[2024-01-24 14:55:07,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:07,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:07,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg8387185b-f85b-42bb-bb83-f8498f1c70c6/dqc_reference
[2024-01-24 14:55:09,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,465] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,465] [INFO] Running command: gunzip -c /var/lib/cwl/stg33319f3b-1dbc-4d7b-add2-ea98d7699a20/GCF_014199395.1_ASM1419939v1_genomic.fna.gz | prodigal -d GCF_014199395.1_ASM1419939v1_genomic.fna/cds.fna -a GCF_014199395.1_ASM1419939v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:21,508] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:21,509] [INFO] Task started: HMMsearch
[2024-01-24 14:55:21,509] [INFO] Running command: hmmsearch --tblout GCF_014199395.1_ASM1419939v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8387185b-f85b-42bb-bb83-f8498f1c70c6/dqc_reference/reference_markers.hmm GCF_014199395.1_ASM1419939v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:21,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:21,765] [INFO] Found 6/6 markers.
[2024-01-24 14:55:21,801] [INFO] Query marker FASTA was written to GCF_014199395.1_ASM1419939v1_genomic.fna/markers.fasta
[2024-01-24 14:55:21,802] [INFO] Task started: Blastn
[2024-01-24 14:55:21,802] [INFO] Running command: blastn -query GCF_014199395.1_ASM1419939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8387185b-f85b-42bb-bb83-f8498f1c70c6/dqc_reference/reference_markers.fasta -out GCF_014199395.1_ASM1419939v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:22,538] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:22,542] [INFO] Selected 29 target genomes.
[2024-01-24 14:55:22,543] [INFO] Target genome list was writen to GCF_014199395.1_ASM1419939v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:22,565] [INFO] Task started: fastANI
[2024-01-24 14:55:22,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg33319f3b-1dbc-4d7b-add2-ea98d7699a20/GCF_014199395.1_ASM1419939v1_genomic.fna.gz --refList GCF_014199395.1_ASM1419939v1_genomic.fna/target_genomes.txt --output GCF_014199395.1_ASM1419939v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:41,582] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:41,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8387185b-f85b-42bb-bb83-f8498f1c70c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:41,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8387185b-f85b-42bb-bb83-f8498f1c70c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:41,603] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:41,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:41,604] [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
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	100.0	1224	1228	95	conclusive
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	80.5804	198	1228	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.8074	193	1228	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	77.6719	148	1228	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	77.6513	144	1228	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.6327	229	1228	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	77.6118	151	1228	95	below_threshold
Celeribacter persicus	strain=DSM 100434	GCA_003050785.1	1651082	1651082	type	True	77.5898	124	1228	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.5343	283	1228	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	77.2525	186	1228	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	77.2402	187	1228	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.2015	167	1228	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	77.1543	183	1228	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	77.1339	187	1228	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	77.1151	199	1228	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.1031	148	1228	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	77.1023	149	1228	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.0432	89	1228	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	77.0146	257	1228	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	76.9865	227	1228	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	76.919	142	1228	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.8187	160	1228	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.7082	99	1228	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	76.6522	102	1228	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	76.2372	145	1228	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	75.8825	56	1228	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.8784	71	1228	95	below_threshold
Paracoccus sulfuroxidans	strain=CGMCC 1.5364	GCA_007830335.1	384678	384678	type	True	75.8737	63	1228	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	75.8169	72	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:41,606] [INFO] DFAST Taxonomy check result was written to GCF_014199395.1_ASM1419939v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:41,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:41,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:41,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8387185b-f85b-42bb-bb83-f8498f1c70c6/dqc_reference/checkm_data
[2024-01-24 14:55:41,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:41,645] [INFO] Task started: CheckM
[2024-01-24 14:55:41,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199395.1_ASM1419939v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199395.1_ASM1419939v1_genomic.fna/checkm_input GCF_014199395.1_ASM1419939v1_genomic.fna/checkm_result
[2024-01-24 14:56:20,168] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:20,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:20,190] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:20,190] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:20,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199395.1_ASM1419939v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:20,191] [INFO] Task started: Blastn
[2024-01-24 14:56:20,191] [INFO] Running command: blastn -query GCF_014199395.1_ASM1419939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8387185b-f85b-42bb-bb83-f8498f1c70c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199395.1_ASM1419939v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:21,382] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:21,386] [INFO] Selected 23 target genomes.
[2024-01-24 14:56:21,387] [INFO] Target genome list was writen to GCF_014199395.1_ASM1419939v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:21,410] [INFO] Task started: fastANI
[2024-01-24 14:56:21,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg33319f3b-1dbc-4d7b-add2-ea98d7699a20/GCF_014199395.1_ASM1419939v1_genomic.fna.gz --refList GCF_014199395.1_ASM1419939v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199395.1_ASM1419939v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:36,173] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:36,194] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:36,195] [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_014199395.1	s__Yoonia ponticola	100.0	1224	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003201935.1	s__Yoonia sp003201935	77.8966	270	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	77.8624	251	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378665.1	s__Yoonia sp002378665	77.8598	254	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	99.59	99.15	0.91	0.87	4	-
GCF_002933395.1	s__Yoonia maritima_A	77.7651	224	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003285.1	s__Yoonia maritima	77.6919	228	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458435.1	s__Thalassobius mediterraneus	77.6719	148	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905182645.1	s__Yoonia sp905182645	77.55	238	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115105.1	s__Yoonia tamlensis	77.5319	283	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058085.1	s__Yoonia sediminilitoris	77.2383	187	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	77.2014	167	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109295.1	s__Cognatiyoonia koreensis	77.1151	199	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	77.0852	149	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003663885.1	s__Litoreibacter meonggei	76.9436	183	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	76.9137	116	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017390475.1	s__Yoonia sp017390475	76.8545	204	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	76.8187	160	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263905.1	s__Loktanella sp018263905	76.7937	205	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	76.7803	196	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCA_003551805.1	s__Yoonia sp003551805	76.7481	169	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	98.26	98.25	0.80	0.77	3	-
GCF_903914075.1	s__Ruegeria sp903914075	76.4103	104	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.16	95.09	0.87	0.84	7	-
GCF_001969365.1	s__Tateyamaria omphalii_A	76.3769	132	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814025.1	s__Tateyamaria sp000814025	76.2005	113	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:36,196] [INFO] GTDB search result was written to GCF_014199395.1_ASM1419939v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:36,197] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:36,202] [INFO] DFAST_QC result json was written to GCF_014199395.1_ASM1419939v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:36,202] [INFO] DFAST_QC completed!
[2024-01-24 14:56:36,202] [INFO] Total running time: 0h1m29s