[2024-01-24 10:47:06,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg7375a14b-a7ad-4f94-9838-696467097f58/dqc_reference
[2024-01-24 10:47:12,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,825] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg6127695a-5e8a-4530-8fcc-7195d8612db9/GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna.gz | prodigal -d GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/cds.fna -a GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:20,760] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:20,760] [INFO] Task started: HMMsearch
[2024-01-24 10:47:20,760] [INFO] Running command: hmmsearch --tblout GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7375a14b-a7ad-4f94-9838-696467097f58/dqc_reference/reference_markers.hmm GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:21,055] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:21,057] [INFO] Found 6/6 markers.
[2024-01-24 10:47:21,091] [INFO] Query marker FASTA was written to GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/markers.fasta
[2024-01-24 10:47:21,092] [INFO] Task started: Blastn
[2024-01-24 10:47:21,092] [INFO] Running command: blastn -query GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7375a14b-a7ad-4f94-9838-696467097f58/dqc_reference/reference_markers.fasta -out GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:21,773] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:21,776] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:21,777] [INFO] Target genome list was writen to GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:22,107] [INFO] Task started: fastANI
[2024-01-24 10:47:22,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg6127695a-5e8a-4530-8fcc-7195d8612db9/GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna.gz --refList GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/target_genomes.txt --output GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:29,564] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:29,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7375a14b-a7ad-4f94-9838-696467097f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:29,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7375a14b-a7ad-4f94-9838-696467097f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:29,572] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 10:47:29,572] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:29,573] [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
Fluoribacter gormanii	strain=LS-13	GCA_900640095.1	464	464	type	True	100.0	1193	1197	95	conclusive
Fluoribacter gormanii	strain=NCTC11401	GCA_900450965.1	464	464	type	True	99.9947	1197	1197	95	conclusive
Fluoribacter gormanii	strain=ATCC 33342	GCA_900156395.1	464	464	type	True	99.9923	1186	1197	95	conclusive
Fluoribacter gormanii	strain=ATCC 33297	GCA_001648685.1	464	464	type	True	99.9885	1180	1197	95	conclusive
Fluoribacter gormanii	strain=LS-13	GCA_001467685.1	464	464	type	True	99.9865	1189	1197	95	conclusive
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	78.5052	248	1197	95	below_threshold
Legionella pneumophila subsp. pneumophila	strain=PartS-Lpneumophila-RM8376	GCA_022870105.1	91891	446	type	True	78.3382	165	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:29,575] [INFO] DFAST Taxonomy check result was written to GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:29,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:29,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:29,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7375a14b-a7ad-4f94-9838-696467097f58/dqc_reference/checkm_data
[2024-01-24 10:47:29,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:29,622] [INFO] Task started: CheckM
[2024-01-24 10:47:29,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/checkm_input GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/checkm_result
[2024-01-24 10:47:59,159] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:59,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:59,183] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:59,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:59,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:59,184] [INFO] Task started: Blastn
[2024-01-24 10:47:59,184] [INFO] Running command: blastn -query GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7375a14b-a7ad-4f94-9838-696467097f58/dqc_reference/reference_markers_gtdb.fasta -out GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:00,263] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:00,269] [INFO] Selected 9 target genomes.
[2024-01-24 10:48:00,270] [INFO] Target genome list was writen to GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:00,349] [INFO] Task started: fastANI
[2024-01-24 10:48:00,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg6127695a-5e8a-4530-8fcc-7195d8612db9/GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna.gz --refList GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:09,057] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,066] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:09,066] [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_900156395.1	s__Legionella gormanii	99.9923	1186	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.78	98.94	0.98	0.92	6	conclusive
GCF_003184185.1	s__Legionella qingyii	91.4972	1070	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.76	0.97	0.97	3	-
GCF_014109825.1	s__Legionella sp014109825	85.0958	941	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648595.1	s__Legionella bozemanae	82.562	797	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_001468035.1	s__Legionella tucsonensis	82.3703	761	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001467525.1	s__Legionella anisa	82.2991	815	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_014109805.1	s__Legionella sp014109805	82.241	808	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635815.1	s__Legionella cherrii	81.231	759	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.61	0.99	0.97	4	-
GCF_001468005.1	s__Legionella steelei	81.1346	721	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.95	98.94	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,068] [INFO] GTDB search result was written to GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:09,070] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:09,073] [INFO] DFAST_QC result json was written to GCF_900640095.1_Leg_gormanii_LS-13.v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:09,073] [INFO] DFAST_QC completed!
[2024-01-24 10:48:09,073] [INFO] Total running time: 0h1m2s