[2024-01-24 13:48:59,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,784] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d59b46c-3936-40c9-b73f-21d3499ad1ed/dqc_reference
[2024-01-24 13:49:01,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,057] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg96a2d1d5-ab7a-4ea1-be59-05919cbdd4b2/GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna.gz | prodigal -d GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/cds.fna -a GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:16,517] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:16,517] [INFO] Task started: HMMsearch
[2024-01-24 13:49:16,517] [INFO] Running command: hmmsearch --tblout GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d59b46c-3936-40c9-b73f-21d3499ad1ed/dqc_reference/reference_markers.hmm GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:16,797] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:16,798] [INFO] Found 6/6 markers.
[2024-01-24 13:49:16,848] [INFO] Query marker FASTA was written to GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/markers.fasta
[2024-01-24 13:49:16,848] [INFO] Task started: Blastn
[2024-01-24 13:49:16,849] [INFO] Running command: blastn -query GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d59b46c-3936-40c9-b73f-21d3499ad1ed/dqc_reference/reference_markers.fasta -out GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:17,498] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:17,503] [INFO] Selected 26 target genomes.
[2024-01-24 13:49:17,503] [INFO] Target genome list was writen to GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:49:17,514] [INFO] Task started: fastANI
[2024-01-24 13:49:17,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg96a2d1d5-ab7a-4ea1-be59-05919cbdd4b2/GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna.gz --refList GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/target_genomes.txt --output GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:41,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:41,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d59b46c-3936-40c9-b73f-21d3499ad1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:41,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d59b46c-3936-40c9-b73f-21d3499ad1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:41,960] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:41,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:41,961] [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
Chryseobacterium populi	strain=CF314	GCA_000282115.1	1144316	1144316	type	True	100.0	1439	1444	95	conclusive
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	81.2088	784	1444	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	81.1155	785	1444	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	81.1034	785	1444	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	81.0379	822	1444	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	80.8775	824	1444	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	80.8765	794	1444	95	below_threshold
Chryseobacterium gleum	strain=NCTC11432	GCA_900636535.1	250	250	type	True	80.8374	761	1444	95	below_threshold
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	80.8296	764	1444	95	below_threshold
Chryseobacterium piperi	strain=CTM	GCA_000737775.1	558152	558152	type	True	80.8102	743	1444	95	below_threshold
Chryseobacterium piperi	strain=ATCC BAA-1782	GCA_002285635.2	558152	558152	type	True	80.7752	753	1444	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	80.7422	770	1444	95	below_threshold
Chryseobacterium paridis	strain=YIM B02567	GCA_016595215.1	2800328	2800328	type	True	80.7091	786	1444	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.7085	679	1444	95	below_threshold
Chryseobacterium soli	strain=DSM 19298	GCA_000737705.1	445961	445961	type	True	80.6767	785	1444	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	80.5895	708	1444	95	below_threshold
Chryseobacterium angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	80.5858	753	1444	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.5016	724	1444	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.468	811	1444	95	below_threshold
Chryseobacterium endalhagicum	strain=L7	GCA_016745235.1	2797638	2797638	type	True	80.4669	772	1444	95	below_threshold
Chryseobacterium luteum	strain=DSM 18605	GCA_000737785.1	421531	421531	type	True	80.463	746	1444	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	80.4031	661	1444	95	below_threshold
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	80.3368	677	1444	95	below_threshold
Chryseobacterium taichungense	strain=DSM 17453	GCA_900109935.1	295069	295069	type	True	80.0747	637	1444	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.6509	509	1444	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:41,975] [INFO] DFAST Taxonomy check result was written to GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:49:41,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:41,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:41,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d59b46c-3936-40c9-b73f-21d3499ad1ed/dqc_reference/checkm_data
[2024-01-24 13:49:41,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:42,019] [INFO] Task started: CheckM
[2024-01-24 13:49:42,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/checkm_input GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/checkm_result
[2024-01-24 13:50:31,016] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:31,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:31,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:31,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:31,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/markers.fasta)
[2024-01-24 13:50:31,032] [INFO] Task started: Blastn
[2024-01-24 13:50:31,033] [INFO] Running command: blastn -query GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d59b46c-3936-40c9-b73f-21d3499ad1ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:31,918] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:31,922] [INFO] Selected 22 target genomes.
[2024-01-24 13:50:31,922] [INFO] Target genome list was writen to GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:31,937] [INFO] Task started: fastANI
[2024-01-24 13:50:31,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg96a2d1d5-ab7a-4ea1-be59-05919cbdd4b2/GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna.gz --refList GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:52,204] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:52,224] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:52,225] [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_000282115.1	s__Chryseobacterium populi	100.0	1439	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCF_008386505.1	s__Chryseobacterium sediminis	81.1213	783	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_900100115.1	s__Chryseobacterium soldanellicola	81.12	783	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111495.1	s__Chryseobacterium wanjuense	81.0304	823	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903969135.1	s__Chryseobacterium sp900156935	81.0179	808	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.11	99.11	0.93	0.93	2	-
GCF_001045455.1	s__Chryseobacterium sp001045455	80.8922	701	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	80.8853	823	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_008274625.1	s__Chryseobacterium sp008274625	80.869	794	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003729955.1	s__Chryseobacterium daecheongense	80.7875	762	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002285635.2	s__Chryseobacterium piperi	80.7689	755	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016595215.1	s__Chryseobacterium sp016595215	80.7091	786	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410675.1	s__Chryseobacterium sp013410675	80.7061	777	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737705.1	s__Chryseobacterium soli	80.6661	787	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979755.1	s__Chryseobacterium culicis_A	80.6164	767	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_002797535.1	s__Chryseobacterium geocarposphaerae	80.5992	706	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.65	95.65	0.87	0.87	2	-
GCF_001045465.1	s__Chryseobacterium angstadtii	80.5944	752	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799235.1	s__Chryseobacterium sp000799235	80.5721	768	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	80.4979	742	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737785.1	s__Chryseobacterium luteum	80.4678	744	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006829085.1	s__Chryseobacterium sp006829085	80.4305	774	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.29	97.29	0.93	0.93	2	-
GCF_003815675.1	s__Chryseobacterium sp003815675	80.3127	739	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204415.1	s__Chryseobacterium defluvii_A	80.3109	657	1444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:52,227] [INFO] GTDB search result was written to GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:52,227] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:52,232] [INFO] DFAST_QC result json was written to GCF_000282115.1_Chryseobacterium.strCF314_v1.0_genomic.fna/dqc_result.json
[2024-01-24 13:50:52,232] [INFO] DFAST_QC completed!
[2024-01-24 13:50:52,232] [INFO] Total running time: 0h1m52s