[2024-01-24 15:19:04,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,049] [INFO] DQC Reference Directory: /var/lib/cwl/stgdef4fbc6-235f-484f-8438-03c4f8b7a1e3/dqc_reference
[2024-01-24 15:19:05,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,324] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c9aed55-7445-4e4a-a834-e6524919fc4e/GCF_018139685.1_ASM1813968v1_genomic.fna.gz | prodigal -d GCF_018139685.1_ASM1813968v1_genomic.fna/cds.fna -a GCF_018139685.1_ASM1813968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:18,241] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:18,241] [INFO] Task started: HMMsearch
[2024-01-24 15:19:18,241] [INFO] Running command: hmmsearch --tblout GCF_018139685.1_ASM1813968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdef4fbc6-235f-484f-8438-03c4f8b7a1e3/dqc_reference/reference_markers.hmm GCF_018139685.1_ASM1813968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:18,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:18,539] [INFO] Found 6/6 markers.
[2024-01-24 15:19:18,583] [INFO] Query marker FASTA was written to GCF_018139685.1_ASM1813968v1_genomic.fna/markers.fasta
[2024-01-24 15:19:18,583] [INFO] Task started: Blastn
[2024-01-24 15:19:18,583] [INFO] Running command: blastn -query GCF_018139685.1_ASM1813968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdef4fbc6-235f-484f-8438-03c4f8b7a1e3/dqc_reference/reference_markers.fasta -out GCF_018139685.1_ASM1813968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:19,318] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:19,322] [INFO] Selected 15 target genomes.
[2024-01-24 15:19:19,323] [INFO] Target genome list was writen to GCF_018139685.1_ASM1813968v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:19,345] [INFO] Task started: fastANI
[2024-01-24 15:19:19,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c9aed55-7445-4e4a-a834-e6524919fc4e/GCF_018139685.1_ASM1813968v1_genomic.fna.gz --refList GCF_018139685.1_ASM1813968v1_genomic.fna/target_genomes.txt --output GCF_018139685.1_ASM1813968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:33,245] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:33,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdef4fbc6-235f-484f-8438-03c4f8b7a1e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:33,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdef4fbc6-235f-484f-8438-03c4f8b7a1e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:33,265] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:33,265] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:33,265] [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
Undibacterium luofuense	strain=LFS511W	GCA_018139685.1	2828733	2828733	type	True	100.0	1415	1417	95	conclusive
Undibacterium squillarum	strain=KCTC 23917	GCA_014652435.1	1131567	1131567	type	True	88.5451	1197	1417	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	78.6442	447	1417	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	78.5703	455	1417	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	78.5061	410	1417	95	below_threshold
Undibacterium griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	78.3008	368	1417	95	below_threshold
Undibacterium oligocarboniphilum	strain=EM 1	GCA_013377855.1	666702	666702	type	True	78.1813	344	1417	95	below_threshold
Undibacterium nitidum	strain=LX22W	GCA_014284155.1	2762298	2762298	type	True	77.5955	115	1417	95	below_threshold
Undibacterium terreum	strain=CGMCC 1.10998	GCA_014636315.1	1224302	1224302	type	True	77.4082	238	1417	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	76.6604	140	1417	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	76.5453	132	1417	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	76.5029	101	1417	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.3276	116	1417	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	76.0085	51	1417	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	75.9748	82	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:33,266] [INFO] DFAST Taxonomy check result was written to GCF_018139685.1_ASM1813968v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:33,267] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:33,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:33,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdef4fbc6-235f-484f-8438-03c4f8b7a1e3/dqc_reference/checkm_data
[2024-01-24 15:19:33,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:33,313] [INFO] Task started: CheckM
[2024-01-24 15:19:33,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018139685.1_ASM1813968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018139685.1_ASM1813968v1_genomic.fna/checkm_input GCF_018139685.1_ASM1813968v1_genomic.fna/checkm_result
[2024-01-24 15:20:14,593] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:14,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 15:20:14,622] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:14,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:14,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018139685.1_ASM1813968v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:14,624] [INFO] Task started: Blastn
[2024-01-24 15:20:14,624] [INFO] Running command: blastn -query GCF_018139685.1_ASM1813968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdef4fbc6-235f-484f-8438-03c4f8b7a1e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_018139685.1_ASM1813968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:15,813] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:15,817] [INFO] Selected 16 target genomes.
[2024-01-24 15:20:15,818] [INFO] Target genome list was writen to GCF_018139685.1_ASM1813968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:15,829] [INFO] Task started: fastANI
[2024-01-24 15:20:15,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c9aed55-7445-4e4a-a834-e6524919fc4e/GCF_018139685.1_ASM1813968v1_genomic.fna.gz --refList GCF_018139685.1_ASM1813968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018139685.1_ASM1813968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:30,250] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:30,264] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:30,264] [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_018139685.1	s__Undibacterium sp018139685	100.0	1415	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014652435.1	s__Undibacterium squillarum	88.5504	1196	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010078235.1	s__Undibacterium crateris	78.6424	446	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284235.1	s__Undibacterium sp014284235	78.5699	454	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284365.1	s__Undibacterium sp014284365	78.5005	409	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.07	99.07	0.95	0.95	2	-
GCF_014284195.1	s__Undibacterium sp014284195	78.3162	369	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377855.1	s__Undibacterium oligocarboniphilum	78.197	342	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014699135.1	s__Undibacterium aquatile	78.1637	338	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	96.61	96.29	0.93	0.93	4	-
GCF_009937955.1	s__Undibacterium sp009937955	77.6707	273	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636315.1	s__Undibacterium terreum	77.4322	236	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257565.1	s__Herbaspirillum sp002257565	77.2371	136	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013625.1	s__Herminiimonas sp000013625	77.019	152	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192645.1	s__Herbaspirillum sp014192645	76.8393	113	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003591035.1	s__Noviherbaspirillum sp003591035	76.6749	139	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191875.1	s__Pseudoduganella violacea	76.5048	132	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013369485.1	s__Pseudoduganella sp013369485	76.2954	140	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:30,266] [INFO] GTDB search result was written to GCF_018139685.1_ASM1813968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:30,267] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:30,273] [INFO] DFAST_QC result json was written to GCF_018139685.1_ASM1813968v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:30,274] [INFO] DFAST_QC completed!
[2024-01-24 15:20:30,274] [INFO] Total running time: 0h1m26s