[2024-01-24 13:58:10,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,231] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,231] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f14d5cb-b431-4470-8949-97fa1979ef0e/dqc_reference
[2024-01-24 13:58:11,365] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,366] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,366] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1545a6b-578f-47f9-b672-c4f6c9ebea9d/GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/cds.fna -a GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:24,585] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:24,585] [INFO] Task started: HMMsearch
[2024-01-24 13:58:24,585] [INFO] Running command: hmmsearch --tblout GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f14d5cb-b431-4470-8949-97fa1979ef0e/dqc_reference/reference_markers.hmm GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:24,770] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:24,771] [INFO] Found 6/6 markers.
[2024-01-24 13:58:24,794] [INFO] Query marker FASTA was written to GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:58:24,795] [INFO] Task started: Blastn
[2024-01-24 13:58:24,795] [INFO] Running command: blastn -query GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f14d5cb-b431-4470-8949-97fa1979ef0e/dqc_reference/reference_markers.fasta -out GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:25,371] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:25,374] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:25,374] [INFO] Target genome list was writen to GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:25,388] [INFO] Task started: fastANI
[2024-01-24 13:58:25,388] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1545a6b-578f-47f9-b672-c4f6c9ebea9d/GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna.gz --refList GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:38,051] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:38,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f14d5cb-b431-4470-8949-97fa1979ef0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:38,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f14d5cb-b431-4470-8949-97fa1979ef0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:38,063] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:38,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:38,064] [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 fontis	strain=DSM 25660	GCA_900129405.1	1124188	1124188	type	True	100.0	1008	1010	95	conclusive
Flavobacterium stagni	strain=WWJ-16	GCA_004122105.1	2506421	2506421	type	True	82.0454	533	1010	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	78.0916	160	1010	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	78.0529	160	1010	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.9385	121	1010	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	77.9372	149	1010	95	below_threshold
Flavobacterium aciduliphilum	strain=DSM 25663	GCA_003268855.1	1101402	1101402	type	True	77.2734	151	1010	95	below_threshold
Flavobacterium silvisoli	strain=RD-2-33	GCA_004329815.1	2529433	2529433	type	True	77.2411	168	1010	95	below_threshold
Flavobacterium phycosphaerae	strain=MK012	GCA_010119235.1	2697515	2697515	type	True	77.2053	175	1010	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	77.147	117	1010	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	77.1216	159	1010	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	77.0422	85	1010	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.0392	117	1010	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	76.9966	97	1010	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	76.9363	105	1010	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	76.8026	130	1010	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	76.7588	103	1010	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	76.668	98	1010	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	76.6015	88	1010	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	76.5827	95	1010	95	below_threshold
Flavobacterium caeni	strain=CGMCC 1.7031	GCA_900101895.1	490189	490189	type	True	76.2273	67	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,065] [INFO] DFAST Taxonomy check result was written to GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:38,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:38,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:38,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f14d5cb-b431-4470-8949-97fa1979ef0e/dqc_reference/checkm_data
[2024-01-24 13:58:38,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:38,097] [INFO] Task started: CheckM
[2024-01-24 13:58:38,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/checkm_input GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:16,845] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:16,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:16,861] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:16,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:16,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:16,862] [INFO] Task started: Blastn
[2024-01-24 13:59:16,862] [INFO] Running command: blastn -query GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f14d5cb-b431-4470-8949-97fa1979ef0e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:17,708] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:17,711] [INFO] Selected 20 target genomes.
[2024-01-24 13:59:17,711] [INFO] Target genome list was writen to GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:17,723] [INFO] Task started: fastANI
[2024-01-24 13:59:17,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1545a6b-578f-47f9-b672-c4f6c9ebea9d/GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna.gz --refList GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:28,029] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:28,040] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:28,041] [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_900129405.1	s__Flavobacterium fontis	100.0	1009	1010	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_004122105.1	s__Flavobacterium sp004122105	82.0571	531	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786385.1	s__Flavobacterium sp002786385	78.5854	190	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.88	0.88	2	-
GCF_013072765.1	s__Flavobacterium sp013072765	78.1045	206	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014486675.1	s__Flavobacterium macrobrachii	78.0752	159	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCA_018267095.1	s__Flavobacterium sp018267095	77.4638	141	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787805.1	s__Flavobacterium sp016787805	77.444	210	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004329815.1	s__Flavobacterium silvisoli	77.2427	167	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119235.1	s__Flavobacterium phycosphaerae	77.2053	175	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362665.1	s__Flavobacterium dankookense	77.1397	157	1010	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	77.1014	82	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018413465.1	s__Flavobacterium sp018413465	77.0822	144	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001800905.1	s__Flavobacterium sp001800905	76.9916	107	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004797125.1	s__Flavobacterium sangjuense	76.8199	129	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483285.1	s__Flavobacterium sp002483285	76.4552	85	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428305.1	s__Flavobacterium sp002428305	76.4153	126	1010	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	76.3832	119	1010	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	76.2273	67	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839195.1	s__Flavobacterium sp903839195	76.153	84	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
GCA_018062725.1	s__Flavobacterium sp018062725	75.7961	99	1010	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 13:59:28,042] [INFO] GTDB search result was written to GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:28,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:28,046] [INFO] DFAST_QC result json was written to GCF_900129405.1_IMG-taxon_2695420946_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:28,046] [INFO] DFAST_QC completed!
[2024-01-24 13:59:28,046] [INFO] Total running time: 0h1m18s