[2024-01-24 10:48:09,177] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,179] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,179] [INFO] DQC Reference Directory: /var/lib/cwl/stga92cef7a-1e34-4964-9362-d2ae3a289d94/dqc_reference
[2024-01-24 10:48:23,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,954] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgd838930f-196b-4144-b830-c454765d313e/GCF_900460175.1_50592_A01_genomic.fna.gz | prodigal -d GCF_900460175.1_50592_A01_genomic.fna/cds.fna -a GCF_900460175.1_50592_A01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:32,099] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:32,099] [INFO] Task started: HMMsearch
[2024-01-24 10:48:32,100] [INFO] Running command: hmmsearch --tblout GCF_900460175.1_50592_A01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga92cef7a-1e34-4964-9362-d2ae3a289d94/dqc_reference/reference_markers.hmm GCF_900460175.1_50592_A01_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:32,381] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:32,382] [INFO] Found 6/6 markers.
[2024-01-24 10:48:32,416] [INFO] Query marker FASTA was written to GCF_900460175.1_50592_A01_genomic.fna/markers.fasta
[2024-01-24 10:48:32,416] [INFO] Task started: Blastn
[2024-01-24 10:48:32,416] [INFO] Running command: blastn -query GCF_900460175.1_50592_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stga92cef7a-1e34-4964-9362-d2ae3a289d94/dqc_reference/reference_markers.fasta -out GCF_900460175.1_50592_A01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:33,068] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:33,072] [INFO] Selected 7 target genomes.
[2024-01-24 10:48:33,073] [INFO] Target genome list was writen to GCF_900460175.1_50592_A01_genomic.fna/target_genomes.txt
[2024-01-24 10:48:33,092] [INFO] Task started: fastANI
[2024-01-24 10:48:33,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgd838930f-196b-4144-b830-c454765d313e/GCF_900460175.1_50592_A01_genomic.fna.gz --refList GCF_900460175.1_50592_A01_genomic.fna/target_genomes.txt --output GCF_900460175.1_50592_A01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:38,960] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:38,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga92cef7a-1e34-4964-9362-d2ae3a289d94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:38,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga92cef7a-1e34-4964-9362-d2ae3a289d94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:38,968] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:48:38,968] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:38,968] [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 maceachernii	strain=NCTC11982	GCA_900460175.1	466	466	type	True	100.0	1217	1218	95	conclusive
Legionella maceachernii	strain=ATCC 35300	GCA_900167045.1	466	466	type	True	99.967	1179	1218	95	conclusive
Legionella maceachernii	strain=PX-1-G2-E2	GCA_001467845.1	466	466	type	True	99.937	1171	1218	95	conclusive
Tatlockia micdadei	strain=ATCC33218	GCA_000953635.1	451	451	type	True	81.2717	721	1218	95	below_threshold
Tatlockia micdadei	strain=ATCC 33218	GCA_900102325.1	451	451	type	True	81.2057	695	1218	95	below_threshold
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	78.1686	85	1218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:38,970] [INFO] DFAST Taxonomy check result was written to GCF_900460175.1_50592_A01_genomic.fna/tc_result.tsv
[2024-01-24 10:48:38,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:38,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:38,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga92cef7a-1e34-4964-9362-d2ae3a289d94/dqc_reference/checkm_data
[2024-01-24 10:48:38,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:39,011] [INFO] Task started: CheckM
[2024-01-24 10:48:39,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460175.1_50592_A01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460175.1_50592_A01_genomic.fna/checkm_input GCF_900460175.1_50592_A01_genomic.fna/checkm_result
[2024-01-24 10:49:12,206] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:12,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:12,232] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:12,232] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:12,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460175.1_50592_A01_genomic.fna/markers.fasta)
[2024-01-24 10:49:12,233] [INFO] Task started: Blastn
[2024-01-24 10:49:12,233] [INFO] Running command: blastn -query GCF_900460175.1_50592_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stga92cef7a-1e34-4964-9362-d2ae3a289d94/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460175.1_50592_A01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:13,284] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:13,288] [INFO] Selected 14 target genomes.
[2024-01-24 10:49:13,289] [INFO] Target genome list was writen to GCF_900460175.1_50592_A01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:13,325] [INFO] Task started: fastANI
[2024-01-24 10:49:13,326] [INFO] Running command: fastANI --query /var/lib/cwl/stgd838930f-196b-4144-b830-c454765d313e/GCF_900460175.1_50592_A01_genomic.fna.gz --refList GCF_900460175.1_50592_A01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460175.1_50592_A01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:23,570] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:23,581] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:23,582] [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_900167045.1	s__Tatlockia maceachernii	99.967	1179	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.96	0.99	0.99	4	conclusive
GCF_001468065.1	s__Legionella steigerwaltii	83.6074	108	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.99	0.99	0.99	3	-
GCF_014109825.1	s__Legionella sp014109825	82.1269	120	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953635.1	s__Tatlockia micdadei	81.2647	718	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.75	0.99	0.96	7	-
GCF_001467945.1	s__Legionella parisiensis	81.0673	133	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.98	1.00	1.00	4	-
GCF_000953655.1	s__Tatlockia hackeliae	80.3717	154	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.95	99.91	0.98	0.96	3	-
GCF_900452385.1	s__Tatlockia donaldsonii	79.5898	168	1218	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	78.4259	362	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001467585.1	s__Tatlockia drozanskii	78.4169	342	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.88	99.79	0.97	0.95	3	-
GCF_002240035.1	s__Tatlockia clemsonensis	78.382	147	1218	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	77.7279	149	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.52	98.18	0.97	0.92	5	-
GCF_000621525.1	s__Tatlockia fairfieldensis	77.4032	143	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.93	99.93	0.99	0.99	2	-
GCA_013812775.1	s__Tatlockia sp013812775	77.1274	138	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:23,590] [INFO] GTDB search result was written to GCF_900460175.1_50592_A01_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:23,591] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:23,597] [INFO] DFAST_QC result json was written to GCF_900460175.1_50592_A01_genomic.fna/dqc_result.json
[2024-01-24 10:49:23,597] [INFO] DFAST_QC completed!
[2024-01-24 10:49:23,597] [INFO] Total running time: 0h1m14s