[2024-01-24 12:44:39,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:39,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:39,974] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3c6a89f-2a39-4cfb-b45c-d9108588615e/dqc_reference
[2024-01-24 12:44:41,237] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:41,237] [INFO] Task started: Prodigal
[2024-01-24 12:44:41,238] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e037e90-7620-441b-8d76-1c57c9fe3428/GCF_002252445.1_ASM225244v1_genomic.fna.gz | prodigal -d GCF_002252445.1_ASM225244v1_genomic.fna/cds.fna -a GCF_002252445.1_ASM225244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:54,560] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:54,560] [INFO] Task started: HMMsearch
[2024-01-24 12:44:54,560] [INFO] Running command: hmmsearch --tblout GCF_002252445.1_ASM225244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3c6a89f-2a39-4cfb-b45c-d9108588615e/dqc_reference/reference_markers.hmm GCF_002252445.1_ASM225244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:54,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:54,952] [INFO] Found 6/6 markers.
[2024-01-24 12:44:54,993] [INFO] Query marker FASTA was written to GCF_002252445.1_ASM225244v1_genomic.fna/markers.fasta
[2024-01-24 12:44:54,994] [INFO] Task started: Blastn
[2024-01-24 12:44:54,994] [INFO] Running command: blastn -query GCF_002252445.1_ASM225244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c6a89f-2a39-4cfb-b45c-d9108588615e/dqc_reference/reference_markers.fasta -out GCF_002252445.1_ASM225244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:55,748] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:55,752] [INFO] Selected 16 target genomes.
[2024-01-24 12:44:55,752] [INFO] Target genome list was writen to GCF_002252445.1_ASM225244v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:55,758] [INFO] Task started: fastANI
[2024-01-24 12:44:55,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e037e90-7620-441b-8d76-1c57c9fe3428/GCF_002252445.1_ASM225244v1_genomic.fna.gz --refList GCF_002252445.1_ASM225244v1_genomic.fna/target_genomes.txt --output GCF_002252445.1_ASM225244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:10,913] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:10,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3c6a89f-2a39-4cfb-b45c-d9108588615e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:10,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3c6a89f-2a39-4cfb-b45c-d9108588615e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:10,926] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:10,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:10,926] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Brucella thiophenivorans	strain=DSM 7216	GCA_002252445.1	571255	571255	type	True	100.0	1419	1421	95	conclusive
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	83.9904	925	1421	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	83.4085	909	1421	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_003049685.2	571256	571256	type	True	83.4029	928	1421	95	below_threshold
Brucella grignonensis	strain=OgA9a	GCA_002252505.1	94627	94627	type	True	83.1844	917	1421	95	below_threshold
[Ochrobactrum] quorumnocens	strain=A44	GCA_002278035.1	271865	271865	type	True	82.9164	968	1421	95	below_threshold
Brucella rhizosphaerae	strain=PR17	GCA_002252475.1	571254	571254	type	True	82.576	922	1421	95	below_threshold
Brucella gallinifaecis	strain=ISO 196	GCA_006476605.1	215590	215590	type	True	82.2209	752	1421	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.7581	260	1421	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.758	260	1421	95	below_threshold
Phyllobacterium zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	76.9849	190	1421	95	below_threshold
Aquamicrobium zhengzhouense	strain=cd-1	GCA_016124105.1	2781738	2781738	type	True	76.8777	107	1421	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	76.5166	172	1421	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	76.474	134	1421	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	76.3988	127	1421	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	76.0281	127	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:10,928] [INFO] DFAST Taxonomy check result was written to GCF_002252445.1_ASM225244v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:10,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:10,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:10,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3c6a89f-2a39-4cfb-b45c-d9108588615e/dqc_reference/checkm_data
[2024-01-24 12:45:10,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:10,982] [INFO] Task started: CheckM
[2024-01-24 12:45:10,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002252445.1_ASM225244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002252445.1_ASM225244v1_genomic.fna/checkm_input GCF_002252445.1_ASM225244v1_genomic.fna/checkm_result
[2024-01-24 12:45:52,240] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:52,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:52,262] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:52,262] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:52,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002252445.1_ASM225244v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:52,263] [INFO] Task started: Blastn
[2024-01-24 12:45:52,263] [INFO] Running command: blastn -query GCF_002252445.1_ASM225244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c6a89f-2a39-4cfb-b45c-d9108588615e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002252445.1_ASM225244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:53,246] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:53,249] [INFO] Selected 12 target genomes.
[2024-01-24 12:45:53,249] [INFO] Target genome list was writen to GCF_002252445.1_ASM225244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:53,260] [INFO] Task started: fastANI
[2024-01-24 12:45:53,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e037e90-7620-441b-8d76-1c57c9fe3428/GCF_002252445.1_ASM225244v1_genomic.fna.gz --refList GCF_002252445.1_ASM225244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002252445.1_ASM225244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:05,219] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:05,233] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:05,233] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002252445.1	s__Ochrobactrum_A thiophenivorans	100.0	1419	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002252525.1	s__Ochrobactrum_A pseudogrignonensis	84.0107	924	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.50	96.15	0.90	0.81	34	-
GCF_018798825.1	s__Ochrobactrum_A sp018798825	83.5028	941	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049685.1	s__Ochrobactrum_A pituitosa	83.3984	927	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	98.27	97.05	0.91	0.82	14	-
GCF_002252505.1	s__Ochrobactrum_A grignonensis	83.1748	918	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	99.78	99.78	1.00	1.00	2	-
GCF_002278035.1	s__Ochrobactrum_A quorumnocens	82.9104	967	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.19	96.78	0.85	0.82	5	-
GCF_014397025.1	s__Ochrobactrum_A sp014397025	82.8997	859	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004368705.1	s__Ochrobactrum_A sp004368705	82.7544	913	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252475.1	s__Ochrobactrum_A rhizosphaerae	82.576	922	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476605.1	s__Ochrobactrum_A gallinifaecis	82.2209	752	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550135.1	s__Ochrobactrum_B haematophila_B	79.8171	659	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470195.1	s__Ochrobactrum sp900470195	79.8028	645	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.22	97.63	0.95	0.85	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:05,235] [INFO] GTDB search result was written to GCF_002252445.1_ASM225244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:05,235] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:05,241] [INFO] DFAST_QC result json was written to GCF_002252445.1_ASM225244v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:05,241] [INFO] DFAST_QC completed!
[2024-01-24 12:46:05,241] [INFO] Total running time: 0h1m25s