found in the NCBI database Acinetobacter_sp._151 was not found in NCBI database, trying to download the next best match Acinetobacter_sp._178 | not found in the NCBI database Acinetobacter_sp._178 was not found in NCBI database, trying to download the next best match Acinetobacter_sp._168 | not found in the NCBI database Acinetobacter_sp._168 was not found in NCBI database, trying to download the next best match Acinetobacter_sp._165 | not found in the NCBI database Acidithiobacillus_ferrivorans_SS3 | successfully downloaded (total 223, 1 more to go) Acaryochloris_sp._MPGRS1 | not found in the NCBI database Acaryochloris_sp._MPGRS1 was not found in NCBI database, trying to download the next best match Acaryochloris_marina | successfully downloaded (total 224, 0 more to go) Downloaded reference(s): /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Acaryochloris_marina.fasta ==> Acaryochloris_marina /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Acidithiobacillus_ferrivorans_SS3.fasta ==> Acidithiobacillus_ferrivorans_SS3 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Actinomyces_sp._oral_taxon_175_str._F0384.fasta ==> Actinomyces_sp._oral_taxon_175_str._F0384 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Ahrensia_kielensis_DSM_5890.fasta ==> Ahrensia_kielensis_DSM_5890 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Akkermansia_muciniphila.fasta ==> Akkermansia_muciniphila /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Altibacter_lentus.fasta ==> Altibacter_lentus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Aphanothece_sacrum.fasta ==> Aphanothece_sacrum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Azospirillum_brasilense.fasta ==> Azospirillum_brasilense /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Bacillus_licheniformis.fasta ==> Bacillus_licheniformis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Bacillus_licheniformis_9945A.fasta ==> Bacillus_licheniformis_9945A /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Bdellovibrionales_bacterium_RKEM611.fasta ==> Bdellovibrionales_bacterium_RKEM611 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Bermanella_marisrubri.fasta ==> Bermanella_marisrubri /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Bizionia_echini.fasta ==> Bizionia_echini /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Burkholderia_rhizoxinica_HKI_454.fasta ==> Burkholderia_rhizoxinica_HKI_454 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Calothrix_sp._PCC_7103.fasta ==> Calothrix_sp._PCC_7103 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Cellulophaga_tyrosinoxydans.fasta ==> Cellulophaga_tyrosinoxydans /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Corynebacterium_durum.fasta ==> Corynebacterium_durum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Crocinitomix_catalasitica.fasta ==> Crocinitomix_catalasitica /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Cryobacterium_psychrophilum.fasta ==> Cryobacterium_psychrophilum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Cyanothece_sp._ATCC_51472.fasta ==> Cyanothece_sp._ATCC_51472 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Cyanothece_sp._PCC_7425.fasta ==> Cyanothece_sp._PCC_7425 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Desulfobacula_sp._TS.fasta ==> Desulfobacula_sp._TS /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Desulfotomaculum_alkaliphilum_DSM_12257.fasta ==> Desulfotomaculum_alkaliphilum_DSM_12257 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Dichotomicrobium_thermohalophilum.fasta ==> Dichotomicrobium_thermohalophilum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Dokdonia_donghaensis_DSW_1.fasta ==> Dokdonia_donghaensis_DSW_1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Endozoicomonas_montiporae.fasta ==> Endozoicomonas_montiporae /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Euzebya_tangerina.fasta ==> Euzebya_tangerina /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Fabibacter_sp._NBRC_110216.fasta ==> Fabibacter_sp._NBRC_110216 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Flavobacterium_psychrophilum.fasta ==> Flavobacterium_psychrophilum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Flavobacterium_psychrophilum_FPG3.fasta ==> Flavobacterium_psychrophilum_FPG3 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Flavobacterium_sp._SCGC_AAA160_P02.fasta ==> Flavobacterium_sp._SCGC_AAA160_P02 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Flexithrix_dorotheae.fasta ==> Flexithrix_dorotheae /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Fluviicola_taffensis_DSM_16823.fasta ==> Fluviicola_taffensis_DSM_16823 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Formosa_sp._AK20.fasta ==> Formosa_sp._AK20 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Gallionella_capsiferriformans_ES_2.fasta ==> Gallionella_capsiferriformans_ES_2 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Geitlerinema_sp._PCC_7105.fasta ==> Geitlerinema_sp._PCC_7105 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Geitlerinema_sp._PCC_7407.fasta ==> Geitlerinema_sp._PCC_7407 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Geobacter_sp._GSS01.fasta ==> Geobacter_sp._GSS01 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Gilvimarinus_chinensis_DSM_19667.fasta ==> Gilvimarinus_chinensis_DSM_19667 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Gilvimarinus_sp._YN3.fasta ==> Gilvimarinus_sp._YN3 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Gimesia_maris.fasta ==> Gimesia_maris /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Gloeocapsopsis_sp._AAB1.fasta ==> Gloeocapsopsis_sp._AAB1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Gracilibacteria_bacterium_JGI_0000069_P22.fasta ==> Gracilibacteria_bacterium_JGI_0000069_P22 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Halioglobus_japonicus.fasta ==> Halioglobus_japonicus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Halorhodospira_halophila_SL1.fasta ==> Halorhodospira_halophila_SL1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Hoeflea_phototrophica_DFL_43.fasta ==> Hoeflea_phototrophica_DFL_43 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Hydrogenophaga_intermedia.fasta ==> Hydrogenophaga_intermedia /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Kordia_algicida.fasta ==> Kordia_algicida /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Kordia_algicida_OT_1.fasta ==> Kordia_algicida_OT_1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Legionella_longbeachae_NSW150.fasta ==> Legionella_longbeachae_NSW150 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Legionella_santicrucis.fasta ==> Legionella_santicrucis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Lentisphaera_araneosa_HTCC2155.fasta ==> Lentisphaera_araneosa_HTCC2155 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Leptolyngbya_sp._PCC_6406.fasta ==> Leptolyngbya_sp._PCC_6406 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Lishizhenia_tianjinensis.fasta ==> Lishizhenia_tianjinensis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Luminiphilus_syltensis_NOR5_1B.fasta ==> Luminiphilus_syltensis_NOR5_1B /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Lutibacter_agarilyticus.fasta ==> Lutibacter_agarilyticus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Lyngbya_confervoides_BDU141951.fasta ==> Lyngbya_confervoides_BDU141951 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Magnetofaba_australis_IT_1.fasta ==> Magnetofaba_australis_IT_1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Magnetovibrio_blakemorei.fasta ==> Magnetovibrio_blakemorei /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Marinobacter_psychrophilus.fasta ==> Marinobacter_psychrophilus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Marinoscillum_furvescens.fasta ==> Marinoscillum_furvescens /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Marivirga_tractuosa_DSM_4126.fasta ==> Marivirga_tractuosa_DSM_4126 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methanocaldococcus_sp._JH146.fasta ==> Methanocaldococcus_sp._JH146 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methanolobus_profundi.fasta ==> Methanolobus_profundi /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methanolobus_psychrophilus.fasta ==> Methanolobus_psychrophilus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methanosaeta_sp.fasta ==> Methanosaeta_sp /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methanothermococcus_okinawensis_IH1.fasta ==> Methanothermococcus_okinawensis_IH1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methylobacillus_glycogenes.fasta ==> Methylobacillus_glycogenes /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methylomonas_clara.fasta ==> Methylomonas_clara /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methylophilus_methylotrophus.fasta ==> Methylophilus_methylotrophus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methylophilus_sp._OH31.fasta ==> Methylophilus_sp._OH31 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methylotenera_mobilis_13.fasta ==> Methylotenera_mobilis_13 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methylotenera_sp._73s.fasta ==> Methylotenera_sp._73s /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Methylotenera_versatilis_79.fasta ==> Methylotenera_versatilis_79 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Microbulbifer_agarilyticus_S89.fasta ==> Microbulbifer_agarilyticus_S89 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Microbulbifer_variabilis.fasta ==> Microbulbifer_variabilis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Moritella_sp._PE36.fasta ==> Moritella_sp._PE36 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Muricauda_ruestringensis_DSM_13258.fasta ==> Muricauda_ruestringensis_DSM_13258 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Nannochloropsis_oceanica.fasta ==> Nannochloropsis_oceanica /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Neisseria_macacae_ATCC_33926.fasta ==> Neisseria_macacae_ATCC_33926 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Neisseria_mucosa_ATCC_25996.fasta ==> Neisseria_mucosa_ATCC_25996 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Neptunomonas_japonica.fasta ==> Neptunomonas_japonica /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Nitrosococcus_halophilus_Nc_4.fasta ==> Nitrosococcus_halophilus_Nc_4 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Nitrosomonas_cryotolerans_ATCC_49181.fasta ==> Nitrosomonas_cryotolerans_ATCC_49181 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Nitrosomonas_sp._Nm86.fasta ==> Nitrosomonas_sp._Nm86 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Nitrosospira_sp._NpAV.fasta ==> Nitrosospira_sp._NpAV /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Nitrospina_gracilis.fasta ==> Nitrospina_gracilis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Nocardioides_terrae.fasta ==> Nocardioides_terrae /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Oceanibaculum_indicum.fasta ==> Oceanibaculum_indicum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Oceanibaculum_indicum_P24.fasta ==> Oceanibaculum_indicum_P24 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Oceanibaculum_pacificum.fasta ==> Oceanibaculum_pacificum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Oceanicola_granulosus_HTCC2516.fasta ==> Oceanicola_granulosus_HTCC2516 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Olavius_algarvensis_Delta_4_endosymbiont.fasta ==> Olavius_algarvensis_Delta_4_endosymbiont /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Oleibacter_marinus.fasta ==> Oleibacter_marinus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Oleispira_antarctica_RB_8.fasta ==> Oleispira_antarctica_RB_8 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Olleya_aquimaris.fasta ==> Olleya_aquimaris /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Olleya_marilimosa_CAM030.fasta ==> Olleya_marilimosa_CAM030 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Olleya_sp._VCSA23.fasta ==> Olleya_sp._VCSA23 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Osedax_symbiont_Rs2.fasta ==> Osedax_symbiont_Rs2 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Owenweeksia_hongkongensis.fasta ==> Owenweeksia_hongkongensis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Owenweeksia_hongkongensis_DSM_17368.fasta ==> Owenweeksia_hongkongensis_DSM_17368 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Parachlamydia_acanthamoebae_UV_7.fasta ==> Parachlamydia_acanthamoebae_UV_7 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Parachlamydiaceae_bacterium_HS_T3.fasta ==> Parachlamydiaceae_bacterium_HS_T3 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Parcubacteria_bacterium_RAAC4_OD1_1.fasta ==> Parcubacteria_bacterium_RAAC4_OD1_1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Parcubacteria_bacterium_SCGC_AAA011_A08.fasta ==> Parcubacteria_bacterium_SCGC_AAA011_A08 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Parcubacteria_bacterium_SCGC_AAA011_N16.fasta ==> Parcubacteria_bacterium_SCGC_AAA011_N16 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pelagibacterium_halotolerans_B2.fasta ==> Pelagibacterium_halotolerans_B2 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pelagibacterium_luteolum.fasta ==> Pelagibacterium_luteolum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Phaeodactylum_tricornutum.fasta ==> Phaeodactylum_tricornutum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Phaeospirillum_molischianum.fasta ==> Phaeospirillum_molischianum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Phaeospirillum_molischianum_DSM_120.fasta ==> Phaeospirillum_molischianum_DSM_120 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Planctomyces_maris_DSM_8797.fasta ==> Planctomyces_maris_DSM_8797 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Planktomarina_temperata_RCA23.fasta ==> Planktomarina_temperata_RCA23 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Planktothrix_agardhii_NIVA_CYA_15.fasta ==> Planktothrix_agardhii_NIVA_CYA_15 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pleionea_mediterranea.fasta ==> Pleionea_mediterranea /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Polaribacter_dokdonensis.fasta ==> Polaribacter_dokdonensis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Polaribacter_irgensii_23_P.fasta ==> Polaribacter_irgensii_23_P /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Polaribacter_sp._Hel1_85.fasta ==> Polaribacter_sp._Hel1_85 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Polycyclovorans_algicola_TG408.fasta ==> Polycyclovorans_algicola_TG408 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Porticoccus_hydrocarbonoclasticus.fasta ==> Porticoccus_hydrocarbonoclasticus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Porticoccus_hydrocarbonoclasticus_MCTG13d.fasta ==> Porticoccus_hydrocarbonoclasticus_MCTG13d /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Propionibacterium_sp._434_HC2.fasta ==> Propionibacterium_sp._434_HC2 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudanabaena_biceps_PCC_7429.fasta ==> Pseudanabaena_biceps_PCC_7429 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudohongiella_spirulinae.fasta ==> Pseudohongiella_spirulinae /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudomonas_fluorescens.fasta ==> Pseudomonas_fluorescens /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudomonas_graminis.fasta ==> Pseudomonas_graminis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudomonas_marincola.fasta ==> Pseudomonas_marincola /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudomonas_mendocina.fasta ==> Pseudomonas_mendocina /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudomonas_parafulva.fasta ==> Pseudomonas_parafulva /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudomonas_psychrophila_HA_4.fasta ==> Pseudomonas_psychrophila_HA_4 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudomonas_putida.fasta ==> Pseudomonas_putida /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudomonas_rhizosphaerae.fasta ==> Pseudomonas_rhizosphaerae /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Pseudomonas_sp._S9.fasta ==> Pseudomonas_sp._S9 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Psychroserpens_burtonensis.fasta ==> Psychroserpens_burtonensis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Psychroserpens_damuponensis.fasta ==> Psychroserpens_damuponensis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Psychroserpens_mesophilus.fasta ==> Psychroserpens_mesophilus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Psychroserpens_sp._PAMC_27130.fasta ==> Psychroserpens_sp._PAMC_27130 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rheinheimera_aquimaris.fasta ==> Rheinheimera_aquimaris /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rheinheimera_baltica_DSM_14885.fasta ==> Rheinheimera_baltica_DSM_14885 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rhodobacter_sphaeroides.fasta ==> Rhodobacter_sphaeroides /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rhodobacterales_bacterium_HTCC2255.fasta ==> Rhodobacterales_bacterium_HTCC2255 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rhodospira_trueperi.fasta ==> Rhodospira_trueperi /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rhodovibrio_salinarum.fasta ==> Rhodovibrio_salinarum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rhodovibrio_salinarum_DSM_9154.fasta ==> Rhodovibrio_salinarum_DSM_9154 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rhodovulum_kholense.fasta ==> Rhodovulum_kholense /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Richelia_intracellularis.fasta ==> Richelia_intracellularis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rickettsia_montanensis_str._OSU_85_930.fasta ==> Rickettsia_montanensis_str._OSU_85_930 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rickettsia_parkeri_str._Portsmouth.fasta ==> Rickettsia_parkeri_str._Portsmouth /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rickettsia_prowazekii_str._Breinl.fasta ==> Rickettsia_prowazekii_str._Breinl /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Riemerella_anatipestifer.fasta ==> Riemerella_anatipestifer /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Roseobacter_sp._SK209_2_6.fasta ==> Roseobacter_sp._SK209_2_6 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rothia_dentocariosa.fasta ==> Rothia_dentocariosa /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Saccharicrinis_fermentans_DSM_9555___JCM_21142.fasta ==> Saccharicrinis_fermentans_DSM_9555___JCM_21142 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Saccharophagus_degradans_2_40.fasta ==> Saccharophagus_degradans_2_40 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sanguibacter_keddieii_DSM_10542.fasta ==> Sanguibacter_keddieii_DSM_10542 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Scytonema_millei_VB511283.fasta ==> Scytonema_millei_VB511283 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sediminitomix_flava.fasta ==> Sediminitomix_flava /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Serratia_symbiotica.fasta ==> Serratia_symbiotica /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Shewanella_morhuae.fasta ==> Shewanella_morhuae /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Shewanella_putrefaciens.fasta ==> Shewanella_putrefaciens /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Shewanella_woodyi_ATCC_51908.fasta ==> Shewanella_woodyi_ATCC_51908 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Simiduia_agarivorans_SA1___DSM_21679.fasta ==> Simiduia_agarivorans_SA1___DSM_21679 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sneathiella_glossodoripedis_JCM_23214.fasta ==> Sneathiella_glossodoripedis_JCM_23214 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Solemya_velum_gill_symbiont.fasta ==> Solemya_velum_gill_symbiont /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sphingobacterium_antarcticus_4BY.fasta ==> Sphingobacterium_antarcticus_4BY /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sphingobium_czechense_LL01.fasta ==> Sphingobium_czechense_LL01 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sphingobium_sp._SYK_6.fasta ==> Sphingobium_sp._SYK_6 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sphingomonas_sanxanigenens_DSM_19645___NX02.fasta ==> Sphingomonas_sanxanigenens_DSM_19645___NX02 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sphingomonas_sp._ERG5.fasta ==> Sphingomonas_sp._ERG5 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sphingomonas_taxi.fasta ==> Sphingomonas_taxi /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sphingopyxis_sp._MC1.fasta ==> Sphingopyxis_sp._MC1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Spongiibacter_tropicus.fasta ==> Spongiibacter_tropicus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Stanieria_cyanosphaera_PCC_7437.fasta ==> Stanieria_cyanosphaera_PCC_7437 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Stenotrophomonas_maltophilia_JV3.fasta ==> Stenotrophomonas_maltophilia_JV3 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Stenotrophomonas_sp._RIT309.fasta ==> Stenotrophomonas_sp._RIT309 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Streptococcus_agalactiae_SS1219.fasta ==> Streptococcus_agalactiae_SS1219 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Streptococcus_sanguinis_SK115.fasta ==> Streptococcus_sanguinis_SK115 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Streptomyces_albulus.fasta ==> Streptomyces_albulus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Streptomyces_indicus.fasta ==> Streptomyces_indicus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Streptomyces_mobaraensis_NBRC_13819___DSM_40847.fasta ==> Streptomyces_mobaraensis_NBRC_13819___DSM_40847 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sulfitobacter_sp._EE_36.fasta ==> Sulfitobacter_sp._EE_36 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Sulfitobacter_sp._NAS_14.1.fasta ==> Sulfitobacter_sp._NAS_14.1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Tenacibaculum_gallaicum.fasta ==> Tenacibaculum_gallaicum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Tenacibaculum_maritimum.fasta ==> Tenacibaculum_maritimum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Tenacibaculum_skagerrakense.fasta ==> Tenacibaculum_skagerrakense /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thalassobaculum_salexigens_DSM_19539.fasta ==> Thalassobaculum_salexigens_DSM_19539 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thalassospira_profundimaris.fasta ==> Thalassospira_profundimaris /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thalassospira_xiamenensis_M_5___DSM_17429.fasta ==> Thalassospira_xiamenensis_M_5___DSM_17429 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thermoplasma_acidophilum.fasta ==> Thermoplasma_acidophilum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thermoplasmatales_archaeon_E_plasma.fasta ==> Thermoplasmatales_archaeon_E_plasma /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thioalkalivibrio_sulfidiphilus_HL_EbGr7.fasta ==> Thioalkalivibrio_sulfidiphilus_HL_EbGr7 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thioflavicoccus_mobilis.fasta ==> Thioflavicoccus_mobilis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thiogranum_longum.fasta ==> Thiogranum_longum /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thiohalobacter_thiocyanaticus.fasta ==> Thiohalobacter_thiocyanaticus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thiorhodococcus_drewsii_AZ1.fasta ==> Thiorhodococcus_drewsii_AZ1 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Thiorhodococcus_sp._AK35.fasta ==> Thiorhodococcus_sp._AK35 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Tistrella_mobilis.fasta ==> Tistrella_mobilis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Tistrella_mobilis_KA081020_065.fasta ==> Tistrella_mobilis_KA081020_065 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Tolypothrix_campylonemoides_VB511288.fasta ==> Tolypothrix_campylonemoides_VB511288 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Umboniibacter_marinipuniceus.fasta ==> Umboniibacter_marinipuniceus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Verrucosispora_maris_AB_18_032.fasta ==> Verrucosispora_maris_AB_18_032 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Vibrio_lentus.fasta ==> Vibrio_lentus /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Vitreoscilla_stercoraria_DSM_513.fasta ==> Vitreoscilla_stercoraria_DSM_513 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Xanthobacter_autotrophicus_Py2.fasta ==> Xanthobacter_autotrophicus_Py2 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Xanthomonas_translucens_pv._graminis.fasta ==> Xanthomonas_translucens_pv._graminis /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Xenococcus_sp._PCC_7305.fasta ==> Xenococcus_sp._PCC_7305 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Zea_mays.fasta ==> Zea_mays /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Zhouia_amylolytica_AD3.fasta ==> Zhouia_amylolytica_AD3 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Zooshikella_ganghwensis_DSM_15267.fasta ==> Zooshikella_ganghwensis_DSM_15267 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/alpha_proteobacterium_SCGC_AAA076_C03.fasta ==> alpha_proteobacterium_SCGC_AAA076_C03 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/bacterium_DY22613.fasta ==> bacterium_DY22613 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/bacterium_KD52.fasta ==> bacterium_KD52 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/endosymbiont_of_Ridgeia_piscesae.fasta ==> endosymbiont_of_Ridgeia_piscesae /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/gamma_proteobacterium_SCGC_AB_629_P17.fasta ==> gamma_proteobacterium_SCGC_AB_629_P17 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/marine_gamma_proteobacterium_HTCC2080.fasta ==> marine_gamma_proteobacterium_HTCC2080 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/mine_drainage_metagenome.fasta ==> mine_drainage_metagenome /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/unidentified_eubacterium_SCB49.fasta ==> unidentified_eubacterium_SCB49 All references were combined in combined_reference.fasta Starting quast.py for the combined reference... (logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/combined_reference/quast.log) Excluding downloaded references with low genome fraction from further analysis.. Filtered reference(s): /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Flavobacterium_sp._SCGC_AAA160_P02.fasta ==> Flavobacterium_sp._SCGC_AAA160_P02 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Planktomarina_temperata_RCA23.fasta ==> Planktomarina_temperata_RCA23 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/Rhodobacterales_bacterium_HTCC2255.fasta ==> Rhodobacterales_bacterium_HTCC2255 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/alpha_proteobacterium_SCGC_AAA076_C03.fasta ==> alpha_proteobacterium_SCGC_AAA076_C03 /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/quast_downloaded_references/marine_gamma_proteobacterium_HTCC2080.fasta ==> marine_gamma_proteobacterium_HTCC2080 All references were combined in combined_reference.fasta Starting quast.py for the corrected combined reference... (logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/combined_reference/quast.log) Partitioning contigs into bins aligned to each reference.. processing MG1_ets processing MG1_sjw processing MG2_ets processing MG2_sjw processing MG3_ets processing MG3_sjw processing MG5_ets processing MG5_sjw processing MG6_ets processing MG6_sjw processing MG7_ets processing MG7_sjw Starting quast.py for the contigs aligned to Flavobacterium_sp._SCGC_AAA160_P02... (logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Flavobacterium_sp._SCGC_AAA160_P02/quast.log) Starting quast.py for the contigs aligned to Planktomarina_temperata_RCA23... (logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Planktomarina_temperata_RCA23/quast.log) Starting quast.py for the contigs aligned to Rhodobacterales_bacterium_HTCC2255... (logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/Rhodobacterales_bacterium_HTCC2255/quast.log) Starting quast.py for the contigs aligned to alpha_proteobacterium_SCGC_AAA076_C03... (logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/alpha_proteobacterium_SCGC_AAA076_C03/quast.log) Starting quast.py for the contigs aligned to marine_gamma_proteobacterium_HTCC2080... (logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/runs_per_reference/marine_gamma_proteobacterium_HTCC2080/quast.log) Starting quast.py for the contigs not aligned anywhere... (logging to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/not_aligned/quast.log) 2019-04-03 15:46:02 Summarizing results... Drawing # contigs metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/num_contigs.pdf Drawing Largest contig metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Largest_contig.pdf Drawing Total length metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Total_length.pdf Drawing Largest alignment metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Largest_alignment.pdf Drawing Total aligned length metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Total_aligned_length.pdf Drawing Total length (>= 1000 bp) metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Total_length_(ge_1000_bp).pdf Drawing Total length (>= 10000 bp) metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Total_length_(ge_10000_bp).pdf Drawing Total length (>= 50000 bp) metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Total_length_(ge_50000_bp).pdf Drawing # misassemblies metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/num_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG1_ets... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG1_ets_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG1_sjw... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG1_sjw_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG2_ets... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG2_ets_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG2_sjw... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG2_sjw_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG3_ets... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG3_ets_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG3_sjw... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG3_sjw_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG5_ets... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG5_ets_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG5_sjw... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG5_sjw_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG6_ets... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG6_ets_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG6_sjw... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG6_sjw_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG7_ets... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG7_ets_misassemblies.pdf Drawing metaQUAST summary misassemblies plot for MG7_sjw... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/MG7_sjw_misassemblies.pdf Drawing Misassembled contigs length metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Misassembled_contigs_length.pdf Drawing # mismatches per 100 kbp metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/num_mismatches_per_100_kbp.pdf Drawing # indels per 100 kbp metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/num_indels_per_100_kbp.pdf Drawing # N's per 100 kbp metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/num_Ns_per_100_kbp.pdf Drawing Genome fraction (%) metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Genome_fraction.pdf Drawing Duplication ratio metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/Duplication_ratio.pdf Drawing NGA50 metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/NGA50.pdf Drawing LGA50 metaQUAST summary plot... saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/PDF/LGA50.pdf Text versions of reports and plots for each metric (for all references and assemblies) are saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/summary/ Icarus (contig browser) is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/icarus.html Drawing interactive Krona plots... Krona chart for MG1_ets is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG1_ets_taxonomy_chart.html Krona chart for MG1_sjw is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG1_sjw_taxonomy_chart.html Krona chart for MG2_ets is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG2_ets_taxonomy_chart.html Krona chart for MG2_sjw is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG2_sjw_taxonomy_chart.html Krona chart for MG3_ets is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG3_ets_taxonomy_chart.html Krona chart for MG3_sjw is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG3_sjw_taxonomy_chart.html Krona chart for MG5_ets is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG5_ets_taxonomy_chart.html Krona chart for MG5_sjw is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG5_sjw_taxonomy_chart.html Krona chart for MG6_ets is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG6_ets_taxonomy_chart.html Krona chart for MG6_sjw is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG6_sjw_taxonomy_chart.html Krona chart for MG7_ets is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG7_ets_taxonomy_chart.html Krona chart for MG7_sjw is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/MG7_sjw_taxonomy_chart.html Summary Krona chart is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/krona_charts/summary_taxonomy_chart.html Extended version of HTML-report (for all references and assemblies) is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/report.html MetaQUAST finished. Log is saved to /home/sam/analyses/20190403_metagenomics_pgen_metaquast_comparisons/quast_results/results_2019_04_03_08_23_17/metaquast.log Finished: 2019-04-03 15:46:15 Elapsed time: 7:22:58.087088 Total NOTICEs: 11; WARNINGs: 1; non-fatal ERRORs: 10 Thank you for using QUAST!