[2024-01-25 18:58:05,893] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:05,894] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:05,894] [INFO] DQC Reference Directory: /var/lib/cwl/stgd515792d-57bd-4753-b92f-ecec38e1ccc4/dqc_reference
[2024-01-25 18:58:07,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:07,038] [INFO] Task started: Prodigal
[2024-01-25 18:58:07,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg21442e0b-f55d-42eb-a2ac-0e6dcfb4af10/GCF_030409835.1_ASM3040983v1_genomic.fna.gz | prodigal -d GCF_030409835.1_ASM3040983v1_genomic.fna/cds.fna -a GCF_030409835.1_ASM3040983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:19,657] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:19,657] [INFO] Task started: HMMsearch
[2024-01-25 18:58:19,657] [INFO] Running command: hmmsearch --tblout GCF_030409835.1_ASM3040983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd515792d-57bd-4753-b92f-ecec38e1ccc4/dqc_reference/reference_markers.hmm GCF_030409835.1_ASM3040983v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:19,915] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:19,916] [INFO] Found 6/6 markers.
[2024-01-25 18:58:19,952] [INFO] Query marker FASTA was written to GCF_030409835.1_ASM3040983v1_genomic.fna/markers.fasta
[2024-01-25 18:58:19,952] [INFO] Task started: Blastn
[2024-01-25 18:58:19,952] [INFO] Running command: blastn -query GCF_030409835.1_ASM3040983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd515792d-57bd-4753-b92f-ecec38e1ccc4/dqc_reference/reference_markers.fasta -out GCF_030409835.1_ASM3040983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:20,613] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:20,616] [INFO] Selected 33 target genomes.
[2024-01-25 18:58:20,616] [INFO] Target genome list was writen to GCF_030409835.1_ASM3040983v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:20,668] [INFO] Task started: fastANI
[2024-01-25 18:58:20,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg21442e0b-f55d-42eb-a2ac-0e6dcfb4af10/GCF_030409835.1_ASM3040983v1_genomic.fna.gz --refList GCF_030409835.1_ASM3040983v1_genomic.fna/target_genomes.txt --output GCF_030409835.1_ASM3040983v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:39,194] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:39,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd515792d-57bd-4753-b92f-ecec38e1ccc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:39,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd515792d-57bd-4753-b92f-ecec38e1ccc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:39,209] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:58:39,209] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:58:39,209] [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
Aureibaculum marinum	strain=BH-SD17	GCA_003813905.1	2487930	2487930	type	True	76.8793	73	1323	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.823	83	1323	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	76.7465	108	1323	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.6001	86	1323	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.5961	90	1323	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.5659	56	1323	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	76.5348	84	1323	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	76.5032	54	1323	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.5011	56	1323	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	76.4276	92	1323	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	76.4096	68	1323	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.4027	112	1323	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	76.3582	110	1323	95	below_threshold
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	76.3146	65	1323	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.1601	72	1323	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.0934	50	1323	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	76.0261	53	1323	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	76.0219	59	1323	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.0214	58	1323	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	76.0191	56	1323	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	75.9323	59	1323	95	below_threshold
Aurantibacter crassamenti	strain=HG732	GCA_016811105.1	1837375	1837375	type	True	75.837	58	1323	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	75.7903	76	1323	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.7836	55	1323	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.7244	53	1323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:39,212] [INFO] DFAST Taxonomy check result was written to GCF_030409835.1_ASM3040983v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:39,212] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:39,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:39,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd515792d-57bd-4753-b92f-ecec38e1ccc4/dqc_reference/checkm_data
[2024-01-25 18:58:39,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:39,253] [INFO] Task started: CheckM
[2024-01-25 18:58:39,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409835.1_ASM3040983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409835.1_ASM3040983v1_genomic.fna/checkm_input GCF_030409835.1_ASM3040983v1_genomic.fna/checkm_result
[2024-01-25 18:59:18,267] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:18,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:18,300] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:18,301] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:18,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409835.1_ASM3040983v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:18,301] [INFO] Task started: Blastn
[2024-01-25 18:59:18,301] [INFO] Running command: blastn -query GCF_030409835.1_ASM3040983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd515792d-57bd-4753-b92f-ecec38e1ccc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409835.1_ASM3040983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:19,202] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:19,205] [INFO] Selected 30 target genomes.
[2024-01-25 18:59:19,205] [INFO] Target genome list was writen to GCF_030409835.1_ASM3040983v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:19,233] [INFO] Task started: fastANI
[2024-01-25 18:59:19,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg21442e0b-f55d-42eb-a2ac-0e6dcfb4af10/GCF_030409835.1_ASM3040983v1_genomic.fna.gz --refList GCF_030409835.1_ASM3040983v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409835.1_ASM3040983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:36,284] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:36,301] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:59:36,301] [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_905479625.1	s__QNYL01 sp905479625	80.154	439	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__QNYL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	77.0048	59	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813905.1	s__Aureibaculum marinum	76.8793	73	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188355.1	s__Lutibacter flavus	76.7465	108	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003449015.1	s__Aureibaculum sp003449015	76.5721	91	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006065315.1	s__Aureibaculum sp006065315	76.561	83	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524075.1	s__Lutibacter sp012524075	76.5377	80	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643655.1	s__Polaribacter_A pacificus	76.5376	53	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954645.1	s__Polaribacter gangjinensis	76.5007	71	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	76.4653	57	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCA_004195315.1	s__Lutibacter sp004195315	76.4489	54	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543325.1	s__Lutibacter profundi	76.4387	67	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181865.1	s__Urechidicola croceus_A	76.406	71	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744615.1	s__QNYL01 sp016744615	76.3501	143	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__QNYL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	76.3501	70	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.3277	59	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861125.1	s__Cellulophaga baltica_A	76.3182	67	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	76.2437	92	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003973375.1	s__QNYL01 sp003973375	76.2136	50	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__QNYL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	76.1557	86	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687935.1	s__Polaribacter sp000687935	76.132	80	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900198195.1	s__Tenacibaculum jejuense	76.0474	55	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	76.0375	52	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767245.1	s__Aureivirga sp015767245	75.8326	57	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767265.1	s__Aureivirga marina	75.7903	76	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:36,303] [INFO] GTDB search result was written to GCF_030409835.1_ASM3040983v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:36,303] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:36,316] [INFO] DFAST_QC result json was written to GCF_030409835.1_ASM3040983v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:36,316] [INFO] DFAST_QC completed!
[2024-01-25 18:59:36,316] [INFO] Total running time: 0h1m30s