[2024-01-24 13:25:29,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,567] [INFO] DQC Reference Directory: /var/lib/cwl/stgc442c77e-5743-45dc-91c3-308f6d277391/dqc_reference
[2024-01-24 13:25:30,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:30,869] [INFO] Task started: Prodigal
[2024-01-24 13:25:30,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg88b7e0bc-245f-47e3-8fb1-397c0b518837/GCF_900187355.1_51342_E02_genomic.fna.gz | prodigal -d GCF_900187355.1_51342_E02_genomic.fna/cds.fna -a GCF_900187355.1_51342_E02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:38,117] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:38,117] [INFO] Task started: HMMsearch
[2024-01-24 13:25:38,117] [INFO] Running command: hmmsearch --tblout GCF_900187355.1_51342_E02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc442c77e-5743-45dc-91c3-308f6d277391/dqc_reference/reference_markers.hmm GCF_900187355.1_51342_E02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:38,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:38,422] [INFO] Found 6/6 markers.
[2024-01-24 13:25:38,453] [INFO] Query marker FASTA was written to GCF_900187355.1_51342_E02_genomic.fna/markers.fasta
[2024-01-24 13:25:38,454] [INFO] Task started: Blastn
[2024-01-24 13:25:38,454] [INFO] Running command: blastn -query GCF_900187355.1_51342_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc442c77e-5743-45dc-91c3-308f6d277391/dqc_reference/reference_markers.fasta -out GCF_900187355.1_51342_E02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:39,122] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:39,125] [INFO] Selected 13 target genomes.
[2024-01-24 13:25:39,126] [INFO] Target genome list was writen to GCF_900187355.1_51342_E02_genomic.fna/target_genomes.txt
[2024-01-24 13:25:39,130] [INFO] Task started: fastANI
[2024-01-24 13:25:39,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg88b7e0bc-245f-47e3-8fb1-397c0b518837/GCF_900187355.1_51342_E02_genomic.fna.gz --refList GCF_900187355.1_51342_E02_genomic.fna/target_genomes.txt --output GCF_900187355.1_51342_E02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:48,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:48,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc442c77e-5743-45dc-91c3-308f6d277391/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:48,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc442c77e-5743-45dc-91c3-308f6d277391/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:48,989] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:25:48,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:48,989] [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
Legionella lansingensis	strain=NCTC12830	GCA_900187355.1	45067	45067	type	True	100.0	994	996	95	conclusive
Legionella lansingensis	strain=1677-MI-H	GCA_900640195.1	45067	45067	type	True	99.946	927	996	95	conclusive
Legionella lansingensis	strain=ATCC 49751	GCA_001467795.1	45067	45067	type	True	99.9436	928	996	95	conclusive
Legionella lansingensis	strain=ATCC 49751	GCA_000622185.1	45067	45067	type	True	99.9196	940	996	95	conclusive
Legionella clemsonensis	strain=CDC-D5610	GCA_002240035.1	1867846	1867846	type	True	78.4367	216	996	95	below_threshold
Legionella brunensis	strain=ATCC 43878	GCA_001467025.1	29422	29422	type	True	78.3528	291	996	95	below_threshold
Legionella hackeliae	strain=ATCC35250	GCA_000953655.1	449	449	type	True	78.2204	236	996	95	below_threshold
Legionella jamestowniensis	strain=DSM 19215	GCA_900114725.1	455	455	type	True	77.6859	214	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:48,991] [INFO] DFAST Taxonomy check result was written to GCF_900187355.1_51342_E02_genomic.fna/tc_result.tsv
[2024-01-24 13:25:48,991] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:48,991] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:48,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc442c77e-5743-45dc-91c3-308f6d277391/dqc_reference/checkm_data
[2024-01-24 13:25:48,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:49,025] [INFO] Task started: CheckM
[2024-01-24 13:25:49,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187355.1_51342_E02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187355.1_51342_E02_genomic.fna/checkm_input GCF_900187355.1_51342_E02_genomic.fna/checkm_result
[2024-01-24 13:26:16,864] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:16,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:16,886] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:16,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:16,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187355.1_51342_E02_genomic.fna/markers.fasta)
[2024-01-24 13:26:16,887] [INFO] Task started: Blastn
[2024-01-24 13:26:16,887] [INFO] Running command: blastn -query GCF_900187355.1_51342_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc442c77e-5743-45dc-91c3-308f6d277391/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187355.1_51342_E02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:17,860] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:17,864] [INFO] Selected 19 target genomes.
[2024-01-24 13:26:17,864] [INFO] Target genome list was writen to GCF_900187355.1_51342_E02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:17,883] [INFO] Task started: fastANI
[2024-01-24 13:26:17,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg88b7e0bc-245f-47e3-8fb1-397c0b518837/GCF_900187355.1_51342_E02_genomic.fna.gz --refList GCF_900187355.1_51342_E02_genomic.fna/target_genomes_gtdb.txt --output GCF_900187355.1_51342_E02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:30,037] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:30,065] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:30,065] [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_900187355.1	s__Tatlockia lansingensis	100.0	993	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.99	99.98	1.00	1.00	4	conclusive
GCF_000512355.1	s__Legionella_A oakridgensis	78.5968	78	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	99.85	99.51	0.97	0.90	5	-
GCF_900637635.1	s__Tatlockia jordanis	78.5217	183	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.59	0.99	0.98	6	-
GCF_002240035.1	s__Tatlockia clemsonensis	78.3924	213	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467025.1	s__Tatlockia brunensis	78.3457	291	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000953655.1	s__Tatlockia hackeliae	78.288	238	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.95	99.91	0.98	0.96	3	-
GCF_001467585.1	s__Tatlockia drozanskii	78.0442	115	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.88	99.79	0.97	0.95	3	-
GCF_900637685.1	s__Legionella sainthelensi	78.0129	77	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.79	95.71	0.95	0.89	8	-
GCF_001467745.1	s__Tatlockia jamestowniensis	77.9516	217	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.71	99.16	0.98	0.95	4	-
GCF_900452415.1	s__Legionella cincinnatiensis	77.9259	97	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000756815.1	s__Tatlockia massiliensis	77.756	119	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900635815.1	s__Legionella cherrii	77.6753	90	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.61	0.99	0.97	4	-
GCF_900640175.1	s__Tatlockia sp900640175	77.6219	139	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467955.1	s__Legionella quateirensis	77.5508	75	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.97	99.97	0.99	0.99	3	-
GCF_000308315.1	s__Tatlockia tunisiensis	77.388	157	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468005.1	s__Legionella steelei	77.3613	86	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.95	98.94	0.93	0.93	3	-
GCF_001468135.1	s__Legionella santicrucis	77.2815	77	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.96	99.96	0.98	0.98	2	-
GCF_003184185.1	s__Legionella qingyii	77.2536	72	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.76	0.97	0.97	3	-
GCF_016786215.1	s__Legionella sp016786215	76.9468	65	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:30,067] [INFO] GTDB search result was written to GCF_900187355.1_51342_E02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:30,067] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:30,084] [INFO] DFAST_QC result json was written to GCF_900187355.1_51342_E02_genomic.fna/dqc_result.json
[2024-01-24 13:26:30,085] [INFO] DFAST_QC completed!
[2024-01-24 13:26:30,085] [INFO] Total running time: 0h1m1s