[2024-01-24 15:26:54,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:54,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:54,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg80e291d3-01f7-44fb-9349-4fe48585ad3b/dqc_reference
[2024-01-24 15:26:55,566] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:55,567] [INFO] Task started: Prodigal
[2024-01-24 15:26:55,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ac9a48c-da01-4787-985f-a76fc76bdc37/GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/cds.fna -a GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:05,753] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:05,754] [INFO] Task started: HMMsearch
[2024-01-24 15:27:05,754] [INFO] Running command: hmmsearch --tblout GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80e291d3-01f7-44fb-9349-4fe48585ad3b/dqc_reference/reference_markers.hmm GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:05,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:06,000] [INFO] Found 6/6 markers.
[2024-01-24 15:27:06,032] [INFO] Query marker FASTA was written to GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:27:06,033] [INFO] Task started: Blastn
[2024-01-24 15:27:06,033] [INFO] Running command: blastn -query GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e291d3-01f7-44fb-9349-4fe48585ad3b/dqc_reference/reference_markers.fasta -out GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:06,670] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:06,674] [INFO] Selected 29 target genomes.
[2024-01-24 15:27:06,675] [INFO] Target genome list was writen to GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:27:06,685] [INFO] Task started: fastANI
[2024-01-24 15:27:06,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac9a48c-da01-4787-985f-a76fc76bdc37/GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna.gz --refList GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:26,331] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:26,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80e291d3-01f7-44fb-9349-4fe48585ad3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:26,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80e291d3-01f7-44fb-9349-4fe48585ad3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:26,352] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:26,352] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:26,352] [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
Cognatiyoonia sediminum	strain=DSM 28715	GCA_900129845.1	1508389	1508389	type	True	100.0	1079	1079	95	conclusive
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	77.6304	185	1079	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	77.6269	205	1079	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.4365	175	1079	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	77.182	118	1079	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	77.0789	151	1079	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	77.0789	151	1079	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	77.0224	122	1079	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	77.0048	79	1079	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	76.9875	99	1079	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.9668	137	1079	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.9383	135	1079	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.8701	144	1079	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.8207	154	1079	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	76.7774	161	1079	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	76.7472	149	1079	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	76.7457	79	1079	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	76.7062	94	1079	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.645	129	1079	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	76.6141	67	1079	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	76.5215	123	1079	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	76.4697	75	1079	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	76.4353	86	1079	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.3623	78	1079	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	76.3543	133	1079	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.3102	110	1079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:26,354] [INFO] DFAST Taxonomy check result was written to GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:27:26,355] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:26,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:26,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80e291d3-01f7-44fb-9349-4fe48585ad3b/dqc_reference/checkm_data
[2024-01-24 15:27:26,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:26,391] [INFO] Task started: CheckM
[2024-01-24 15:27:26,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/checkm_input GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:28:00,307] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:00,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:00,326] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:00,326] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:00,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:28:00,327] [INFO] Task started: Blastn
[2024-01-24 15:28:00,327] [INFO] Running command: blastn -query GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e291d3-01f7-44fb-9349-4fe48585ad3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:01,238] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:01,242] [INFO] Selected 24 target genomes.
[2024-01-24 15:28:01,242] [INFO] Target genome list was writen to GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:01,258] [INFO] Task started: fastANI
[2024-01-24 15:28:01,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac9a48c-da01-4787-985f-a76fc76bdc37/GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna.gz --refList GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:15,816] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:15,835] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:15,835] [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_900129845.1	s__Cognatiyoonia sediminum	100.0	1079	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900109295.1	s__Cognatiyoonia koreensis	77.6468	205	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797915.1	s__Yoonia maricola	77.6457	184	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169435.1	s__Yoonia sp000169435	77.5712	182	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	77.4632	200	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114675.1	s__Yoonia litorea	77.4365	175	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	77.434	207	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500215.1	s__Aliiroseovarius sp010500215	77.3795	104	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115725.1	s__Marivita cryptomonadis	77.0025	122	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCA_015689745.1	s__Roseicyclus sp015689745	76.9833	82	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	76.967	138	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000382265.1	s__Yoonia vestfoldensis	76.7869	162	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	76.7783	157	1079	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	76.7665	162	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	99.59	99.15	0.91	0.87	4	-
GCF_004364805.1	s__Pelagimonas phthalicica	76.7617	148	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	97.63	95.26	0.94	0.87	3	-
GCF_004345735.1	s__Rhodovulum adriaticum	76.7457	79	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014196795.1	s__Sagittula marina	76.7062	94	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634885.1	s__Sulfitobacter sp001634885	76.704	107	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	-
GCF_900129345.1	s__Ruegeria intermedia	76.6083	129	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	76.5546	131	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_005434965.1	s__Marimonas lutisalis	76.543	107	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243445.1	s__Gemmobacter_B straminiformis	76.4287	85	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128995.1	s__Loktanella atrilutea	76.343	131	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854675.1	s__Sulfitobacter sp017854675	76.1891	89	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:15,837] [INFO] GTDB search result was written to GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:15,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:15,845] [INFO] DFAST_QC result json was written to GCF_900129845.1_IMG-taxon_2695421013_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:28:15,846] [INFO] DFAST_QC completed!
[2024-01-24 15:28:15,846] [INFO] Total running time: 0h1m22s