[2023-06-18 11:25:12,274] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:25:12,278] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:25:12,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b16f2b6-6eaa-427a-9c75-7c826c909ad2/dqc_reference
[2023-06-18 11:25:14,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:25:14,179] [INFO] Task started: Prodigal
[2023-06-18 11:25:14,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg855980a7-aa13-4fe1-bc9a-95be1a62601a/GCA_018456185.1_ASM1845618v1_genomic.fna.gz | prodigal -d GCA_018456185.1_ASM1845618v1_genomic.fna/cds.fna -a GCA_018456185.1_ASM1845618v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:25:27,388] [INFO] Task succeeded: Prodigal
[2023-06-18 11:25:27,389] [INFO] Task started: HMMsearch
[2023-06-18 11:25:27,389] [INFO] Running command: hmmsearch --tblout GCA_018456185.1_ASM1845618v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b16f2b6-6eaa-427a-9c75-7c826c909ad2/dqc_reference/reference_markers.hmm GCA_018456185.1_ASM1845618v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:25:27,738] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:25:27,740] [INFO] Found 6/6 markers.
[2023-06-18 11:25:27,775] [INFO] Query marker FASTA was written to GCA_018456185.1_ASM1845618v1_genomic.fna/markers.fasta
[2023-06-18 11:25:27,775] [INFO] Task started: Blastn
[2023-06-18 11:25:27,775] [INFO] Running command: blastn -query GCA_018456185.1_ASM1845618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b16f2b6-6eaa-427a-9c75-7c826c909ad2/dqc_reference/reference_markers.fasta -out GCA_018456185.1_ASM1845618v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:25:28,456] [INFO] Task succeeded: Blastn
[2023-06-18 11:25:28,460] [INFO] Selected 39 target genomes.
[2023-06-18 11:25:28,460] [INFO] Target genome list was writen to GCA_018456185.1_ASM1845618v1_genomic.fna/target_genomes.txt
[2023-06-18 11:25:28,462] [INFO] Task started: fastANI
[2023-06-18 11:25:28,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg855980a7-aa13-4fe1-bc9a-95be1a62601a/GCA_018456185.1_ASM1845618v1_genomic.fna.gz --refList GCA_018456185.1_ASM1845618v1_genomic.fna/target_genomes.txt --output GCA_018456185.1_ASM1845618v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:25:53,814] [INFO] Task succeeded: fastANI
[2023-06-18 11:25:53,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b16f2b6-6eaa-427a-9c75-7c826c909ad2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:25:53,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b16f2b6-6eaa-427a-9c75-7c826c909ad2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:25:53,843] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:25:53,843] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:25:53,843] [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
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	77.0693	51	983	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	76.4925	58	983	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.4609	88	983	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	76.4515	50	983	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	76.3951	68	983	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.3526	59	983	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	76.3454	80	983	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.2324	74	983	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	76.2168	81	983	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.1619	63	983	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.0974	53	983	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	76.0469	69	983	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	76.0256	95	983	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.0104	96	983	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.882	60	983	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	75.88	68	983	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	75.8754	66	983	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	75.7698	83	983	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	75.7446	63	983	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	75.692	66	983	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	75.6572	51	983	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:25:53,861] [INFO] DFAST Taxonomy check result was written to GCA_018456185.1_ASM1845618v1_genomic.fna/tc_result.tsv
[2023-06-18 11:25:53,862] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:25:53,863] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:25:53,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b16f2b6-6eaa-427a-9c75-7c826c909ad2/dqc_reference/checkm_data
[2023-06-18 11:25:53,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:25:53,904] [INFO] Task started: CheckM
[2023-06-18 11:25:53,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018456185.1_ASM1845618v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018456185.1_ASM1845618v1_genomic.fna/checkm_input GCA_018456185.1_ASM1845618v1_genomic.fna/checkm_result
[2023-06-18 11:26:34,716] [INFO] Task succeeded: CheckM
[2023-06-18 11:26:34,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 24.48%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:26:34,746] [INFO] ===== Completeness check finished =====
[2023-06-18 11:26:34,747] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:26:34,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018456185.1_ASM1845618v1_genomic.fna/markers.fasta)
[2023-06-18 11:26:34,748] [INFO] Task started: Blastn
[2023-06-18 11:26:34,748] [INFO] Running command: blastn -query GCA_018456185.1_ASM1845618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b16f2b6-6eaa-427a-9c75-7c826c909ad2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018456185.1_ASM1845618v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:26:35,619] [INFO] Task succeeded: Blastn
[2023-06-18 11:26:35,624] [INFO] Selected 45 target genomes.
[2023-06-18 11:26:35,624] [INFO] Target genome list was writen to GCA_018456185.1_ASM1845618v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:26:35,640] [INFO] Task started: fastANI
[2023-06-18 11:26:35,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg855980a7-aa13-4fe1-bc9a-95be1a62601a/GCA_018456185.1_ASM1845618v1_genomic.fna.gz --refList GCA_018456185.1_ASM1845618v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018456185.1_ASM1845618v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:27:02,020] [INFO] Task succeeded: fastANI
[2023-06-18 11:27:02,039] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 11:27:02,039] [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
GCA_018456245.1	s__Tenacibaculum sp018456245	77.6831	100	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610735.1	s__Tenacibaculum lutimaris	77.0702	50	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCF_012524075.1	s__Lutibacter sp012524075	76.6514	87	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	76.5122	87	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900106565.1	s__Lutibacter oricola	76.4609	88	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664185.1	s__Tenacibaculum discolor	76.4483	58	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_003867015.1	s__Tenacibaculum singaporense	76.3857	67	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_009832745.1	s__Polaribacter sp009832745	76.3526	59	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543325.1	s__Lutibacter profundi	76.24	80	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105455.1	s__Tenacibaculum sp900105455	76.1771	51	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	76.1213	63	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	76.0915	97	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767265.1	s__Aureivirga marina	76.0469	69	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	76.0256	95	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014784055.1	s__Polaribacter haliotis	75.9423	71	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018861005.1	s__Polaribacter vadi_A	75.9058	62	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041805.1	s__Lutibacter sp013041805	75.8694	78	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002954685.1	s__Polaribacter porphyrae	75.6547	68	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293165.1	s__Flavobacterium sp004293165	75.5052	51	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.30	97.30	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-18 11:27:02,041] [INFO] GTDB search result was written to GCA_018456185.1_ASM1845618v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:27:02,042] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:27:02,046] [INFO] DFAST_QC result json was written to GCA_018456185.1_ASM1845618v1_genomic.fna/dqc_result.json
[2023-06-18 11:27:02,047] [INFO] DFAST_QC completed!
[2023-06-18 11:27:02,047] [INFO] Total running time: 0h1m50s