[2024-01-25 18:09:06,400] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:06,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:06,407] [INFO] DQC Reference Directory: /var/lib/cwl/stgd840c2ae-d206-40d2-95a7-636cb1736a1f/dqc_reference
[2024-01-25 18:09:07,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:07,563] [INFO] Task started: Prodigal
[2024-01-25 18:09:07,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b361c49-3609-45de-8d92-484bf2fb55b0/GCF_015767265.1_ASM1576726v1_genomic.fna.gz | prodigal -d GCF_015767265.1_ASM1576726v1_genomic.fna/cds.fna -a GCF_015767265.1_ASM1576726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:17,318] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:17,319] [INFO] Task started: HMMsearch
[2024-01-25 18:09:17,319] [INFO] Running command: hmmsearch --tblout GCF_015767265.1_ASM1576726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd840c2ae-d206-40d2-95a7-636cb1736a1f/dqc_reference/reference_markers.hmm GCF_015767265.1_ASM1576726v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:17,538] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:17,539] [INFO] Found 6/6 markers.
[2024-01-25 18:09:17,574] [INFO] Query marker FASTA was written to GCF_015767265.1_ASM1576726v1_genomic.fna/markers.fasta
[2024-01-25 18:09:17,574] [INFO] Task started: Blastn
[2024-01-25 18:09:17,575] [INFO] Running command: blastn -query GCF_015767265.1_ASM1576726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd840c2ae-d206-40d2-95a7-636cb1736a1f/dqc_reference/reference_markers.fasta -out GCF_015767265.1_ASM1576726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:18,193] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:18,197] [INFO] Selected 31 target genomes.
[2024-01-25 18:09:18,198] [INFO] Target genome list was writen to GCF_015767265.1_ASM1576726v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:18,216] [INFO] Task started: fastANI
[2024-01-25 18:09:18,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b361c49-3609-45de-8d92-484bf2fb55b0/GCF_015767265.1_ASM1576726v1_genomic.fna.gz --refList GCF_015767265.1_ASM1576726v1_genomic.fna/target_genomes.txt --output GCF_015767265.1_ASM1576726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:37,236] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:37,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd840c2ae-d206-40d2-95a7-636cb1736a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:37,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd840c2ae-d206-40d2-95a7-636cb1736a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:37,254] [INFO] Found 31 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:37,254] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:37,254] [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
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	100.0	1298	1298	95	conclusive
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	77.0359	174	1298	95	below_threshold
Wenyingzhuangia marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	76.8539	132	1298	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.8278	234	1298	95	below_threshold
Wenyingzhuangia marina	strain=DSM 100572	GCA_900130035.1	1195760	1195760	type	True	76.8219	134	1298	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.7945	220	1298	95	below_threshold
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	76.7215	209	1298	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	76.6836	211	1298	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	76.6821	147	1298	95	below_threshold
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	76.624	151	1298	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	76.5754	186	1298	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	76.5718	188	1298	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.5684	225	1298	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.5546	191	1298	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.552	201	1298	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.5289	227	1298	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	76.5286	228	1298	95	below_threshold
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	76.511	180	1298	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.4675	230	1298	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.4256	204	1298	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	76.4211	241	1298	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	76.3705	170	1298	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.3065	91	1298	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.2847	208	1298	95	below_threshold
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	76.0416	66	1298	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	75.9972	63	1298	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	75.9478	134	1298	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	75.7799	101	1298	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	75.5823	92	1298	95	below_threshold
Cloacibacterium rupense	strain=CGMCC 1.7656	GCA_014645495.1	517423	517423	type	True	75.4891	62	1298	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	74.7547	63	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:37,255] [INFO] DFAST Taxonomy check result was written to GCF_015767265.1_ASM1576726v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:37,256] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:37,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:37,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd840c2ae-d206-40d2-95a7-636cb1736a1f/dqc_reference/checkm_data
[2024-01-25 18:09:37,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:37,299] [INFO] Task started: CheckM
[2024-01-25 18:09:37,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015767265.1_ASM1576726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015767265.1_ASM1576726v1_genomic.fna/checkm_input GCF_015767265.1_ASM1576726v1_genomic.fna/checkm_result
[2024-01-25 18:10:09,428] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:09,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:09,467] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:09,467] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:09,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015767265.1_ASM1576726v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:09,469] [INFO] Task started: Blastn
[2024-01-25 18:10:09,469] [INFO] Running command: blastn -query GCF_015767265.1_ASM1576726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd840c2ae-d206-40d2-95a7-636cb1736a1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_015767265.1_ASM1576726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:10,628] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:10,631] [INFO] Selected 25 target genomes.
[2024-01-25 18:10:10,631] [INFO] Target genome list was writen to GCF_015767265.1_ASM1576726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:10,660] [INFO] Task started: fastANI
[2024-01-25 18:10:10,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b361c49-3609-45de-8d92-484bf2fb55b0/GCF_015767265.1_ASM1576726v1_genomic.fna.gz --refList GCF_015767265.1_ASM1576726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015767265.1_ASM1576726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:28,359] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:28,373] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:28,373] [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_015767265.1	s__Aureivirga marina	100.0	1298	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015767245.1	s__Aureivirga sp015767245	84.0901	924	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867015.1	s__Tenacibaculum singaporense	77.048	172	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_900106565.1	s__Lutibacter oricola	76.8273	233	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130035.1	s__Wenyingzhuangia marina	76.8219	134	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002733665.1	s__Urechidicola sp002733665	76.8203	147	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116115.1	s__Lutibacter maritimus	76.8053	219	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761325.1	s__Urechidicola croceus	76.7215	209	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693415.1	s__Tenacibaculum soleae	76.7001	198	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	76.6478	146	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927765.1	s__Wenyingzhuangia aestuarii	76.6163	150	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	76.5517	188	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	76.5421	212	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006381105.1	s__Flavicella sediminum	76.5188	179	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	76.4868	238	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188355.1	s__Lutibacter flavus	76.4768	223	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337695.1	s__Tenacibaculum sp004337695	76.4407	196	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	76.4181	240	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004121075.1	s__Lutibacter sp004121075	76.2663	197	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862805.1	s__Flavobacterium sp002862805	76.2499	145	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911605.1	s__Flavobacterium sp012911605	75.7669	100	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842575.1	s__Planktosalinus sp002842575	75.7394	77	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Planktosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	75.5946	91	1298	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:28,375] [INFO] GTDB search result was written to GCF_015767265.1_ASM1576726v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:28,375] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:28,379] [INFO] DFAST_QC result json was written to GCF_015767265.1_ASM1576726v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:28,380] [INFO] DFAST_QC completed!
[2024-01-25 18:10:28,380] [INFO] Total running time: 0h1m22s