[2024-01-24 13:31:26,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:26,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:26,305] [INFO] DQC Reference Directory: /var/lib/cwl/stge3c4d378-a35e-40e4-8a1e-ecb1564e74b5/dqc_reference
[2024-01-24 13:31:27,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:27,553] [INFO] Task started: Prodigal
[2024-01-24 13:31:27,553] [INFO] Running command: gunzip -c /var/lib/cwl/stgeffc963a-077c-4242-8830-6a69e376fc8a/GCF_030849025.1_ASM3084902v1_genomic.fna.gz | prodigal -d GCF_030849025.1_ASM3084902v1_genomic.fna/cds.fna -a GCF_030849025.1_ASM3084902v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:38,883] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:38,884] [INFO] Task started: HMMsearch
[2024-01-24 13:31:38,884] [INFO] Running command: hmmsearch --tblout GCF_030849025.1_ASM3084902v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3c4d378-a35e-40e4-8a1e-ecb1564e74b5/dqc_reference/reference_markers.hmm GCF_030849025.1_ASM3084902v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:39,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:39,163] [INFO] Found 6/6 markers.
[2024-01-24 13:31:39,197] [INFO] Query marker FASTA was written to GCF_030849025.1_ASM3084902v1_genomic.fna/markers.fasta
[2024-01-24 13:31:39,197] [INFO] Task started: Blastn
[2024-01-24 13:31:39,198] [INFO] Running command: blastn -query GCF_030849025.1_ASM3084902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c4d378-a35e-40e4-8a1e-ecb1564e74b5/dqc_reference/reference_markers.fasta -out GCF_030849025.1_ASM3084902v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:40,149] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:40,153] [INFO] Selected 13 target genomes.
[2024-01-24 13:31:40,153] [INFO] Target genome list was writen to GCF_030849025.1_ASM3084902v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:40,309] [INFO] Task started: fastANI
[2024-01-24 13:31:40,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgeffc963a-077c-4242-8830-6a69e376fc8a/GCF_030849025.1_ASM3084902v1_genomic.fna.gz --refList GCF_030849025.1_ASM3084902v1_genomic.fna/target_genomes.txt --output GCF_030849025.1_ASM3084902v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:51,139] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:51,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3c4d378-a35e-40e4-8a1e-ecb1564e74b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:51,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3c4d378-a35e-40e4-8a1e-ecb1564e74b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:51,156] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:31:51,156] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:31:51,157] [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
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	89.3889	890	1197	95	below_threshold
Oceanimonas doudoroffii	strain=ATCC 27123	GCA_002242685.1	84158	84158	type	True	88.6067	943	1197	95	below_threshold
Oceanimonas smirnovii	strain=ATCC BAA-899	GCA_000381965.1	264574	264574	type	True	84.7135	826	1197	95	below_threshold
Zobellella denitrificans	strain=ZD1	GCA_002237365.1	347534	347534	type	True	84.0167	763	1197	95	below_threshold
Oceanimonas baumannii	strain=ATCC 700832	GCA_002245495.1	129578	129578	type	True	83.5871	849	1197	95	below_threshold
Oceanimonas baumannii	strain=DSM 15594	GCA_004365405.1	129578	129578	type	True	83.5479	851	1197	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	83.4313	799	1197	95	below_threshold
Oceanisphaera psychrotolerans	strain=LAM-WHM-ZC	GCA_001870485.1	1414654	1414654	type	True	82.1173	768	1197	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.3724	204	1197	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.8013	191	1197	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.4122	135	1197	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.2849	181	1197	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.2518	195	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:51,158] [INFO] DFAST Taxonomy check result was written to GCF_030849025.1_ASM3084902v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:51,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:51,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:51,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3c4d378-a35e-40e4-8a1e-ecb1564e74b5/dqc_reference/checkm_data
[2024-01-24 13:31:51,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:51,197] [INFO] Task started: CheckM
[2024-01-24 13:31:51,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030849025.1_ASM3084902v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030849025.1_ASM3084902v1_genomic.fna/checkm_input GCF_030849025.1_ASM3084902v1_genomic.fna/checkm_result
[2024-01-24 13:32:27,885] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:27,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:27,907] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:27,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:27,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030849025.1_ASM3084902v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:27,908] [INFO] Task started: Blastn
[2024-01-24 13:32:27,909] [INFO] Running command: blastn -query GCF_030849025.1_ASM3084902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c4d378-a35e-40e4-8a1e-ecb1564e74b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_030849025.1_ASM3084902v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:29,612] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:29,616] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:29,616] [INFO] Target genome list was writen to GCF_030849025.1_ASM3084902v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:29,650] [INFO] Task started: fastANI
[2024-01-24 13:32:29,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgeffc963a-077c-4242-8830-6a69e376fc8a/GCF_030849025.1_ASM3084902v1_genomic.fna.gz --refList GCF_030849025.1_ASM3084902v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030849025.1_ASM3084902v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:38,879] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:38,893] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:32:38,894] [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_003049725.1	s__Oceanimonas marisflavi	89.4058	889	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243075.1	s__Oceanimonas sp000243075	89.1401	943	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002242685.1	s__Oceanimonas doudoroffii	88.6066	943	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	98.80	98.80	0.94	0.94	2	-
GCF_000381965.1	s__Oceanimonas smirnovii	84.7255	825	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012795.1	s__Zobellella_D taiwanensis	84.1717	804	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237365.1	s__Zobellella denitrificans	84.0141	763	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella	95.0	98.78	98.78	0.93	0.93	2	-
GCF_002245495.1	s__Oceanimonas baumannii	83.5925	849	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003012775.1	s__Zobellella_C endophytica	83.4613	796	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016746085.1	s__CGMCC-1-18722 sp016746085	83.3884	794	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__CGMCC-1-18722	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075035.1	s__Zobellella_A maritima	80.8277	660	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:38,896] [INFO] GTDB search result was written to GCF_030849025.1_ASM3084902v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:38,897] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:38,900] [INFO] DFAST_QC result json was written to GCF_030849025.1_ASM3084902v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:38,901] [INFO] DFAST_QC completed!
[2024-01-24 13:32:38,901] [INFO] Total running time: 0h1m13s