[2024-01-24 13:40:42,878] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,884] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,884] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ec733fe-9ba5-4135-bf3b-937f75245433/dqc_reference
[2024-01-24 13:40:44,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,134] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg98c32e95-ef58-4868-b1ac-554bf4eb57ee/GCF_003076475.1_ASM307647v1_genomic.fna.gz | prodigal -d GCF_003076475.1_ASM307647v1_genomic.fna/cds.fna -a GCF_003076475.1_ASM307647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:01,852] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:01,852] [INFO] Task started: HMMsearch
[2024-01-24 13:41:01,852] [INFO] Running command: hmmsearch --tblout GCF_003076475.1_ASM307647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ec733fe-9ba5-4135-bf3b-937f75245433/dqc_reference/reference_markers.hmm GCF_003076475.1_ASM307647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:02,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:02,136] [INFO] Found 6/6 markers.
[2024-01-24 13:41:02,181] [INFO] Query marker FASTA was written to GCF_003076475.1_ASM307647v1_genomic.fna/markers.fasta
[2024-01-24 13:41:02,182] [INFO] Task started: Blastn
[2024-01-24 13:41:02,182] [INFO] Running command: blastn -query GCF_003076475.1_ASM307647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ec733fe-9ba5-4135-bf3b-937f75245433/dqc_reference/reference_markers.fasta -out GCF_003076475.1_ASM307647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:02,896] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:02,902] [INFO] Selected 27 target genomes.
[2024-01-24 13:41:02,903] [INFO] Target genome list was writen to GCF_003076475.1_ASM307647v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:03,005] [INFO] Task started: fastANI
[2024-01-24 13:41:03,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c32e95-ef58-4868-b1ac-554bf4eb57ee/GCF_003076475.1_ASM307647v1_genomic.fna.gz --refList GCF_003076475.1_ASM307647v1_genomic.fna/target_genomes.txt --output GCF_003076475.1_ASM307647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:21,689] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:21,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ec733fe-9ba5-4135-bf3b-937f75245433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:21,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ec733fe-9ba5-4135-bf3b-937f75245433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:21,707] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:21,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:21,707] [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
Flavobacterium kingsejongi	strain=WV39	GCA_003076475.1	1678728	1678728	type	True	100.0	1403	1408	95	conclusive
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	78.4921	155	1408	95	below_threshold
Flavobacterium gossypii	strain=DSM 100397	GCA_014138495.1	1646119	1646119	type	True	78.3085	199	1408	95	below_threshold
Flavobacterium soli	strain=DSM 19725	GCA_000422705.1	344881	344881	type	True	78.1909	187	1408	95	below_threshold
Flavobacterium macacae	strain=YIM 102600	GCA_003865365.1	2488993	2488993	type	True	78.1539	211	1408	95	below_threshold
Flavobacterium endophyticum	strain=DSM 29537	GCA_003634455.1	1540163	1540163	type	True	78.1001	190	1408	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.0826	116	1408	95	below_threshold
Flavobacterium inviolabile	strain=P2-65	GCA_013389455.1	2748320	2748320	type	True	77.9135	228	1408	95	below_threshold
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	77.8831	224	1408	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	77.7129	108	1408	95	below_threshold
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	77.6834	186	1408	95	below_threshold
Flavobacterium noncentrifugens	strain=CGMCC 1.10076	GCA_900100375.1	1128970	1128970	type	True	77.5933	156	1408	95	below_threshold
Flavobacterium lotistagni	strain=CYK-4	GCA_011392125.1	2709660	2709660	type	True	77.5825	78	1408	95	below_threshold
Flavobacterium noncentrifugens	strain=NBRC 108844	GCA_007992475.1	1128970	1128970	type	True	77.5771	155	1408	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	77.5352	155	1408	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	77.4974	181	1408	95	below_threshold
Flavobacterium bomense	strain=RB1N8	GCA_003970355.1	2497483	2497483	type	True	77.4179	136	1408	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	77.2731	180	1408	95	below_threshold
Flavobacterium orientale	strain=CGMCC 1.12506	GCA_014638005.1	1756020	1756020	type	True	77.1811	126	1408	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	77.16	181	1408	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	76.5487	91	1408	95	below_threshold
Flavobacterium silvaticum	strain=SE-s28	GCA_012911565.1	1852020	1852020	type	True	76.394	75	1408	95	below_threshold
Flavobacterium caeni	strain=CGMCC 1.7031	GCA_900101895.1	490189	490189	type	True	76.3813	60	1408	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:21,709] [INFO] DFAST Taxonomy check result was written to GCF_003076475.1_ASM307647v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:21,709] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:21,709] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:21,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ec733fe-9ba5-4135-bf3b-937f75245433/dqc_reference/checkm_data
[2024-01-24 13:41:21,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:21,750] [INFO] Task started: CheckM
[2024-01-24 13:41:21,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003076475.1_ASM307647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003076475.1_ASM307647v1_genomic.fna/checkm_input GCF_003076475.1_ASM307647v1_genomic.fna/checkm_result
[2024-01-24 13:42:13,752] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:13,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,773] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:13,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:13,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003076475.1_ASM307647v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:13,774] [INFO] Task started: Blastn
[2024-01-24 13:42:13,774] [INFO] Running command: blastn -query GCF_003076475.1_ASM307647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ec733fe-9ba5-4135-bf3b-937f75245433/dqc_reference/reference_markers_gtdb.fasta -out GCF_003076475.1_ASM307647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:14,738] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:14,743] [INFO] Selected 25 target genomes.
[2024-01-24 13:42:14,743] [INFO] Target genome list was writen to GCF_003076475.1_ASM307647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:14,838] [INFO] Task started: fastANI
[2024-01-24 13:42:14,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c32e95-ef58-4868-b1ac-554bf4eb57ee/GCF_003076475.1_ASM307647v1_genomic.fna.gz --refList GCF_003076475.1_ASM307647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003076475.1_ASM307647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:32,170] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:32,194] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:32,194] [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_003076475.1	s__Flavobacterium kingsejongi	100.0	1402	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004349145.1	s__Flavobacterium hiemivividum	78.4921	155	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	-
GCF_000422705.1	s__Flavobacterium soli	78.1909	187	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865365.1	s__Flavobacterium macacae	78.1592	210	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846575.1	s__Flavobacterium lindanitolerans	78.1388	211	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.86	97.14	0.91	0.85	11	-
GCF_003634455.1	s__Flavobacterium endophyticum	78.1058	189	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.19	97.19	0.95	0.95	2	-
GCF_013389455.1	s__Flavobacterium sp001898245	77.9611	230	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.49	98.42	0.93	0.92	4	-
GCF_006385255.1	s__Flavobacterium microcysteis	77.8831	224	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016645.1	s__Flavobacterium johnsoniae	77.8736	189	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_000735715.2	s__Flavobacterium chungangense	77.6916	170	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_017833855.1	s__Flavobacterium sp017833855	77.6845	175	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011392125.1	s__Flavobacterium lotistagni	77.6596	76	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100375.1	s__Flavobacterium noncentrifugens	77.5771	156	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003350545.1	s__Flavobacterium glaciei	77.5678	146	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_015752255.1	s__Flavobacterium sp015752255	77.5646	160	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016525.1	s__Flavobacterium sufflavum	77.5552	154	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711135.1	s__Flavobacterium sp009711135	77.54	159	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217435.1	s__Flavobacterium reichenbachii	77.5035	179	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003968755.1	s__Flavobacterium sp003968755	77.4567	134	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.86	96.58	0.85	0.82	9	-
GCF_004349315.1	s__Flavobacterium sp004349315	77.3091	163	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.90	0.90	2	-
GCA_002483285.1	s__Flavobacterium sp002483285	77.2152	88	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638005.1	s__Flavobacterium orientale	77.1824	125	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243255.1	s__Flavobacterium psychrophilum_B	76.9354	141	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101895.1	s__Flavobacterium caeni	76.4962	60	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823965.1	s__Flavobacterium sp013823965	76.3562	95	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:32,196] [INFO] GTDB search result was written to GCF_003076475.1_ASM307647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:32,197] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:32,202] [INFO] DFAST_QC result json was written to GCF_003076475.1_ASM307647v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:32,202] [INFO] DFAST_QC completed!
[2024-01-24 13:42:32,202] [INFO] Total running time: 0h1m49s