[2024-01-24 12:31:34,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,189] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,189] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eadbfc2-f473-4fc0-8b43-63df3c492808/dqc_reference
[2024-01-24 12:31:35,430] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,431] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,431] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a77fad9-b177-4656-919d-8ff70e8c7ff1/GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna.gz | prodigal -d GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/cds.fna -a GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:42,786] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:42,786] [INFO] Task started: HMMsearch
[2024-01-24 12:31:42,786] [INFO] Running command: hmmsearch --tblout GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eadbfc2-f473-4fc0-8b43-63df3c492808/dqc_reference/reference_markers.hmm GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:43,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:43,126] [INFO] Found 6/6 markers.
[2024-01-24 12:31:43,160] [INFO] Query marker FASTA was written to GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/markers.fasta
[2024-01-24 12:31:43,160] [INFO] Task started: Blastn
[2024-01-24 12:31:43,160] [INFO] Running command: blastn -query GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eadbfc2-f473-4fc0-8b43-63df3c492808/dqc_reference/reference_markers.fasta -out GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:43,814] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:43,817] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:43,817] [INFO] Target genome list was writen to GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:43,820] [INFO] Task started: fastANI
[2024-01-24 12:31:43,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a77fad9-b177-4656-919d-8ff70e8c7ff1/GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna.gz --refList GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/target_genomes.txt --output GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:51,607] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:51,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eadbfc2-f473-4fc0-8b43-63df3c492808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:51,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eadbfc2-f473-4fc0-8b43-63df3c492808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:51,623] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:51,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:51,624] [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 drozanskii	strain=LLAP-1	GCA_900640075.1	96228	96228	type	True	100.0	1153	1155	95	conclusive
Legionella drozanskii	strain=ATCC 700990	GCA_001467585.1	96228	96228	type	True	99.9693	1146	1155	95	conclusive
Legionella nautarum	strain=1224	GCA_900639935.1	45070	45070	type	True	86.5642	889	1155	95	below_threshold
Legionella nautarum	strain=ATCC 49506	GCA_001467895.1	45070	45070	type	True	86.5281	902	1155	95	below_threshold
Legionella maceachernii	strain=PX-1-G2-E2	GCA_001467845.1	466	466	type	True	78.3565	344	1155	95	below_threshold
Tatlockia micdadei	strain=ATCC 33218	GCA_900102325.1	451	451	type	True	78.3139	361	1155	95	below_threshold
Legionella massiliensis	strain=LegA	GCA_000756815.1	1034943	1034943	type	True	77.9736	215	1155	95	below_threshold
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	77.2762	71	1155	95	below_threshold
Legionella rowbothamii	strain=LLAP6	GCA_900639985.1	96229	96229	type	True	76.7425	86	1155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:51,625] [INFO] DFAST Taxonomy check result was written to GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:51,626] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:51,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:51,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eadbfc2-f473-4fc0-8b43-63df3c492808/dqc_reference/checkm_data
[2024-01-24 12:31:51,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:51,667] [INFO] Task started: CheckM
[2024-01-24 12:31:51,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/checkm_input GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/checkm_result
[2024-01-24 12:32:19,890] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:19,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:19,915] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:19,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:19,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:19,916] [INFO] Task started: Blastn
[2024-01-24 12:32:19,917] [INFO] Running command: blastn -query GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eadbfc2-f473-4fc0-8b43-63df3c492808/dqc_reference/reference_markers_gtdb.fasta -out GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:20,916] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:20,920] [INFO] Selected 12 target genomes.
[2024-01-24 12:32:20,921] [INFO] Target genome list was writen to GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:20,925] [INFO] Task started: fastANI
[2024-01-24 12:32:20,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a77fad9-b177-4656-919d-8ff70e8c7ff1/GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna.gz --refList GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:28,816] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:28,837] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:28,838] [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_001467585.1	s__Tatlockia drozanskii	99.9693	1146	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.88	99.79	0.97	0.95	3	conclusive
GCF_001467895.1	s__Tatlockia nautarum	86.5243	902	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000953635.1	s__Tatlockia micdadei	78.3929	355	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.75	0.99	0.96	7	-
GCF_900167045.1	s__Tatlockia maceachernii	78.3213	354	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.96	0.99	0.99	4	-
GCF_000756815.1	s__Tatlockia massiliensis	77.9692	216	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013812775.1	s__Tatlockia sp013812775	77.8342	165	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467945.1	s__Legionella parisiensis	77.7896	100	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.98	1.00	1.00	4	-
GCF_900452385.1	s__Tatlockia donaldsonii	77.4611	177	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648595.1	s__Legionella bozemanae	77.2805	92	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_016786215.1	s__Legionella sp016786215	77.2058	93	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
GCF_014109805.1	s__Legionella sp014109805	77.088	91	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467525.1	s__Legionella anisa	76.8228	99	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:28,840] [INFO] GTDB search result was written to GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:28,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:28,847] [INFO] DFAST_QC result json was written to GCF_900640075.1_Leg_drozanskii_LLAP-1.v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:28,847] [INFO] DFAST_QC completed!
[2024-01-24 12:32:28,847] [INFO] Total running time: 0h0m55s