[2023-03-15 17:39:54,063] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:39:54,063] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:39:54,063] [INFO] DQC Reference Directory: /var/lib/cwl/stge1e923c7-ad3d-48b1-be21-49b042871769/dqc_reference
[2023-03-15 17:39:55,224] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:39:55,224] [INFO] Task started: Prodigal
[2023-03-15 17:39:55,224] [INFO] Running command: cat /var/lib/cwl/stgbfa3e516-68bc-4620-a898-f85983e5b38e/OceanDNA-b41304.fa | prodigal -d OceanDNA-b41304/cds.fna -a OceanDNA-b41304/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:40:31,893] [INFO] Task succeeded: Prodigal
[2023-03-15 17:40:31,893] [INFO] Task started: HMMsearch
[2023-03-15 17:40:31,893] [INFO] Running command: hmmsearch --tblout OceanDNA-b41304/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1e923c7-ad3d-48b1-be21-49b042871769/dqc_reference/reference_markers.hmm OceanDNA-b41304/protein.faa > /dev/null
[2023-03-15 17:40:32,134] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:40:32,134] [INFO] Found 6/6 markers.
[2023-03-15 17:40:32,164] [INFO] Query marker FASTA was written to OceanDNA-b41304/markers.fasta
[2023-03-15 17:40:32,166] [INFO] Task started: Blastn
[2023-03-15 17:40:32,166] [INFO] Running command: blastn -query OceanDNA-b41304/markers.fasta -db /var/lib/cwl/stge1e923c7-ad3d-48b1-be21-49b042871769/dqc_reference/reference_markers.fasta -out OceanDNA-b41304/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:40:33,025] [INFO] Task succeeded: Blastn
[2023-03-15 17:40:33,025] [INFO] Selected 25 target genomes.
[2023-03-15 17:40:33,026] [INFO] Target genome list was writen to OceanDNA-b41304/target_genomes.txt
[2023-03-15 17:40:33,040] [INFO] Task started: fastANI
[2023-03-15 17:40:33,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfa3e516-68bc-4620-a898-f85983e5b38e/OceanDNA-b41304.fa --refList OceanDNA-b41304/target_genomes.txt --output OceanDNA-b41304/fastani_result.tsv --threads 1
[2023-03-15 17:41:04,028] [INFO] Task succeeded: fastANI
[2023-03-15 17:41:04,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1e923c7-ad3d-48b1-be21-49b042871769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:41:04,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1e923c7-ad3d-48b1-be21-49b042871769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:41:04,042] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:41:04,042] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:41:04,042] [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
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	88.7567	1129	1884	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	85.432	1200	1884	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	85.3572	1250	1884	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	84.9066	1161	1884	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	84.8059	1148	1884	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	84.7623	1239	1884	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	84.7454	1214	1884	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	84.6729	1241	1884	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	83.8785	1075	1884	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	83.8283	1151	1884	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	83.3245	1171	1884	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	83.3197	1159	1884	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	83.294	1173	1884	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	83.2109	941	1884	95	below_threshold
Pseudomonas arcuscaelestis	strain=P66	GCA_016881005.1	2710591	2710591	type	True	82.8379	1052	1884	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	82.6094	1036	1884	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	82.3209	1020	1884	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	82.1965	1049	1884	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	82.0967	1022	1884	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	81.6585	984	1884	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	81.3703	971	1884	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	80.6071	789	1884	95	below_threshold
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	75.6143	72	1884	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:41:04,042] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41304/tc_result.tsv
[2023-03-15 17:41:04,043] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:41:04,043] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:41:04,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1e923c7-ad3d-48b1-be21-49b042871769/dqc_reference/checkm_data
[2023-03-15 17:41:04,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:41:04,050] [INFO] Task started: CheckM
[2023-03-15 17:41:04,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41304/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41304/checkm_input OceanDNA-b41304/checkm_result
[2023-03-15 17:42:39,017] [INFO] Task succeeded: CheckM
[2023-03-15 17:42:39,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.55%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:42:39,022] [INFO] ===== Completeness check finished =====
[2023-03-15 17:42:39,022] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:42:39,022] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41304/markers.fasta)
[2023-03-15 17:42:39,023] [INFO] Task started: Blastn
[2023-03-15 17:42:39,023] [INFO] Running command: blastn -query OceanDNA-b41304/markers.fasta -db /var/lib/cwl/stge1e923c7-ad3d-48b1-be21-49b042871769/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41304/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:42:40,689] [INFO] Task succeeded: Blastn
[2023-03-15 17:42:40,690] [INFO] Selected 19 target genomes.
[2023-03-15 17:42:40,690] [INFO] Target genome list was writen to OceanDNA-b41304/target_genomes_gtdb.txt
[2023-03-15 17:42:41,211] [INFO] Task started: fastANI
[2023-03-15 17:42:41,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfa3e516-68bc-4620-a898-f85983e5b38e/OceanDNA-b41304.fa --refList OceanDNA-b41304/target_genomes_gtdb.txt --output OceanDNA-b41304/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:43:07,311] [INFO] Task succeeded: fastANI
[2023-03-15 17:43:07,322] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:43:07,322] [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_002806685.1	s__Pseudomonas_E qingdaonensis	99.1211	1718	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	conclusive
GCF_019168305.1	s__Pseudomonas_E sp019168305	89.289	1386	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010671725.1	s__Pseudomonas_E brassicae	88.7787	1126	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.75	0.94	0.94	2	-
GCF_900497695.1	s__Pseudomonas_E wadenswilerensis	85.9218	1306	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.26	0.95	0.95	2	-
GCF_000259195.1	s__Pseudomonas_E donghuensis	85.8992	1255	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.33	99.30	0.94	0.92	5	-
GCF_003105155.1	s__Pseudomonas_E sp003105155	85.8528	1150	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800615.1	s__Pseudomonas_E putida_F	85.838	1285	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.83	99.76	0.97	0.96	3	-
GCF_900188455.1	s__Pseudomonas_E japonica	85.3768	1248	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001941965.1	s__Pseudomonas_E putida_L	85.2304	1263	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187455.1	s__Pseudomonas_E sp900187455	84.921	1286	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746525.1	s__Pseudomonas_E alkylphenolica	84.8022	1148	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.61	96.52	0.84	0.83	3	-
GCF_000621225.1	s__Pseudomonas_E mosselii	84.7689	1238	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
GCF_003231275.1	s__Pseudomonas_E huaxiensis	84.6748	1287	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.93	95.93	0.85	0.85	2	-
GCF_002906855.1	s__Pseudomonas_E putida_N	84.4824	1170	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003024385.1	s__Pseudomonas_E sp003024385	84.4501	1102	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009391885.1	s__Pseudomonas_E sp009391885	84.3656	1183	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730605.1	s__Pseudomonas_E monteilii	83.9431	1119	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	-
GCF_002113595.1	s__Pseudomonas_E sp002113595	83.6761	1107	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	96.42	0.97	0.93	16	-
GCF_900109995.1	s__Pseudomonas_E sp900109995	82.5038	972	1884	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:43:07,322] [INFO] GTDB search result was written to OceanDNA-b41304/result_gtdb.tsv
[2023-03-15 17:43:07,322] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:43:07,324] [INFO] DFAST_QC result json was written to OceanDNA-b41304/dqc_result.json
[2023-03-15 17:43:07,325] [INFO] DFAST_QC completed!
[2023-03-15 17:43:07,325] [INFO] Total running time: 0h3m13s