Outputs

Below are all the outputs when using the taxons table example

📂taxons
 ┣ 📂download
 ┃ ┣ 📂GCF_000008865.2
 ┃ ┃ ┗ 📜GCF_000008865.2_ASM886v2_genomic.fna.gz
 ┃ ┣ 📂GCF_000013425.1
 ┃ ┃ ┗ 📜GCF_000013425.1_ASM1342v1_genomic.fna.gz
 ┃ ┣ 📂GCF_003812505.1
 ┃ ┃ ┗ 📜GCF_003812505.1_ASM381250v1_genomic.fna.gz
 ┃ ┗ 📜.snakemake_timestamp
 ┣ 📂logs
 ┃ ┣ 📂taxons
 ┃ ┃ ┣ 📜1290.log
 ┃ ┃ ┣ 📜562.log
 ┃ ┃ ┗ 📜staphylococcus_aureus.log
 ┃ ┣ 📜archive.log
 ┃ ┣ 📜lineage.log
 ┃ ┣ 📜rsync.log
 ┃ ┗ 📜unzip.log
 ┣ 📜archive.zip
 ┣ 📜assembly_finder.log
 ┣ 📜assembly_summary.tsv
 ┣ 📜config.yaml
 ┗ 📜taxonomy.tsv

Download directory

Downloaded files (genomic.fna.gz by default) are located in the download directory as shown below

 ┣ 📂download
 ┃ ┣ 📂GCF_000008865.2
 ┃ ┃ ┗ 📜GCF_000008865.2_ASM886v2_genomic.fna.gz
 ┃ ┣ 📂GCF_000013425.1
 ┃ ┃ ┗ 📜GCF_000013425.1_ASM1342v1_genomic.fna.gz
 ┃ ┣ 📂GCF_003812505.1
 ┃ ┃ ┗ 📜GCF_003812505.1_ASM381250v1_genomic.fna.gz

Assembly summary

Table with assembly informations such as assembly level, reference category, checkM and BUSCO completeness, sequencing technology, number of contigs ...

taxon	accession	current_accession	paired_accession	source_database	annotation_info.method	annotation_info.name	annotation_info.pipeline	annotation_info.provider	annotation_info.release_date	annotation_info.software_version	annotation_info.stats.gene_counts.non_coding	annotation_info.stats.gene_counts.protein_coding	annotation_info.stats.gene_counts.pseudogene	annotation_info.stats.gene_counts.total	assembly_level	assembly_method	assembly_name	assembly_status	assembly_type	bioproject_accession	biosample.accession	biosample.bioprojects	biosample.description.organism_name	biosample.description.tax_id	biosample.description.title	biosample.last_updated	biosample.models	biosample.owner.contacts	biosample.owner.name	biosample.package	biosample.publication_date	biosample.status.status	biosample.status.when	biosample.submission_date	paired_assembly.accession	paired_assembly.annotation_name	paired_assembly.status	refseq_category	release_date	sequencing_tech	submitter	contig_l50	contig_n50	gc_count	gc_percent	genome_coverage	number_of_component_sequences	number_of_contigs	number_of_scaffolds	scaffold_l50	scaffold_n50	total_number_of_chromosomes	total_sequence_length	total_ungapped_length	average_nucleotide_identity.best_ani_match.ani	average_nucleotide_identity.best_ani_match.assembly	average_nucleotide_identity.best_ani_match.assembly_coverage	average_nucleotide_identity.best_ani_match.category	average_nucleotide_identity.best_ani_match.organism_name	average_nucleotide_identity.best_ani_match.type_assembly_coverage	average_nucleotide_identity.category	average_nucleotide_identity.comment	average_nucleotide_identity.match_status	average_nucleotide_identity.submitted_ani_match.ani	average_nucleotide_identity.submitted_ani_match.assembly	average_nucleotide_identity.submitted_ani_match.assembly_coverage	average_nucleotide_identity.submitted_ani_match.category	average_nucleotide_identity.submitted_ani_match.organism_name	average_nucleotide_identity.submitted_ani_match.type_assembly_coverage	average_nucleotide_identity.submitted_organism	average_nucleotide_identity.submitted_species	average_nucleotide_identity.taxonomy_check_status	checkm_info.checkm_marker_set	checkm_info.checkm_marker_set_rank	checkm_info.checkm_species_tax_id	checkm_info.checkm_version	checkm_info.completeness	checkm_info.completeness_percentile	checkm_info.contamination	infraspecific_names.strain	organism_name	tax_id	path
staphylococcus_aureus	GCF_000013425.1	GCF_000013425.1	GCA_000013425.1	SOURCE_DATABASE_REFSEQ	na	Annotation submitted by NCBI RefSeq	na	NCBI RefSeq	2016-08-03	na	75	2767	30	2872	Complete Genome	na	ASM1342v1	current	haploid	PRJNA237	SAMN02604235	[{'accession': 'PRJNA237'}]	Staphylococcus aureus subsp. aureus NCTC 8325	93061	Sample from Staphylococcus aureus subsp. aureus NCTC 8325	2015-05-18T13:21:01.110	['Generic']	na	NCBI	Generic.1.0	2014-01-30T15:13:19.920	live	2014-01-30T15:13:19.920	2014-01-30T15:13:19.920	GCA_000013425.1	Annotation submitted by University of Oklahoma Health Sciences Center	current	reference genome	2006-02-13	na	University of Oklahoma Health Sciences Center	1	2821361	927332	33	na	1	1	1	1	2821361	1	2821361	2821361	99.94	GCA_006094915.1	96.32	type	Staphylococcus aureus	97.66	category_na	na	species_match	99.94	GCA_006094915.1	96.32	type	Staphylococcus aureus	97.66	Staphylococcus aureus subsp. aureus NCTC 8325	Staphylococcus aureus	OK	Staphylococcus aureus	species	1280	v1.2.2	97.59	19.683367	0.39	NCTC 8325	Staphylococcus aureus subsp. aureus NCTC 8325	93061	/path/to/genome/GCF_000013425.1/GCF_000013425.1_ASM1342v1_genomic.fna.gz
562	GCF_000008865.2	GCF_000008865.2	GCA_000008865.2	SOURCE_DATABASE_REFSEQ	na	Annotation submitted by NCBI RefSeq	na	NCBI RefSeq	2021-02-12	na	126	5155	136	5417	Complete Genome	na	ASM886v2	current	haploid	PRJNA226	SAMN01911278	[{'accession': 'PRJNA226'}]	Escherichia coli O157:H7 str. Sakai	386585	Bacterial, clinical or host-associated sample for Escherichia coli O157:H7 str. SAKAI (EHEC)	2019-05-23T15:25:40.989	['Pathogen.ba-cl']	[{}]	ATCC	Pathogen.cl.1.0	2013-02-05T00:00:00.000	live	2014-11-20T09:44:57	2013-02-05T09:09:06.203	GCA_000008865.2	Annotation submitted by GIRC	current	reference genome	2018-06-08	na	GIRC	1	5498578	2824389	50.5	na	3	3	3	1	5498578	3	5594605	5594605	99.97	GCA_001281725.1	94.32	claderef	Escherichia coli	99.57	category_na	na	species_match	99.97	GCA_001281725.1	94.32	claderef	Escherichia coli	99.57	Escherichia coli O157:H7 str. Sakai	Escherichia coli	OK	Escherichia coli	species	562	v1.2.2	99.51	92.85564	0.15	Sakai substr. RIMD 0509952	Escherichia coli O157:H7 str. Sakai	386585	/path/to/genome/GCF_000008865.2/GCF_000008865.2_ASM886v2_genomic.fna.gz
1290	GCF_003812505.1	GCF_003812505.1	GCA_003812505.1	SOURCE_DATABASE_REFSEQ	Best-placed reference protein set; GeneMarkS-2+	GCF_003812505.1-RS_2024_03_28	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)	NCBI RefSeq	2024-03-28	6.7	85	2142	35	2262	Complete Genome	SMRT v. 2.3.0, HGAP v. 3.0	ASM381250v1	current	haploid	PRJNA231221	SAMN10163251	[{'accession': 'PRJNA231221'}]	Staphylococcus hominis	1290	Pathogen: clinical or host-associated sample from Staphylococcus hominis	2019-05-14T13:08:20.304	['Pathogen.cl']	[{}]	US Food and Drug Administration	Pathogen.cl.1.0	2018-10-02T00:00:00.000	live	2018-10-02T12:23:11.101	2018-10-02T12:23:11.100	GCA_003812505.1	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)	current	representative genome	2018-11-21	PacBio; Illumina	US Food and Drug Administration	1	2220494	713682	31.5	19.6x	3	3	3	1	2220494	3	2257431	2257431	99.99	GCA_900458635.1	98.99	type	Staphylococcus hominis	99.01	category_na	na	species_match	99.99	GCA_900458635.1	98.99	type	Staphylococcus hominis	99.01	Staphylococcus hominis	Staphylococcus hominis	OK	Staphylococcus hominis	species	1290	v1.2.2	90.97	47.945206	2.63	FDAARGOS_575	Staphylococcus hominis	1290	/path/to/genome/GCF_003812505.1/GCF_003812505.1_ASM381250v1_genomic.fna.gz

Note

Some columns were removed for visual clarity

Taxonomy

Table containing the full lineage from kingdom to species of each tax_id

accession	tax_id	name	rank	kingdom	phylum	class	order	family	genus	species
GCF_000013425.1	93061	Staphylococcus aureus subsp. aureus NCTC 8325	strain	Bacteria	Bacillota	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	Staphylococcus aureus
GCF_000008865.2	386585	Escherichia coli O157:H7 str. Sakai	strain	Bacteria	Pseudomonadota	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	Escherichia coli
GCF_003812505.1	1290	Staphylococcus hominis	species	Bacteria	Bacillota	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	Staphylococcus hominis