[2024-01-24 11:35:11,296] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,299] [INFO] DQC Reference Directory: /var/lib/cwl/stge7fe8392-a9aa-446d-9839-93ae96ca945a/dqc_reference
[2024-01-24 11:35:12,726] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,727] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,727] [INFO] Running command: gunzip -c /var/lib/cwl/stgba68c205-1801-43c1-91b0-a410e71ac1bc/GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna.gz | prodigal -d GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/cds.fna -a GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:18,385] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:18,385] [INFO] Task started: HMMsearch
[2024-01-24 11:35:18,385] [INFO] Running command: hmmsearch --tblout GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7fe8392-a9aa-446d-9839-93ae96ca945a/dqc_reference/reference_markers.hmm GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:18,662] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:18,663] [INFO] Found 6/6 markers.
[2024-01-24 11:35:18,689] [INFO] Query marker FASTA was written to GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/markers.fasta
[2024-01-24 11:35:18,689] [INFO] Task started: Blastn
[2024-01-24 11:35:18,690] [INFO] Running command: blastn -query GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7fe8392-a9aa-446d-9839-93ae96ca945a/dqc_reference/reference_markers.fasta -out GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:19,351] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:19,356] [INFO] Selected 20 target genomes.
[2024-01-24 11:35:19,356] [INFO] Target genome list was writen to GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:19,386] [INFO] Task started: fastANI
[2024-01-24 11:35:19,386] [INFO] Running command: fastANI --query /var/lib/cwl/stgba68c205-1801-43c1-91b0-a410e71ac1bc/GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna.gz --refList GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/target_genomes.txt --output GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:32,813] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:32,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7fe8392-a9aa-446d-9839-93ae96ca945a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:32,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7fe8392-a9aa-446d-9839-93ae96ca945a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:32,824] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:32,825] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:32,825] [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 yabuuchiae	strain=OA1-2	GCA_900640115.1	376727	376727	type	True	100.0	842	845	95	conclusive
Legionella impletisoli	strain=OA1-1	GCA_900639875.1	343510	343510	type	True	79.8901	449	845	95	below_threshold
Legionella impletisoli	strain=JCM 13919	GCA_014646855.1	343510	343510	type	True	79.7705	464	845	95	below_threshold
Legionella oakridgensis	strain=Oak Ridge-10	GCA_001467925.1	29423	29423	type	True	78.1651	82	845	95	below_threshold
Legionella maceachernii	strain=PX-1-G2-E2	GCA_001467845.1	466	466	type	True	77.9124	59	845	95	below_threshold
Legionella longbeachae	strain=FDAARGOS_1481	GCA_019930685.1	450	450	type	True	77.6596	52	845	95	below_threshold
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	77.4386	51	845	95	below_threshold
Legionella adelaidensis	strain=1762-AUS-E	GCA_001467055.1	45056	45056	type	True	77.3513	58	845	95	below_threshold
Legionella bononiensis	strain=30cs62	GCA_016786415.1	2793102	2793102	type	True	77.3149	54	845	95	below_threshold
Legionella septentrionalis	strain=km711	GCA_003989745.1	2498109	2498109	type	True	77.2996	73	845	95	below_threshold
Legionella nagasakiensis	strain=JCM 15315	GCA_900639915.1	535290	535290	type	True	77.2201	85	845	95	below_threshold
Legionella anisa	strain=WA-316-C3	GCA_001467525.1	28082	28082	type	True	76.8342	66	845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:32,827] [INFO] DFAST Taxonomy check result was written to GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:32,827] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:32,827] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:32,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7fe8392-a9aa-446d-9839-93ae96ca945a/dqc_reference/checkm_data
[2024-01-24 11:35:32,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:32,858] [INFO] Task started: CheckM
[2024-01-24 11:35:32,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/checkm_input GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/checkm_result
[2024-01-24 11:35:56,803] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:56,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:56,824] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:56,824] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:56,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:56,825] [INFO] Task started: Blastn
[2024-01-24 11:35:56,825] [INFO] Running command: blastn -query GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7fe8392-a9aa-446d-9839-93ae96ca945a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:57,815] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:57,819] [INFO] Selected 23 target genomes.
[2024-01-24 11:35:57,820] [INFO] Target genome list was writen to GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:57,841] [INFO] Task started: fastANI
[2024-01-24 11:35:57,842] [INFO] Running command: fastANI --query /var/lib/cwl/stgba68c205-1801-43c1-91b0-a410e71ac1bc/GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna.gz --refList GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:10,504] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:10,518] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:10,518] [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_900640115.1	s__Legionella_A yabuuchiae	100.0	842	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004571175.1	s__Legionella_D israelensis	80.2828	76	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_D	95.0	99.34	97.95	0.96	0.86	7	-
GCF_900639875.1	s__Legionella_A impletisoli	79.8901	449	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000512355.1	s__Legionella_A oakridgensis	78.318	80	845	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_001467745.1	s__Tatlockia jamestowniensis	77.8615	52	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.71	99.16	0.98	0.95	4	-
GCF_900167045.1	s__Tatlockia maceachernii	77.727	56	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.96	0.99	0.99	4	-
GCF_014109805.1	s__Legionella sp014109805	77.5554	54	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467615.1	s__Legionella_C erythra	77.5507	56	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.95	99.95	0.98	0.98	2	-
GCA_004283175.1	s__Legionella longbeachae	77.5002	50	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.77	99.22	0.96	0.94	9	-
GCF_003989745.1	s__Legionella_A septentrionalis	77.3364	72	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	99.39	99.22	0.94	0.93	4	-
GCF_016786215.1	s__Legionella sp016786215	77.2421	55	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
GCF_900639985.1	s__Legionella rowbothamii	77.1969	53	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900639915.1	s__Legionella_A nagasakiensis	77.1908	86	845	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_001467525.1	s__Legionella anisa	76.8687	65	845	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 11:36:10,520] [INFO] GTDB search result was written to GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:10,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:10,524] [INFO] DFAST_QC result json was written to GCF_900640115.1_Leg_yabuuchiae_OA1-2.v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:10,524] [INFO] DFAST_QC completed!
[2024-01-24 11:36:10,524] [INFO] Total running time: 0h0m59s