Merge pull request #341 from erikrikarddaniel/magmap

testdata/bac120_metadata.tsv

@@ -0,0 +1,11 @@
+accession	ambiguous_bases	checkm_completeness	checkm_contamination	checkm_marker_count	checkm_marker_lineage	checkm_marker_set_count	checkm_strain_heterogeneity	coding_bases	coding_density	contig_count	gc_count	gc_percentage	genome_size	gtdb_genome_representative	gtdb_representative	gtdb_taxonomy	gtdb_type_designation	gtdb_type_designation_sources	gtdb_type_species_of_genus	l50_contigs	l50_scaffolds	longest_contig	longest_scaffold	lsu_23s_contig_len	lsu_23s_count	lsu_23s_length	lsu_23s_query_id	lsu_5s_contig_len	lsu_5s_count	lsu_5s_length	lsu_5s_query_id	lsu_silva_23s_blast_align_len	lsu_silva_23s_blast_bitscore	lsu_silva_23s_blast_evalue	lsu_silva_23s_blast_perc_identity	lsu_silva_23s_blast_subject_id	lsu_silva_23s_taxonomy	mean_contig_length	mean_scaffold_length	mimag_high_quality	mimag_low_quality	mimag_medium_quality	n50_contigs	n50_scaffolds	ncbi_assembly_level	ncbi_assembly_name	ncbi_assembly_type	ncbi_bioproject	ncbi_biosample	ncbi_contig_count	ncbi_contig_n50	ncbi_country	ncbi_date	ncbi_genbank_assembly_accession	ncbi_genome_category	ncbi_genome_representation	ncbi_isolate	ncbi_isolation_source	ncbi_lat_lon	ncbi_molecule_count	ncbi_ncrna_count	ncbi_organism_name	ncbi_protein_count	ncbi_refseq_category	ncbi_rrna_count	ncbi_scaffold_count	ncbi_scaffold_l50	ncbi_scaffold_n50	ncbi_scaffold_n75	ncbi_scaffold_n90	ncbi_seq_rel_date	ncbi_spanned_gaps	ncbi_species_taxid	ncbi_ssu_count	ncbi_strain_identifiers	ncbi_submitter	ncbi_taxid	ncbi_taxonomy	ncbi_taxonomy_unfiltered	ncbi_total_gap_length	ncbi_total_length	ncbi_translation_table	ncbi_trna_count	ncbi_type_material_designation	ncbi_ungapped_length	ncbi_unspanned_gaps	ncbi_wgs_master	protein_count	scaffold_count	ssu_contig_len	ssu_count	ssu_gg_blast_align_len	ssu_gg_blast_bitscore	ssu_gg_blast_evalue	ssu_gg_blast_perc_identity	ssu_gg_blast_subject_id	ssu_gg_taxonomy	ssu_length	ssu_query_id	ssu_silva_blast_align_len	ssu_silva_blast_bitscore	ssu_silva_blast_evalue	ssu_silva_blast_perc_identity	ssu_silva_blast_subject_id	ssu_silva_taxonomy	total_gap_length	trna_aa_count	trna_count	trna_selenocysteine_count
+GB_GCA_002687715.1	98	75.31	0	143	k__Bacteria (UID2565)	88	0	5376616	92.3442251882955	288	3903627	67.0465360130465	5822363	GB_GCA_002687715.1	t	d__Bacteria;p__Planctomycetota;c__GCA-002687715;o__GCA-002687715;f__GCA-002687715;g__GCA-2687715;s__GCA-2687715 sp002687715	not type material	none	f	73	73	74926	74926	none	0	none	none	none	0	none	none	none	none	none	none	none	none	20216	20216	f	f	t	27159	27159	Contig	ASM268771v1	na	PRJNA391943	SAMN07619727	288	27159	none	2017-10-24	GCA_002687715.1	derived from metagenome	full	ARS1434	none	none	0	0	Planctomycetes bacterium	4575	na	0	none	none	none	none	none	2017/10/24	0	2026780	0	ARS1434	Tara Oceans Consortium	2026780	d__Bacteria;p__Planctomycetes;c__;o__;f__;g__;s__	d__Bacteria;x__PVC group;p__Planctomycetes;x__unclassified Planctomycetes;s__Planctomycetes bacterium	0	5822363	11	29	none	5822363	0	NZBC00000000.1	4663	288	none	0	none	none	none	none	none	none	none	none	none	none	none	none	none	none	0	14	29	1
+GB_GCA_002688175.1	15	79.43	3.24	544	c__Gammaproteobacteria (UID4267)	284	0	2356507	90.4275620394933	84	1384405	53.1248536999615	2605961	GB_GCA_002688175.1	t	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__GCA-002729875;s__GCA-002729875 sp002688175	not type material	none	f	20	20	106947	106947	none	0	none	none	none	0	none	none	none	none	none	none	none	none	31023	31023	f	f	t	41005	41005	Contig	ASM268817v1	na	PRJNA391943	SAMN07618542	84	41005	none	2017-10-24	GCA_002688175.1	derived from metagenome	full	ARS1279	none	none	0	1	Chromatiales bacterium	2421	na	1	none	none	none	none	none	2017/10/24	0	2026725	1	ARS1279	Tara Oceans Consortium	2026725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__;g__;s__	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;x__unclassified Chromatiales;s__Chromatiales bacterium	0	2605961	11	36	none	2605961	0	NZCC00000000.1	2461	84	6094	1	none	none	none	none	none	none	939	NZCC01000038.1	927	1400	0	94.067	AQTV01000144.6373.7900	Bacteria;Poribacteria;Candidatus Poribacteria sp. WGA-4E	0	18	36	0
+GB_GCA_002688505.1	2	77.08	0	136	k__Bacteria (UID2495)	80	0	243051	89.6288374665806	1	41722	15.3857500562372	271175	GB_GCA_002688505.1	t	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Stammera;s__Stammera capleta	not type material	none	f	1	1	271175	271175	271175	1	2926	CP024013.1	271175	1	100	CP024013.1	2918	5389	0	100	CP024013.86157.89078	Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Morganellaceae;Candidatus Purcelliella;Enterobacteriaceae bacterium NZ1215	271175	271175	f	f	t	271175	271175	Complete Genome	ASM268850v1	na	PRJNA413589	SAMN07758087	none	none	none	2017-10-24	GCA_002688505.1	derived from metagenome	full	NZ1215	none	none	1	none	Candidatus Stammera capleta	0	na	none	none	none	none	none	none	2017/10/24	0	2608262	none	NZ1215	University of Luxembourg	2608262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Candidatus Stammera;s__Candidatus Stammera capleta	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;x__Enterobacteriaceae incertae sedis;x__ant, tsetse, mealybug, aphid, etc. endosymbionts;g__Candidatus Stammera;s__Candidatus Stammera capleta	0	271175	none	none	none	271175	0	none	257	1	271175	1	none	none	none	none	none	none	1606	CP024013.1	1391	1580	0	87.419	AP018160.219472.221029	Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Morganellaceae;endosymbionts;endosymbiont of Pachyrhynchus infernalis	0	20	29	0
+GB_GCA_002689725.1	5000	56.43	1.1	147	k__Bacteria (UID2495)	91	0	777598	95.0823841577863	62	246230	30.293486217651	817815	GB_GCA_002169685.1	f	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__TMED211;s__TMED211 sp002169685	not type material	none	f	22	22	33046	33046	none	0	none	none	none	0	none	none	none	none	none	none	none	none	13190	13190	f	f	t	13554	13554	Contig	ASM268972v1	na	PRJNA391943	SAMN07620281	62	13554	none	2017-10-24	GCA_002689725.1	derived from metagenome	full	MED639	none	none	0	0	Rickettsiales bacterium	870	na	0	none	none	none	none	none	2017/10/24	0	2026788	0	MED639	Tara Oceans Consortium	2026788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__;g__;s__	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;x__unclassified Rickettsiales;s__Rickettsiales bacterium	0	817815	11	22	none	817815	0	NZHR00000000.1	894	62	none	0	none	none	none	none	none	none	none	none	none	none	none	none	none	none	0	15	21	0
+GB_GCA_002690175.1	8013	90.29	5.21	171	k__Bacteria (UID1453)	117	55.56	1761769	94.5797413908803	82	831940	44.8552639453589	1862734	GB_GCA_002380145.1	f	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__MedAcidi-G2A;s__MedAcidi-G2A sp002380145	not type material	none	f	16	16	139868	139868	28425	1	367	NZDQ01000008.1	28425	1	110	NZDQ01000008.1	367	678	0	100	AACY020104695.1521.4600	Bacteria;Actinobacteriota;Acidimicrobiia;Microtrichales;uncultured;marine metagenome	22716	22716	f	f	t	38545	38545	Contig	ASM269017v1	na	PRJNA391943	SAMN07618149	82	38545	none	2017-10-24	GCA_002690175.1	derived from metagenome	full	ARS1034	none	none	0	0	Acidimicrobiaceae bacterium	1861	na	2	none	none	none	none	none	2017/10/24	0	2024894	0	ARS1034	Tara Oceans Consortium	2024894	d__Bacteria;p__Actinobacteria;c__Acidimicrobiia;o__Acidimicrobiales;f__Acidimicrobiaceae;g__;s__	d__Bacteria;x__Terrabacteria group;p__Actinobacteria;c__Acidimicrobiia;o__Acidimicrobiales;f__Acidimicrobiaceae;x__unclassified Acidimicrobiaceae;s__Acidimicrobiaceae bacterium	0	1862734	11	35	none	1862734	0	NZDQ00000000.1	1890	82	none	0	none	none	none	none	none	none	none	none	none	none	none	none	none	none	0	17	34	0
+RS_GCF_004294725.1	0	100	0.12	1312	g__Klebsiella (UID5140)	336	0	4945546	88.1737235298543	115	3216028	57.3382926245697	5608866	RS_GCF_000742135.1	f	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella pneumoniae	not type material	none	f	10	10	498595	498595	2798	1	2736	NZ_SHTY01000072.1	498595	3	110	NZ_SHTY01000001.1	2736	5053	0	100	CP033242.5421784.5424706	Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Klebsiella;Klebsiella pneumoniae	48772	48772	f	f	t	176018	176018	Contig	ASM429472v1	na	PRJNA224116	SAMN10956213	115	176018	none	2019-02-24	GCA_004294725.1	none	full	none	none	none	0	7	Klebsiella pneumoniae	none	na	6	none	none	none	none	none	2019/02/24	0	573	2	MGF011	Deakin University	573	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella pneumoniae	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella pneumoniae	0	5608866	11	77	none	5608866	0	SHTY00000000.1	5391	115	980	2	none	none	none	none	none	none	978	NZ_SHTY01000094.1	978	1807	0	100	CP033396.457925.459474	Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Klebsiella;Klebsiella pneumoniae	0	20	77	1
+RS_GCF_004296275.1	0	98.41	0.61	1193	g__Acinetobacter (UID4685)	254	0	3432027	88.3869432496935	203	1517070	39.069966522936	3882957	RS_GCF_009759685.1	f	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter;s__Acinetobacter baumannii	not type material	none	f	19	19	215562	215562	1994	6	1671	NZ_SGSF01000146.1	1994	2	111	NZ_SGSF01000146.1	1671	3086	0	100	CU459141.489578.492479	Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Acinetobacter;Acinetobacter baumannii	19127	19127	f	f	t	55522	55522	Contig	ASM429627v1	na	PRJNA224116	SAMN10910649	203	55522	none	2019-02-18	GCA_004296275.1	none	full	none	none	none	0	1	Acinetobacter baumannii	none	na	13	none	none	none	none	none	2019/02/18	0	470	3	H350	UNAM	470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter;s__Acinetobacter baumannii	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter;x__Acinetobacter calcoaceticus/baumannii complex;s__Acinetobacter baumannii	0	3882957	11	65	none	3882957	0	SGSF00000000.1	3762	203	52379	2	none	none	none	none	none	none	1532	NZ_SGSF01000139.1	1532	2830	0	100	CP012006.3900324.3901867	Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Acinetobacter;Acinetobacter baumannii	0	20	65	0
+RS_GCF_004296495.1	0	64.89	0	136	k__Bacteria (UID2495)	80	0	186535	93.1203698156912	1	30680	15.3158010343657	200316	RS_GCF_004296495.1	t	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Nardonella;s__Nardonella dryophthoridicola	not type material	none	f	1	1	200316	200316	200316	1	2927	NZ_AP018161.1	none	0	none	none	2927	5406	0	100	AP018161.195153.198095	Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Morganellaceae;Candidatus Purcelliella;endosymbiont of Rhynchophorus ferrugineus	200316	200316	f	f	t	200316	200316	Complete Genome	ASM429649v1	na	PRJNA224116	SAMD00080335	none	none	none	2017-10-21	GCA_004296495.1	none	full	NARRFE1	none	none	1	0	endosymbiont of Rhynchophorus ferrugineus	none	na	3	none	none	none	none	none	2017/10/21	0	1971485	1	NARRFE1	The Open University of Japan	1972133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__;f__;g__Candidatus Nardonella;s__Candidatus Nardonella dryophthoridicola	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;x__Gammaproteobacteria incertae sedis;g__Candidatus Nardonella;s__Candidatus Nardonella dryophthoridicola;x__endosymbiont of Rhynchophorus ferrugineus	0	200316	11	28	none	200316	0	none	198	1	200316	1	none	none	none	none	none	none	1603	NZ_AP018161.1	1603	2961	0	100	AP018161.193362.194973	Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Morganellaceae;endosymbionts;endosymbiont of Rhynchophorus ferrugineus	0	18	24	0
+RS_GCF_004296555.1	0	99.41	0	675	o__Thiotrichales (UID4410)	243	0	1611687	88.6965351002708	101	586098	32.2549364915139	1817080	RS_GCF_000008985.1	f	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella;s__Francisella tularensis	not type material	none	f	17	17	113051	113051	5559	1	2878	NZ_SGWP01000064.1	5559	2	110	NZ_SGWP01000064.1	2878	5315	0	100	GU073995.1.2992	Bacteria;Proteobacteria;Gammaproteobacteria;Francisellales;Francisellaceae;Francisella;Francisella tularensis subsp. mediasiatica FSC147	17990	17990	t	f	f	35350	35350	Contig	ASM429655v1	na	PRJNA224116	SAMN10924158	101	35350	none	2019-02-19	GCA_004296555.1	none	full	none	none	none	0	1	Francisella tularensis subsp. mediasiatica	none	na	4	none	none	none	none	none	2019/02/19	0	263	1	SCPM-O-B-7175(A-554)	SRCAMB	135248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Francisellaceae;g__Francisella;s__Francisella tularensis	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Francisellaceae;g__Francisella;s__Francisella tularensis;sb__Francisella tularensis subsp. mediasiatica	0	1817080	11	34	none	1817080	0	SGWP00000000.1	2037	101	5559	1	none	none	none	none	none	none	1523	NZ_SGWP01000064.1	1521	2809	0	100	CP000915.1823129.1824652	Bacteria;Proteobacteria;Gammaproteobacteria;Francisellales;Francisellaceae;Francisella;Francisella tularensis subsp. mediasiatica FSC147	0	20	34	0
+RS_GCF_004298225.1	0	100	0.04	1169	f__Enterobacteriaceae (UID5139)	340	0	4196472	87.8610828812011	97	2492282	52.1806401580484	4776258	RS_GCF_000006945.2	f	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella enterica	not type material	none	f	19	19	300074	300074	none	0	none	none	45529	7	355	NZ_SIIC01000038.1	none	none	none	none	none	none	49239	49239	f	f	t	74482	74482	Contig	ASM429822v1	na	PRJNA224116	SAMN10887076	97	74482	none	2019-02-25	GCA_004298225.1	none	full	none	none	none	0	11	Salmonella enterica subsp. enterica serovar Typhimurium	none	na	19	none	none	none	none	none	2019/02/25	0	28901	6	3160	Agriculture and Agri-Food Canada	90371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella enterica	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella;s__Salmonella enterica;sb__Salmonella enterica subsp. enterica;x__Salmonella enterica subsp. enterica serovar Typhimurium	0	4776258	11	75	none	4776258	0	SIIC00000000.1	4496	97	none	0	none	none	none	none	none	none	none	none	none	none	none	none	none	none	0	18	75	1