[2024-01-24 10:56:34,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:56:34,376] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:56:34,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg783ae04e-5aed-4b39-83b7-fea5ecc6f0ab/dqc_reference
[2024-01-24 10:56:36,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:56:36,717] [INFO] Task started: Prodigal
[2024-01-24 10:56:36,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg5215595e-8b3b-4c97-8625-263625f11248/GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/cds.fna -a GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:56:56,619] [INFO] Task succeeded: Prodigal
[2024-01-24 10:56:56,620] [INFO] Task started: HMMsearch
[2024-01-24 10:56:56,620] [INFO] Running command: hmmsearch --tblout GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg783ae04e-5aed-4b39-83b7-fea5ecc6f0ab/dqc_reference/reference_markers.hmm GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:56:56,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:56:56,911] [INFO] Found 6/6 markers.
[2024-01-24 10:56:56,945] [INFO] Query marker FASTA was written to GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:56:56,945] [INFO] Task started: Blastn
[2024-01-24 10:56:56,945] [INFO] Running command: blastn -query GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg783ae04e-5aed-4b39-83b7-fea5ecc6f0ab/dqc_reference/reference_markers.fasta -out GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:56:57,612] [INFO] Task succeeded: Blastn
[2024-01-24 10:56:57,617] [INFO] Selected 25 target genomes.
[2024-01-24 10:56:57,617] [INFO] Target genome list was writen to GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:56:57,628] [INFO] Task started: fastANI
[2024-01-24 10:56:57,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg5215595e-8b3b-4c97-8625-263625f11248/GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna.gz --refList GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:14,839] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:14,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg783ae04e-5aed-4b39-83b7-fea5ecc6f0ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:14,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg783ae04e-5aed-4b39-83b7-fea5ecc6f0ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:14,874] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:14,875] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:14,875] [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 noncentrifugens	strain=CGMCC 1.10076	GCA_900100375.1	1128970	1128970	type	True	100.0	1336	1337	95	conclusive
Flavobacterium noncentrifugens	strain=NBRC 108844	GCA_007992475.1	1128970	1128970	type	True	99.9653	1312	1337	95	conclusive
Flavobacterium soli	strain=DSM 19725	GCA_000422705.1	344881	344881	type	True	77.7754	231	1337	95	below_threshold
Flavobacterium macacae	strain=YIM 102600	GCA_003865365.1	2488993	2488993	type	True	77.6953	235	1337	95	below_threshold
Flavobacterium turcicum	strain=F-339	GCA_011365745.1	2764718	2764718	type	True	77.6324	150	1337	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	77.5884	174	1337	95	below_threshold
Flavobacterium pallidum	strain=HYN0049	GCA_003097535.1	2172098	2172098	type	True	77.5736	245	1337	95	below_threshold
Flavobacterium erciyesense	strain=F-328	GCA_018069925.1	2825842	2825842	type	True	77.5517	141	1337	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	77.4317	170	1337	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	77.4211	184	1337	95	below_threshold
Flavobacterium magnum	strain=HYN0048	GCA_003055625.1	2162713	2162713	type	True	77.3997	173	1337	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	77.3986	202	1337	95	below_threshold
Flavobacterium bomense	strain=RB1N8	GCA_003970355.1	2497483	2497483	type	True	77.3856	152	1337	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.38	157	1337	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.358	167	1337	95	below_threshold
Flavobacterium xanthum	strain=DSM 3661	GCA_900142695.1	69322	69322	type	True	77.3195	151	1337	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	77.311	151	1337	95	below_threshold
Flavobacterium caeni	strain=CGMCC 1.7031	GCA_900101895.1	490189	490189	type	True	77.2942	262	1337	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	77.2571	137	1337	95	below_threshold
Flavobacterium agri	strain=MAH-1	GCA_013401995.1	2743471	2743471	type	True	77.0745	209	1337	95	below_threshold
Flavobacterium suncheonense	strain=GH29-5	GCA_000769835.1	350894	350894	type	True	76.8858	161	1337	95	below_threshold
Flavobacterium silvaticum	strain=SE-s28	GCA_012911565.1	1852020	1852020	type	True	76.831	177	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:14,877] [INFO] DFAST Taxonomy check result was written to GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:57:14,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:14,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:14,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg783ae04e-5aed-4b39-83b7-fea5ecc6f0ab/dqc_reference/checkm_data
[2024-01-24 10:57:14,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:14,927] [INFO] Task started: CheckM
[2024-01-24 10:57:14,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/checkm_input GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:58:12,646] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:12,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:12,669] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:12,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:12,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:58:12,670] [INFO] Task started: Blastn
[2024-01-24 10:58:12,670] [INFO] Running command: blastn -query GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg783ae04e-5aed-4b39-83b7-fea5ecc6f0ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:13,634] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:13,638] [INFO] Selected 23 target genomes.
[2024-01-24 10:58:13,639] [INFO] Target genome list was writen to GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:13,672] [INFO] Task started: fastANI
[2024-01-24 10:58:13,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg5215595e-8b3b-4c97-8625-263625f11248/GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna.gz --refList GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:28,136] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:28,157] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:28,158] [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_900100375.1	s__Flavobacterium noncentrifugens	100.0	1336	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002483285.1	s__Flavobacterium sp002483285	77.8877	291	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097635.1	s__Flavobacterium psychrotolerans	77.7089	190	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014844035.1	s__Flavobacterium sp014844035	77.6996	177	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754315.1	s__Flavobacterium sp002754315	77.6693	173	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_011365745.1	s__Flavobacterium turcicum	77.6324	150	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003097535.1	s__Flavobacterium pallidum	77.5704	246	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742145.1	s__Flavobacterium sp011742145	77.5636	184	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002256285.1	s__Flavobacterium sp002256285	77.5578	211	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069925.1	s__Flavobacterium sp018069925	77.5517	141	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097365.1	s__Flavobacterium franklandianum	77.5176	176	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCA_002413745.1	s__Flavobacterium sp002413745	77.4467	181	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
GCF_015752255.1	s__Flavobacterium sp015752255	77.411	180	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478765.1	s__Flavobacterium sp015478765	77.4028	144	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004797125.1	s__Flavobacterium sangjuense	77.3986	202	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003105115.1	s__Flavobacterium sp003105115	77.3414	172	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883065.1	s__Flavobacterium sp018883065	77.3373	121	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	77.3227	151	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142695.1	s__Flavobacterium xanthum	77.3059	151	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.99	97.99	0.90	0.90	2	-
GCF_003968755.1	s__Flavobacterium sp003968755	77.2927	153	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.86	96.58	0.85	0.82	9	-
GCA_903861155.1	s__Flavobacterium sp903861155	77.1158	140	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.81	99.81	0.91	0.91	2	-
GCA_004295795.1	s__Flavobacterium sp004295795	76.9086	199	1337	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842575.1	s__Flavobacterium sp903842575	76.8798	131	1337	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 10:58:28,160] [INFO] GTDB search result was written to GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:28,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:28,170] [INFO] DFAST_QC result json was written to GCF_900100375.1_IMG-taxon_2619618994_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:58:28,170] [INFO] DFAST_QC completed!
[2024-01-24 10:58:28,170] [INFO] Total running time: 0h1m54s