[2024-01-24 14:14:20,164] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f7c42e7-591d-4597-b688-bf6371835a90/dqc_reference
[2024-01-24 14:14:21,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,519] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,520] [INFO] Running command: gunzip -c /var/lib/cwl/stg2293c2ce-2b0b-4770-a4ca-0c8fe799df10/GCF_004366355.1_ASM436635v1_genomic.fna.gz | prodigal -d GCF_004366355.1_ASM436635v1_genomic.fna/cds.fna -a GCF_004366355.1_ASM436635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:59,799] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:59,800] [INFO] Task started: HMMsearch
[2024-01-24 14:14:59,800] [INFO] Running command: hmmsearch --tblout GCF_004366355.1_ASM436635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f7c42e7-591d-4597-b688-bf6371835a90/dqc_reference/reference_markers.hmm GCF_004366355.1_ASM436635v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:00,106] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:00,108] [INFO] Found 6/6 markers.
[2024-01-24 14:15:00,163] [INFO] Query marker FASTA was written to GCF_004366355.1_ASM436635v1_genomic.fna/markers.fasta
[2024-01-24 14:15:00,164] [INFO] Task started: Blastn
[2024-01-24 14:15:00,164] [INFO] Running command: blastn -query GCF_004366355.1_ASM436635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f7c42e7-591d-4597-b688-bf6371835a90/dqc_reference/reference_markers.fasta -out GCF_004366355.1_ASM436635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:00,782] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:00,786] [INFO] Selected 22 target genomes.
[2024-01-24 14:15:00,786] [INFO] Target genome list was writen to GCF_004366355.1_ASM436635v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:00,809] [INFO] Task started: fastANI
[2024-01-24 14:15:00,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg2293c2ce-2b0b-4770-a4ca-0c8fe799df10/GCF_004366355.1_ASM436635v1_genomic.fna.gz --refList GCF_004366355.1_ASM436635v1_genomic.fna/target_genomes.txt --output GCF_004366355.1_ASM436635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:21,949] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:21,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f7c42e7-591d-4597-b688-bf6371835a90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:21,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f7c42e7-591d-4597-b688-bf6371835a90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:21,960] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:21,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:21,960] [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
Dinghuibacter silviterrae	strain=DSM 100059	GCA_004366355.1	1539049	1539049	type	True	100.0	2163	2163	95	conclusive
Puia dinghuensis	strain=CGMCC 1.15448	GCA_014642875.1	1792502	1792502	type	True	76.8885	140	2163	95	below_threshold
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	76.7448	65	2163	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	76.1492	78	2163	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	75.9888	85	2163	95	below_threshold
Flaviaesturariibacter aridisoli	strain=17J68-15	GCA_004343705.1	2545761	2545761	type	True	75.9789	92	2163	95	below_threshold
Chitinophaga parva	strain=LY-1	GCA_003071345.1	2169414	2169414	type	True	75.9563	67	2163	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	75.9267	67	2163	95	below_threshold
Chitinophaga agrisoli	strain=BN140078	GCA_008386695.1	2607653	2607653	type	True	75.8512	69	2163	95	below_threshold
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	75.7262	53	2163	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	75.5452	59	2163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:21,962] [INFO] DFAST Taxonomy check result was written to GCF_004366355.1_ASM436635v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:21,962] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:21,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:21,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f7c42e7-591d-4597-b688-bf6371835a90/dqc_reference/checkm_data
[2024-01-24 14:15:21,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:22,023] [INFO] Task started: CheckM
[2024-01-24 14:15:22,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004366355.1_ASM436635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004366355.1_ASM436635v1_genomic.fna/checkm_input GCF_004366355.1_ASM436635v1_genomic.fna/checkm_result
[2024-01-24 14:16:58,751] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:58,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:58,771] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:58,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:58,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004366355.1_ASM436635v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:58,772] [INFO] Task started: Blastn
[2024-01-24 14:16:58,772] [INFO] Running command: blastn -query GCF_004366355.1_ASM436635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f7c42e7-591d-4597-b688-bf6371835a90/dqc_reference/reference_markers_gtdb.fasta -out GCF_004366355.1_ASM436635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:59,650] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:59,654] [INFO] Selected 27 target genomes.
[2024-01-24 14:16:59,654] [INFO] Target genome list was writen to GCF_004366355.1_ASM436635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:59,733] [INFO] Task started: fastANI
[2024-01-24 14:16:59,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg2293c2ce-2b0b-4770-a4ca-0c8fe799df10/GCF_004366355.1_ASM436635v1_genomic.fna.gz --refList GCF_004366355.1_ASM436635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004366355.1_ASM436635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:24,534] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:24,549] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:24,549] [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_004366355.1	s__Dinghuibacter silviterrae	100.0	2163	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Dinghuibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014642875.1	s__Puia dinghuensis	76.9065	139	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337505.1	s__Flaviaesturariibacter flavus	76.7816	64	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970475.1	s__Dinghuibacter sp903970475	76.7729	189	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Dinghuibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267545.1	s__Puia sp018267545	76.0886	101	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898505.1	s__Puia sp001898505	76.0666	103	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004343705.1	s__Flaviaesturariibacter aridisoli	75.9964	91	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167015.1	s__Puia sp003167015	75.9901	84	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813775.1	s__Chitinophaga lutea	75.9888	85	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628535.1	s__Flavisolibacter nicotianae	75.95	66	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267585.1	s__Puia sp018267585	75.9228	105	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386695.1	s__Chitinophaga agrisoli	75.8512	69	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529945.1	s__Chitinophaga varians	75.7262	53	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830125.1	s__Chitinophaga japonensis	75.717	91	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654595.1	s__Puia sp015654595	75.703	67	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849455.1	s__Pseudobacter sp017849455	75.6221	54	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015069695.1	s__JADCRZ01 sp015069695	75.6142	59	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JADCRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192105.1	s__JJ008 sp016192105	75.5449	52	2163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:24,551] [INFO] GTDB search result was written to GCF_004366355.1_ASM436635v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:24,552] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:24,555] [INFO] DFAST_QC result json was written to GCF_004366355.1_ASM436635v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:24,555] [INFO] DFAST_QC completed!
[2024-01-24 14:17:24,555] [INFO] Total running time: 0h3m4s