[2024-01-25 18:14:20,499] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:20,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:20,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg99788941-ebd6-4a1e-8a53-b7f45715f0f6/dqc_reference
[2024-01-25 18:14:21,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:21,600] [INFO] Task started: Prodigal
[2024-01-25 18:14:21,601] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb513b42-cbde-4283-b60d-eb0c9806cc68/GCF_001467795.1_ASM146779v1_genomic.fna.gz | prodigal -d GCF_001467795.1_ASM146779v1_genomic.fna/cds.fna -a GCF_001467795.1_ASM146779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:27,166] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:27,167] [INFO] Task started: HMMsearch
[2024-01-25 18:14:27,167] [INFO] Running command: hmmsearch --tblout GCF_001467795.1_ASM146779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99788941-ebd6-4a1e-8a53-b7f45715f0f6/dqc_reference/reference_markers.hmm GCF_001467795.1_ASM146779v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:27,385] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:27,386] [INFO] Found 6/6 markers.
[2024-01-25 18:14:27,415] [INFO] Query marker FASTA was written to GCF_001467795.1_ASM146779v1_genomic.fna/markers.fasta
[2024-01-25 18:14:27,415] [INFO] Task started: Blastn
[2024-01-25 18:14:27,415] [INFO] Running command: blastn -query GCF_001467795.1_ASM146779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99788941-ebd6-4a1e-8a53-b7f45715f0f6/dqc_reference/reference_markers.fasta -out GCF_001467795.1_ASM146779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:28,015] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:28,018] [INFO] Selected 13 target genomes.
[2024-01-25 18:14:28,019] [INFO] Target genome list was writen to GCF_001467795.1_ASM146779v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:28,025] [INFO] Task started: fastANI
[2024-01-25 18:14:28,025] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb513b42-cbde-4283-b60d-eb0c9806cc68/GCF_001467795.1_ASM146779v1_genomic.fna.gz --refList GCF_001467795.1_ASM146779v1_genomic.fna/target_genomes.txt --output GCF_001467795.1_ASM146779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:37,579] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:37,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99788941-ebd6-4a1e-8a53-b7f45715f0f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:37,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99788941-ebd6-4a1e-8a53-b7f45715f0f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:37,587] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:14:37,587] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:37,587] [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=ATCC 49751	GCA_001467795.1	45067	45067	type	True	100.0	934	935	95	conclusive
Legionella lansingensis	strain=ATCC 49751	GCA_000622185.1	45067	45067	type	True	99.9862	928	935	95	conclusive
Legionella lansingensis	strain=1677-MI-H	GCA_900640195.1	45067	45067	type	True	99.9861	922	935	95	conclusive
Legionella lansingensis	strain=NCTC12830	GCA_900187355.1	45067	45067	type	True	99.9811	934	935	95	conclusive
Legionella clemsonensis	strain=CDC-D5610	GCA_002240035.1	1867846	1867846	type	True	78.1626	205	935	95	below_threshold
Legionella brunensis	strain=ATCC 43878	GCA_001467025.1	29422	29422	type	True	78.1574	287	935	95	below_threshold
Legionella hackeliae	strain=ATCC35250	GCA_000953655.1	449	449	type	True	77.8297	227	935	95	below_threshold
Legionella jamestowniensis	strain=DSM 19215	GCA_900114725.1	455	455	type	True	77.6635	209	935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:37,588] [INFO] DFAST Taxonomy check result was written to GCF_001467795.1_ASM146779v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:37,589] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:37,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:37,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99788941-ebd6-4a1e-8a53-b7f45715f0f6/dqc_reference/checkm_data
[2024-01-25 18:14:37,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:37,621] [INFO] Task started: CheckM
[2024-01-25 18:14:37,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001467795.1_ASM146779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001467795.1_ASM146779v1_genomic.fna/checkm_input GCF_001467795.1_ASM146779v1_genomic.fna/checkm_result
[2024-01-25 18:14:59,654] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:59,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:59,670] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:59,671] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:59,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001467795.1_ASM146779v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:59,671] [INFO] Task started: Blastn
[2024-01-25 18:14:59,671] [INFO] Running command: blastn -query GCF_001467795.1_ASM146779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99788941-ebd6-4a1e-8a53-b7f45715f0f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001467795.1_ASM146779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:00,635] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:00,637] [INFO] Selected 19 target genomes.
[2024-01-25 18:15:00,637] [INFO] Target genome list was writen to GCF_001467795.1_ASM146779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:00,646] [INFO] Task started: fastANI
[2024-01-25 18:15:00,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb513b42-cbde-4283-b60d-eb0c9806cc68/GCF_001467795.1_ASM146779v1_genomic.fna.gz --refList GCF_001467795.1_ASM146779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001467795.1_ASM146779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:13,360] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:13,372] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:13,373] [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	99.9811	934	935	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_002240035.1	s__Tatlockia clemsonensis	78.1631	205	935	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	78.1626	286	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900637635.1	s__Tatlockia jordanis	78.1264	175	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.59	0.99	0.98	6	-
GCF_001467745.1	s__Tatlockia jamestowniensis	77.8276	208	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.71	99.16	0.98	0.95	4	-
GCF_000953655.1	s__Tatlockia hackeliae	77.8156	228	935	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	77.7346	113	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.88	99.79	0.97	0.95	3	-
GCF_900640175.1	s__Tatlockia sp900640175	77.6786	139	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512355.1	s__Legionella_A oakridgensis	77.6037	78	935	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_000756815.1	s__Tatlockia massiliensis	77.5079	113	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000308315.1	s__Tatlockia tunisiensis	77.4863	152	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637685.1	s__Legionella sainthelensi	77.3773	65	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.79	95.71	0.95	0.89	8	-
GCF_900452415.1	s__Legionella cincinnatiensis	77.3657	83	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_001468135.1	s__Legionella santicrucis	77.3428	75	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001468005.1	s__Legionella steelei	77.1073	92	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.95	98.94	0.93	0.93	3	-
GCF_900635815.1	s__Legionella cherrii	77.041	90	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.61	0.99	0.97	4	-
GCF_001467955.1	s__Legionella quateirensis	77.0005	74	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.97	99.97	0.99	0.99	3	-
GCF_003184185.1	s__Legionella qingyii	76.9525	69	935	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	76.8779	67	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:13,374] [INFO] GTDB search result was written to GCF_001467795.1_ASM146779v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:13,374] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:13,377] [INFO] DFAST_QC result json was written to GCF_001467795.1_ASM146779v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:13,377] [INFO] DFAST_QC completed!
[2024-01-25 18:15:13,377] [INFO] Total running time: 0h0m53s