[2024-01-24 13:02:04,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:04,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:04,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg88dddec0-3705-4a2f-ace6-0b83ca74aeb8/dqc_reference
[2024-01-24 13:02:05,313] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,314] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,314] [INFO] Running command: gunzip -c /var/lib/cwl/stg43f47849-3536-4931-97bd-6c892c8768c6/GCF_007990815.1_ASM799081v1_genomic.fna.gz | prodigal -d GCF_007990815.1_ASM799081v1_genomic.fna/cds.fna -a GCF_007990815.1_ASM799081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:19,334] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:19,334] [INFO] Task started: HMMsearch
[2024-01-24 13:02:19,334] [INFO] Running command: hmmsearch --tblout GCF_007990815.1_ASM799081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88dddec0-3705-4a2f-ace6-0b83ca74aeb8/dqc_reference/reference_markers.hmm GCF_007990815.1_ASM799081v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:19,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:19,555] [INFO] Found 6/6 markers.
[2024-01-24 13:02:19,587] [INFO] Query marker FASTA was written to GCF_007990815.1_ASM799081v1_genomic.fna/markers.fasta
[2024-01-24 13:02:19,587] [INFO] Task started: Blastn
[2024-01-24 13:02:19,587] [INFO] Running command: blastn -query GCF_007990815.1_ASM799081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88dddec0-3705-4a2f-ace6-0b83ca74aeb8/dqc_reference/reference_markers.fasta -out GCF_007990815.1_ASM799081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:20,242] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:20,247] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:20,247] [INFO] Target genome list was writen to GCF_007990815.1_ASM799081v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:20,253] [INFO] Task started: fastANI
[2024-01-24 13:02:20,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg43f47849-3536-4931-97bd-6c892c8768c6/GCF_007990815.1_ASM799081v1_genomic.fna.gz --refList GCF_007990815.1_ASM799081v1_genomic.fna/target_genomes.txt --output GCF_007990815.1_ASM799081v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:32,334] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:32,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88dddec0-3705-4a2f-ace6-0b83ca74aeb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:32,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88dddec0-3705-4a2f-ace6-0b83ca74aeb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:32,351] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:02:32,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:32,352] [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 branchiophilum	strain=NBRC 15030	GCA_007990815.1	55197	55197	type	True	100.0	1100	1104	95	conclusive
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	99.9959	1103	1104	95	conclusive
Flavobacterium branchiophilum	strain=ATCC 35035	GCA_002217205.1	55197	55197	type	True	99.9301	1031	1104	95	conclusive
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	77.4971	164	1104	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	77.4416	191	1104	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	77.4197	179	1104	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.3963	124	1104	95	below_threshold
Flavobacterium crassostreae	strain=LPB0076	GCA_001831475.1	1763534	1763534	type	True	77.3366	144	1104	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	77.3361	165	1104	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	77.3236	148	1104	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	77.3216	174	1104	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	77.27	165	1104	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.1347	194	1104	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.1237	123	1104	95	below_threshold
Flavobacterium ichthyis	strain=NST-5	GCA_009915155.1	2698827	2698827	type	True	77.0784	130	1104	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	76.9628	161	1104	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.5015	139	1104	95	below_threshold
Flavobacterium columnare	strain=NBRC 100251	GCA_007990835.1	996	996	type	True	76.4577	111	1104	95	below_threshold
Flavobacterium columnare	strain=ATCC 23463	GCA_002530675.1	996	996	type	True	76.3966	116	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:32,353] [INFO] DFAST Taxonomy check result was written to GCF_007990815.1_ASM799081v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:32,354] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:32,354] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:32,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88dddec0-3705-4a2f-ace6-0b83ca74aeb8/dqc_reference/checkm_data
[2024-01-24 13:02:32,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:32,393] [INFO] Task started: CheckM
[2024-01-24 13:02:32,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990815.1_ASM799081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990815.1_ASM799081v1_genomic.fna/checkm_input GCF_007990815.1_ASM799081v1_genomic.fna/checkm_result
[2024-01-24 13:03:14,241] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:14,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:14,263] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:14,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:14,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990815.1_ASM799081v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:14,263] [INFO] Task started: Blastn
[2024-01-24 13:03:14,263] [INFO] Running command: blastn -query GCF_007990815.1_ASM799081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88dddec0-3705-4a2f-ace6-0b83ca74aeb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990815.1_ASM799081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:15,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:15,105] [INFO] Selected 29 target genomes.
[2024-01-24 13:03:15,105] [INFO] Target genome list was writen to GCF_007990815.1_ASM799081v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:15,152] [INFO] Task started: fastANI
[2024-01-24 13:03:15,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg43f47849-3536-4931-97bd-6c892c8768c6/GCF_007990815.1_ASM799081v1_genomic.fna.gz --refList GCF_007990815.1_ASM799081v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990815.1_ASM799081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:30,960] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:30,980] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:30,980] [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_002217205.1	s__Flavobacterium branchiophilum	99.9301	1031	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.60	97.23	0.92	0.84	5	conclusive
GCF_007109225.1	s__Flavobacterium sp007109225	77.8413	109	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001005.1	s__Flavobacterium sp002001005	77.5753	156	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097265.1	s__Flavobacterium gawalongense	77.4197	179	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_001831475.1	s__Flavobacterium crassostreae	77.3431	146	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018069925.1	s__Flavobacterium sp018069925	77.3364	152	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425425.1	s__Flavobacterium daejeonense	77.3043	149	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182285.1	s__Flavobacterium sp015182285	77.284	149	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293165.1	s__Flavobacterium sp004293165	77.2344	134	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.30	97.30	0.81	0.81	2	-
GCA_903839195.1	s__Flavobacterium sp903839195	77.2238	139	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
GCF_000708595.2	s__Flavobacterium sp000708595	77.1508	164	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	98.27	0.95	0.93	3	-
GCF_008806775.1	s__Flavobacterium luteum	77.1217	195	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707955.1	s__Flavobacterium sp009707955	77.0982	189	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009915155.1	s__Flavobacterium sp009915155	77.0784	130	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009495755.1	s__Flavobacterium sp009495755	77.0187	137	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	77.0163	111	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903819815.1	s__Flavobacterium sp903819815	77.0071	107	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497625.1	s__Flavobacterium sp003497625	76.9932	121	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000812945.1	s__Flavobacterium sp000812945	76.9655	193	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903879875.1	s__Flavobacterium sp903879875	76.9479	159	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.40	99.40	0.86	0.86	2	-
GCA_002352205.1	s__Flavobacterium sp002352205	76.855	140	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
GCA_002217245.1	s__Flavobacterium columnare_A	76.8244	120	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.08	98.79	0.92	0.89	11	-
GCF_004122145.1	s__Flavobacterium piscinae	76.7518	133	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.76	99.76	1.00	1.00	2	-
GCA_002482975.1	s__Flavobacterium sp002482975	76.6615	168	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888655.1	s__Flavobacterium sp903888655	76.5953	92	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903824755.1	s__Flavobacterium sp903824755	76.4364	138	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002530675.1	s__Flavobacterium columnare	76.4125	115	1104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.33	99.02	0.96	0.93	39	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:30,982] [INFO] GTDB search result was written to GCF_007990815.1_ASM799081v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:30,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:30,987] [INFO] DFAST_QC result json was written to GCF_007990815.1_ASM799081v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:30,987] [INFO] DFAST_QC completed!
[2024-01-24 13:03:30,987] [INFO] Total running time: 0h1m27s