[2024-01-24 13:27:46,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg32a5afa6-0efc-452e-8e69-fb71668af84e/dqc_reference
[2024-01-24 13:27:47,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,793] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg5009b86b-b5e1-43c8-a03b-74a37faca6a6/GCF_000621525.1_ASM62152v1_genomic.fna.gz | prodigal -d GCF_000621525.1_ASM62152v1_genomic.fna/cds.fna -a GCF_000621525.1_ASM62152v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:53,462] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:53,463] [INFO] Task started: HMMsearch
[2024-01-24 13:27:53,463] [INFO] Running command: hmmsearch --tblout GCF_000621525.1_ASM62152v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32a5afa6-0efc-452e-8e69-fb71668af84e/dqc_reference/reference_markers.hmm GCF_000621525.1_ASM62152v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:53,780] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:53,781] [INFO] Found 6/6 markers.
[2024-01-24 13:27:53,809] [INFO] Query marker FASTA was written to GCF_000621525.1_ASM62152v1_genomic.fna/markers.fasta
[2024-01-24 13:27:53,810] [INFO] Task started: Blastn
[2024-01-24 13:27:53,810] [INFO] Running command: blastn -query GCF_000621525.1_ASM62152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32a5afa6-0efc-452e-8e69-fb71668af84e/dqc_reference/reference_markers.fasta -out GCF_000621525.1_ASM62152v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:54,478] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:54,481] [INFO] Selected 20 target genomes.
[2024-01-24 13:27:54,481] [INFO] Target genome list was writen to GCF_000621525.1_ASM62152v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:54,498] [INFO] Task started: fastANI
[2024-01-24 13:27:54,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg5009b86b-b5e1-43c8-a03b-74a37faca6a6/GCF_000621525.1_ASM62152v1_genomic.fna.gz --refList GCF_000621525.1_ASM62152v1_genomic.fna/target_genomes.txt --output GCF_000621525.1_ASM62152v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:04,763] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:04,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32a5afa6-0efc-452e-8e69-fb71668af84e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:04,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32a5afa6-0efc-452e-8e69-fb71668af84e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:04,777] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:04,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:04,778] [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 fairfieldensis	strain=ATCC 49588	GCA_000621525.1	45064	45064	type	True	100.0	851	855	95	conclusive
Legionella fairfieldensis	strain=1725-Aus-E	GCA_900640125.1	45064	45064	type	True	99.9287	836	855	95	conclusive
Legionella quateirensis	strain=NCTC12376	GCA_900452695.1	45072	45072	type	True	78.1058	86	855	95	below_threshold
Legionella gratiana	strain=NCTC12388	GCA_900452545.1	45066	45066	type	True	77.9816	84	855	95	below_threshold
Legionella quateirensis	strain=ATCC 49507	GCA_001467955.1	45072	45072	type	True	77.9573	85	855	95	below_threshold
Legionella gratiana	strain=Lyon 8420412	GCA_900639855.1	45066	45066	type	True	77.8548	82	855	95	below_threshold
Legionella massiliensis	strain=LegA	GCA_000756815.1	1034943	1034943	type	True	77.7997	148	855	95	below_threshold
Legionella gratiana	strain=Lyon 8420412	GCA_001467695.1	45066	45066	type	True	77.7542	85	855	95	below_threshold
Legionella drozanskii	strain=ATCC 700990	GCA_001467585.1	96228	96228	type	True	77.6785	151	855	95	below_threshold
Legionella nautarum	strain=ATCC 49506	GCA_001467895.1	45070	45070	type	True	77.4822	145	855	95	below_threshold
Legionella feeleii	strain=NCTC12022	GCA_900452475.1	453	453	type	True	77.4615	157	855	95	below_threshold
Legionella bononiensis	strain=30cs62	GCA_016786415.1	2793102	2793102	type	True	77.4416	98	855	95	below_threshold
Legionella feeleii	strain=WO-44C	GCA_001467625.1	453	453	type	True	77.3532	153	855	95	below_threshold
Legionella nautarum	strain=1224	GCA_900639935.1	45070	45070	type	True	77.3223	150	855	95	below_threshold
Legionella feeleii	strain=ATCC 35072	GCA_001648615.1	453	453	type	True	77.3124	151	855	95	below_threshold
Legionella adelaidensis	strain=NCTC12735	GCA_900637865.1	45056	45056	type	True	77.1141	60	855	95	below_threshold
Legionella adelaidensis	strain=1762-AUS-E	GCA_001467055.1	45056	45056	type	True	76.888	66	855	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:04,780] [INFO] DFAST Taxonomy check result was written to GCF_000621525.1_ASM62152v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:04,781] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:04,781] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:04,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32a5afa6-0efc-452e-8e69-fb71668af84e/dqc_reference/checkm_data
[2024-01-24 13:28:04,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:04,811] [INFO] Task started: CheckM
[2024-01-24 13:28:04,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621525.1_ASM62152v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621525.1_ASM62152v1_genomic.fna/checkm_input GCF_000621525.1_ASM62152v1_genomic.fna/checkm_result
[2024-01-24 13:28:29,431] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:29,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:29,479] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:29,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:29,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621525.1_ASM62152v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:29,480] [INFO] Task started: Blastn
[2024-01-24 13:28:29,481] [INFO] Running command: blastn -query GCF_000621525.1_ASM62152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32a5afa6-0efc-452e-8e69-fb71668af84e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621525.1_ASM62152v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:30,297] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:30,304] [INFO] Selected 23 target genomes.
[2024-01-24 13:28:30,304] [INFO] Target genome list was writen to GCF_000621525.1_ASM62152v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:30,314] [INFO] Task started: fastANI
[2024-01-24 13:28:30,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg5009b86b-b5e1-43c8-a03b-74a37faca6a6/GCF_000621525.1_ASM62152v1_genomic.fna.gz --refList GCF_000621525.1_ASM62152v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621525.1_ASM62152v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:43,093] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:43,114] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:43,114] [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_000621525.1	s__Tatlockia fairfieldensis	100.0	851	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.93	99.93	0.99	0.99	2	conclusive
GCF_014109805.1	s__Legionella sp014109805	80.7587	106	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467025.1	s__Tatlockia brunensis	79.4249	143	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000308315.1	s__Tatlockia tunisiensis	78.3854	159	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002240035.1	s__Tatlockia clemsonensis	78.0904	131	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467955.1	s__Legionella quateirensis	78.0406	83	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.97	99.97	0.99	0.99	3	-
GCF_000756815.1	s__Tatlockia massiliensis	77.8226	147	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001467695.1	s__Legionella gratiana	77.7497	85	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001467585.1	s__Tatlockia drozanskii	77.722	149	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.88	99.79	0.97	0.95	3	-
GCF_900452415.1	s__Legionella cincinnatiensis	77.6313	93	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_900452385.1	s__Tatlockia donaldsonii	77.559	150	855	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	77.5248	143	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900640175.1	s__Tatlockia sp900640175	77.4636	135	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467625.1	s__Tatlockia feeleii	77.3343	154	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.52	98.18	0.97	0.92	5	-
GCA_013812775.1	s__Tatlockia sp013812775	77.2742	118	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697645.1	s__Tatlockia sp013697645	77.2326	110	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167045.1	s__Tatlockia maceachernii	77.1532	147	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.96	0.99	0.99	4	-
GCF_000162755.2	s__Legionella drancourtii	77.0707	92	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637865.1	s__Legionella_A adelaidensis	77.0702	61	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	99.95	99.94	0.97	0.97	3	-
GCA_013697725.1	s__Tatlockia sp013697725	76.9803	118	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863045.1	s__GCA-2863045 sp002863045	76.6136	53	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__GCA-2863045	95.0	98.31	98.18	0.88	0.83	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:43,122] [INFO] GTDB search result was written to GCF_000621525.1_ASM62152v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:43,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:43,131] [INFO] DFAST_QC result json was written to GCF_000621525.1_ASM62152v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:43,131] [INFO] DFAST_QC completed!
[2024-01-24 13:28:43,131] [INFO] Total running time: 0h0m57s