[2024-01-24 11:59:12,129] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:12,131] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:12,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg36bba219-91c0-43d4-89b5-1a3205c87110/dqc_reference
[2024-01-24 11:59:13,495] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:13,496] [INFO] Task started: Prodigal
[2024-01-24 11:59:13,496] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ec2f372-8b2d-4e94-a6a7-254daee9ee3f/GCF_010671725.1_ASM1067172v1_genomic.fna.gz | prodigal -d GCF_010671725.1_ASM1067172v1_genomic.fna/cds.fna -a GCF_010671725.1_ASM1067172v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:29,828] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:29,829] [INFO] Task started: HMMsearch
[2024-01-24 11:59:29,829] [INFO] Running command: hmmsearch --tblout GCF_010671725.1_ASM1067172v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36bba219-91c0-43d4-89b5-1a3205c87110/dqc_reference/reference_markers.hmm GCF_010671725.1_ASM1067172v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:30,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:30,222] [INFO] Found 6/6 markers.
[2024-01-24 11:59:30,275] [INFO] Query marker FASTA was written to GCF_010671725.1_ASM1067172v1_genomic.fna/markers.fasta
[2024-01-24 11:59:30,276] [INFO] Task started: Blastn
[2024-01-24 11:59:30,276] [INFO] Running command: blastn -query GCF_010671725.1_ASM1067172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36bba219-91c0-43d4-89b5-1a3205c87110/dqc_reference/reference_markers.fasta -out GCF_010671725.1_ASM1067172v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:31,307] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:31,311] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:31,311] [INFO] Target genome list was writen to GCF_010671725.1_ASM1067172v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:31,318] [INFO] Task started: fastANI
[2024-01-24 11:59:31,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ec2f372-8b2d-4e94-a6a7-254daee9ee3f/GCF_010671725.1_ASM1067172v1_genomic.fna.gz --refList GCF_010671725.1_ASM1067172v1_genomic.fna/target_genomes.txt --output GCF_010671725.1_ASM1067172v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:55,950] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:55,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36bba219-91c0-43d4-89b5-1a3205c87110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:55,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36bba219-91c0-43d4-89b5-1a3205c87110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:55,969] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:55,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:55,970] [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	100.0	1509	1527	95	conclusive
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	84.9722	989	1527	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	84.9333	1035	1527	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	84.9226	980	1527	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	84.9144	1034	1527	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	84.4204	1004	1527	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	83.8526	914	1527	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	83.8201	965	1527	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	83.553	791	1527	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	83.3899	932	1527	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	83.3525	941	1527	95	below_threshold
Pseudomonas laurentiana	strain=JCM 32154	GCA_014648275.1	2364649	2364649	type	True	83.3409	856	1527	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	83.2824	946	1527	95	below_threshold
Pseudomonas arcuscaelestis	strain=P66	GCA_016881005.1	2710591	2710591	type	True	83.1016	905	1527	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	82.901	856	1527	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	82.3677	893	1527	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	82.2872	879	1527	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	81.9568	818	1527	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	81.5735	833	1527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:55,972] [INFO] DFAST Taxonomy check result was written to GCF_010671725.1_ASM1067172v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:55,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:55,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:55,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36bba219-91c0-43d4-89b5-1a3205c87110/dqc_reference/checkm_data
[2024-01-24 11:59:55,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:56,099] [INFO] Task started: CheckM
[2024-01-24 11:59:56,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010671725.1_ASM1067172v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010671725.1_ASM1067172v1_genomic.fna/checkm_input GCF_010671725.1_ASM1067172v1_genomic.fna/checkm_result
[2024-01-24 12:00:44,040] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:44,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:44,062] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:44,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:44,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010671725.1_ASM1067172v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:44,063] [INFO] Task started: Blastn
[2024-01-24 12:00:44,063] [INFO] Running command: blastn -query GCF_010671725.1_ASM1067172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36bba219-91c0-43d4-89b5-1a3205c87110/dqc_reference/reference_markers_gtdb.fasta -out GCF_010671725.1_ASM1067172v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:45,734] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:45,738] [INFO] Selected 16 target genomes.
[2024-01-24 12:00:45,739] [INFO] Target genome list was writen to GCF_010671725.1_ASM1067172v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:45,749] [INFO] Task started: fastANI
[2024-01-24 12:00:45,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ec2f372-8b2d-4e94-a6a7-254daee9ee3f/GCF_010671725.1_ASM1067172v1_genomic.fna.gz --refList GCF_010671725.1_ASM1067172v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010671725.1_ASM1067172v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:04,949] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:04,967] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:04,968] [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_010671725.1	s__Pseudomonas_E brassicae	100.0	1509	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.75	0.94	0.94	2	conclusive
GCF_019168305.1	s__Pseudomonas_E sp019168305	92.1197	1299	1527	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_002806685.1	s__Pseudomonas_E qingdaonensis	88.9623	1185	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	-
GCF_018417635.1	s__Pseudomonas_E sp900101695	85.9306	1087	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.49	97.27	0.95	0.94	5	-
GCF_003105155.1	s__Pseudomonas_E sp003105155	85.8233	994	1527	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_900497695.1	s__Pseudomonas_E wadenswilerensis	85.7613	1078	1527	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	85.7207	1046	1527	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_000800615.1	s__Pseudomonas_E putida_F	85.7031	1075	1527	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	84.9107	1036	1527	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_000746525.1	s__Pseudomonas_E alkylphenolica	84.8991	983	1527	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_001941965.1	s__Pseudomonas_E putida_L	84.7212	1075	1527	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_003024385.1	s__Pseudomonas_E sp003024385	84.5732	920	1527	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_000955815.1	s__Pseudomonas_E sp000955815	83.8972	945	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.49	99.49	0.96	0.96	2	-
GCF_004353925.1	s__Pseudomonas_E sp004353925	83.69	920	1527	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_002113595.1	s__Pseudomonas_E sp002113595	83.4854	938	1527	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	82.787	791	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:04,970] [INFO] GTDB search result was written to GCF_010671725.1_ASM1067172v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:04,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:04,975] [INFO] DFAST_QC result json was written to GCF_010671725.1_ASM1067172v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:04,976] [INFO] DFAST_QC completed!
[2024-01-24 12:01:04,976] [INFO] Total running time: 0h1m53s