[2023-06-18 13:19:22,925] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:19:22,932] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:19:22,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg2580c0d3-be68-43fc-a426-8f2a18f70a3f/dqc_reference
[2023-06-18 13:19:24,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:19:24,101] [INFO] Task started: Prodigal
[2023-06-18 13:19:24,101] [INFO] Running command: gunzip -c /var/lib/cwl/stga1ba7f8b-9cbd-4fe7-80cb-45239d3d35d0/GCA_018971285.1_ASM1897128v1_genomic.fna.gz | prodigal -d GCA_018971285.1_ASM1897128v1_genomic.fna/cds.fna -a GCA_018971285.1_ASM1897128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:19:28,739] [INFO] Task succeeded: Prodigal
[2023-06-18 13:19:28,739] [INFO] Task started: HMMsearch
[2023-06-18 13:19:28,739] [INFO] Running command: hmmsearch --tblout GCA_018971285.1_ASM1897128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2580c0d3-be68-43fc-a426-8f2a18f70a3f/dqc_reference/reference_markers.hmm GCA_018971285.1_ASM1897128v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:19:28,924] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:19:28,926] [INFO] Found 6/6 markers.
[2023-06-18 13:19:28,951] [INFO] Query marker FASTA was written to GCA_018971285.1_ASM1897128v1_genomic.fna/markers.fasta
[2023-06-18 13:19:28,951] [INFO] Task started: Blastn
[2023-06-18 13:19:28,951] [INFO] Running command: blastn -query GCA_018971285.1_ASM1897128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2580c0d3-be68-43fc-a426-8f2a18f70a3f/dqc_reference/reference_markers.fasta -out GCA_018971285.1_ASM1897128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:19:29,740] [INFO] Task succeeded: Blastn
[2023-06-18 13:19:29,746] [INFO] Selected 35 target genomes.
[2023-06-18 13:19:29,746] [INFO] Target genome list was writen to GCA_018971285.1_ASM1897128v1_genomic.fna/target_genomes.txt
[2023-06-18 13:19:29,752] [INFO] Task started: fastANI
[2023-06-18 13:19:29,753] [INFO] Running command: fastANI --query /var/lib/cwl/stga1ba7f8b-9cbd-4fe7-80cb-45239d3d35d0/GCA_018971285.1_ASM1897128v1_genomic.fna.gz --refList GCA_018971285.1_ASM1897128v1_genomic.fna/target_genomes.txt --output GCA_018971285.1_ASM1897128v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:19:51,831] [INFO] Task succeeded: fastANI
[2023-06-18 13:19:51,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2580c0d3-be68-43fc-a426-8f2a18f70a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:19:51,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2580c0d3-be68-43fc-a426-8f2a18f70a3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:19:51,852] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:19:51,852] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 13:19:51,853] [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
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.2908	83	411	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.0292	66	411	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	76.8188	87	411	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	76.789	78	411	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	76.6459	82	411	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	76.6442	66	411	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	76.6264	82	411	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.6261	63	411	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	76.593	74	411	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	76.593	86	411	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	76.5872	82	411	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	76.5832	68	411	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	76.5667	75	411	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	76.5597	61	411	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	76.4347	73	411	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	76.4274	68	411	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	76.4054	74	411	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.3877	59	411	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	76.3401	62	411	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	76.2374	58	411	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	76.2374	58	411	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.2114	87	411	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	76.2081	63	411	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	76.1691	60	411	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.0872	64	411	95	below_threshold
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	75.8127	64	411	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	75.7215	62	411	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 13:19:51,856] [INFO] DFAST Taxonomy check result was written to GCA_018971285.1_ASM1897128v1_genomic.fna/tc_result.tsv
[2023-06-18 13:19:51,856] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:19:51,856] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:19:51,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2580c0d3-be68-43fc-a426-8f2a18f70a3f/dqc_reference/checkm_data
[2023-06-18 13:19:51,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:19:51,879] [INFO] Task started: CheckM
[2023-06-18 13:19:51,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018971285.1_ASM1897128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018971285.1_ASM1897128v1_genomic.fna/checkm_input GCA_018971285.1_ASM1897128v1_genomic.fna/checkm_result
[2023-06-18 13:20:11,708] [INFO] Task succeeded: CheckM
[2023-06-18 13:20:11,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.65%
Contamintation: 6.94%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 13:20:11,738] [INFO] ===== Completeness check finished =====
[2023-06-18 13:20:11,738] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:20:11,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018971285.1_ASM1897128v1_genomic.fna/markers.fasta)
[2023-06-18 13:20:11,739] [INFO] Task started: Blastn
[2023-06-18 13:20:11,739] [INFO] Running command: blastn -query GCA_018971285.1_ASM1897128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2580c0d3-be68-43fc-a426-8f2a18f70a3f/dqc_reference/reference_markers_gtdb.fasta -out GCA_018971285.1_ASM1897128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:20:13,121] [INFO] Task succeeded: Blastn
[2023-06-18 13:20:13,135] [INFO] Selected 28 target genomes.
[2023-06-18 13:20:13,135] [INFO] Target genome list was writen to GCA_018971285.1_ASM1897128v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:20:13,172] [INFO] Task started: fastANI
[2023-06-18 13:20:13,172] [INFO] Running command: fastANI --query /var/lib/cwl/stga1ba7f8b-9cbd-4fe7-80cb-45239d3d35d0/GCA_018971285.1_ASM1897128v1_genomic.fna.gz --refList GCA_018971285.1_ASM1897128v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018971285.1_ASM1897128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:20:32,308] [INFO] Task succeeded: fastANI
[2023-06-18 13:20:32,325] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 13:20:32,326] [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_004801305.1	s__Thauera_A rhizosphaerae	77.2756	82	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903863375.1	s__CAIVHB01 sp903863375	77.2122	80	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ferrovaceae;g__CAIVHB01	95.0	99.77	99.77	0.92	0.92	2	-
GCA_016183615.1	s__JACPEG01 sp016183615	76.9379	74	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA6910;g__JACPEG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893215.1	s__CAIVHB01 sp903893215	76.6772	76	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ferrovaceae;g__CAIVHB01	95.0	99.91	99.87	0.93	0.92	3	-
GCF_002924365.1	s__Chromobacterium sp002924365	76.6442	66	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336195.1	s__JAGXQV01 sp018336195	76.6003	56	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__JAGXQV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094595.1	s__Cupriavidus alkaliphilus	76.5961	86	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	-
GCF_001598055.1	s__Cupriavidus nantongensis	76.5872	82	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.73	95.73	0.81	0.78	3	-
GCF_900249755.1	s__Cupriavidus taiwanensis_D	76.4956	78	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.80	98.80	0.92	0.92	2	-
GCF_007833355.1	s__Denitratisoma sp007833355	76.4733	81	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitratisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000876015.1	s__Cupriavidus basilensis_B	76.4533	98	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.55	98.55	0.88	0.88	2	-
GCA_016219425.1	s__PFJX01 sp016219425	76.4263	63	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018119395.1	s__Massilia sp018119395	76.2617	64	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_000620105.1	s__Microvirgula aerodenitrificans	76.2216	57	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Microvirgula	95.0	99.13	99.12	0.93	0.93	3	-
GCF_003325475.1	s__Chromobacterium phragmitis	76.2081	63	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
GCF_000423285.1	s__Laribacter hongkongensis	76.1774	62	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Laribacter	95.0	98.14	97.82	0.92	0.90	5	-
GCF_000711885.1	s__Chromobacterium haemolyticum	76.1337	63	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	96.93	96.05	0.88	0.85	14	-
GCA_903909415.1	s__CAIVVS01 sp903909415	76.1019	62	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__CAIVVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202035.1	s__Aquitalea magnusonii	76.0847	67	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	99.21	98.53	0.95	0.91	3	-
GCF_003416985.1	s__Duganella sp003416985	76.0118	70	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.63	95.41	0.92	0.79	7	-
GCF_003416895.1	s__Duganella sp003416895	76.0101	63	411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	99.92	99.92	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-18 13:20:32,328] [INFO] GTDB search result was written to GCA_018971285.1_ASM1897128v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:20:32,330] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:20:32,336] [INFO] DFAST_QC result json was written to GCA_018971285.1_ASM1897128v1_genomic.fna/dqc_result.json
[2023-06-18 13:20:32,336] [INFO] DFAST_QC completed!
[2023-06-18 13:20:32,336] [INFO] Total running time: 0h1m9s