[2024-01-25 20:12:05,373] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg3771c8a8-dbe8-4822-b4c0-363ad9b47a71/dqc_reference
[2024-01-25 20:12:06,499] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:06,500] [INFO] Task started: Prodigal
[2024-01-25 20:12:06,500] [INFO] Running command: gunzip -c /var/lib/cwl/stg89bef524-fad3-4f54-95b7-537b84394d18/GCF_014646855.1_ASM1464685v1_genomic.fna.gz | prodigal -d GCF_014646855.1_ASM1464685v1_genomic.fna/cds.fna -a GCF_014646855.1_ASM1464685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:11,151] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:11,151] [INFO] Task started: HMMsearch
[2024-01-25 20:12:11,151] [INFO] Running command: hmmsearch --tblout GCF_014646855.1_ASM1464685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3771c8a8-dbe8-4822-b4c0-363ad9b47a71/dqc_reference/reference_markers.hmm GCF_014646855.1_ASM1464685v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:11,343] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:11,344] [INFO] Found 6/6 markers.
[2024-01-25 20:12:11,364] [INFO] Query marker FASTA was written to GCF_014646855.1_ASM1464685v1_genomic.fna/markers.fasta
[2024-01-25 20:12:11,365] [INFO] Task started: Blastn
[2024-01-25 20:12:11,365] [INFO] Running command: blastn -query GCF_014646855.1_ASM1464685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3771c8a8-dbe8-4822-b4c0-363ad9b47a71/dqc_reference/reference_markers.fasta -out GCF_014646855.1_ASM1464685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:11,957] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:11,965] [INFO] Selected 18 target genomes.
[2024-01-25 20:12:11,965] [INFO] Target genome list was writen to GCF_014646855.1_ASM1464685v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:11,975] [INFO] Task started: fastANI
[2024-01-25 20:12:11,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg89bef524-fad3-4f54-95b7-537b84394d18/GCF_014646855.1_ASM1464685v1_genomic.fna.gz --refList GCF_014646855.1_ASM1464685v1_genomic.fna/target_genomes.txt --output GCF_014646855.1_ASM1464685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:22,551] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:22,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3771c8a8-dbe8-4822-b4c0-363ad9b47a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:22,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3771c8a8-dbe8-4822-b4c0-363ad9b47a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:22,559] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:12:22,560] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:22,560] [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 impletisoli	strain=JCM 13919	GCA_014646855.1	343510	343510	type	True	100.0	819	819	95	conclusive
Legionella impletisoli	strain=OA1-1	GCA_900639875.1	343510	343510	type	True	99.998	817	819	95	conclusive
Legionella yabuuchiae	strain=OA1-2	GCA_900640115.1	376727	376727	type	True	79.8907	446	819	95	below_threshold
Legionella nagasakiensis	strain=JCM 15315	GCA_900639915.1	535290	535290	type	True	77.8378	109	819	95	below_threshold
Legionella anisa	strain=WA-316-C3	GCA_001467525.1	28082	28082	type	True	76.74	62	819	95	below_threshold
Legionella anisa	strain=FDAARGOS_1480	GCA_019930885.1	28082	28082	type	True	76.7249	63	819	95	below_threshold
Legionella clemsonensis	strain=CDC-D5610	GCA_002240035.1	1867846	1867846	type	True	76.6313	60	819	95	below_threshold
Legionella nautarum	strain=1224	GCA_900639935.1	45070	45070	type	True	76.4868	63	819	95	below_threshold
Legionella drancourtii	strain=LLAP12	GCA_000162755.2	168933	168933	type	True	76.2736	68	819	95	below_threshold
Legionella fallonii	strain=LLAP-10	GCA_000953135.1	96230	96230	type	True	76.155	58	819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:22,562] [INFO] DFAST Taxonomy check result was written to GCF_014646855.1_ASM1464685v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:22,563] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:22,563] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:22,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3771c8a8-dbe8-4822-b4c0-363ad9b47a71/dqc_reference/checkm_data
[2024-01-25 20:12:22,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:22,591] [INFO] Task started: CheckM
[2024-01-25 20:12:22,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646855.1_ASM1464685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646855.1_ASM1464685v1_genomic.fna/checkm_input GCF_014646855.1_ASM1464685v1_genomic.fna/checkm_result
[2024-01-25 20:12:42,083] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:42,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:42,103] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:42,103] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:42,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646855.1_ASM1464685v1_genomic.fna/markers.fasta)
[2024-01-25 20:12:42,103] [INFO] Task started: Blastn
[2024-01-25 20:12:42,103] [INFO] Running command: blastn -query GCF_014646855.1_ASM1464685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3771c8a8-dbe8-4822-b4c0-363ad9b47a71/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646855.1_ASM1464685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:43,084] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:43,087] [INFO] Selected 17 target genomes.
[2024-01-25 20:12:43,087] [INFO] Target genome list was writen to GCF_014646855.1_ASM1464685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:43,109] [INFO] Task started: fastANI
[2024-01-25 20:12:43,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg89bef524-fad3-4f54-95b7-537b84394d18/GCF_014646855.1_ASM1464685v1_genomic.fna.gz --refList GCF_014646855.1_ASM1464685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646855.1_ASM1464685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:51,599] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:51,607] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:51,607] [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_900639875.1	s__Legionella_A impletisoli	99.998	817	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900640115.1	s__Legionella_A yabuuchiae	79.877	448	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900639915.1	s__Legionella_A nagasakiensis	77.8378	109	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697725.1	s__Tatlockia sp013697725	76.8592	57	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003989735.1	s__Legionella sp003989735	76.7735	59	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900452385.1	s__Tatlockia donaldsonii	76.7336	61	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467525.1	s__Legionella anisa	76.7031	63	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_002240035.1	s__Tatlockia clemsonensis	76.6667	59	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467895.1	s__Tatlockia nautarum	76.4129	63	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCA_013697645.1	s__Tatlockia sp013697645	76.3176	50	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467585.1	s__Tatlockia drozanskii	76.2987	61	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.88	99.79	0.97	0.95	3	-
GCF_000162755.2	s__Legionella drancourtii	76.2736	68	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953135.1	s__Legionella fallonii	76.155	58	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:51,610] [INFO] GTDB search result was written to GCF_014646855.1_ASM1464685v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:51,611] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:51,614] [INFO] DFAST_QC result json was written to GCF_014646855.1_ASM1464685v1_genomic.fna/dqc_result.json
[2024-01-25 20:12:51,614] [INFO] DFAST_QC completed!
[2024-01-25 20:12:51,614] [INFO] Total running time: 0h0m46s