[2024-01-24 12:13:53,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:53,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:53,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg01c7db7c-dcd2-4f5f-bac7-e435dcb5a8a0/dqc_reference
[2024-01-24 12:13:54,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:54,361] [INFO] Task started: Prodigal
[2024-01-24 12:13:54,361] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8dcf770-c5a5-4ed6-a4aa-7da0c2ba34ec/GCF_004571175.1_ASM457117v1_genomic.fna.gz | prodigal -d GCF_004571175.1_ASM457117v1_genomic.fna/cds.fna -a GCF_004571175.1_ASM457117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:01,871] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:01,872] [INFO] Task started: HMMsearch
[2024-01-24 12:14:01,872] [INFO] Running command: hmmsearch --tblout GCF_004571175.1_ASM457117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01c7db7c-dcd2-4f5f-bac7-e435dcb5a8a0/dqc_reference/reference_markers.hmm GCF_004571175.1_ASM457117v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:02,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:02,147] [INFO] Found 6/6 markers.
[2024-01-24 12:14:02,179] [INFO] Query marker FASTA was written to GCF_004571175.1_ASM457117v1_genomic.fna/markers.fasta
[2024-01-24 12:14:02,180] [INFO] Task started: Blastn
[2024-01-24 12:14:02,180] [INFO] Running command: blastn -query GCF_004571175.1_ASM457117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c7db7c-dcd2-4f5f-bac7-e435dcb5a8a0/dqc_reference/reference_markers.fasta -out GCF_004571175.1_ASM457117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:02,833] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:02,837] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:02,837] [INFO] Target genome list was writen to GCF_004571175.1_ASM457117v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:02,859] [INFO] Task started: fastANI
[2024-01-24 12:14:02,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8dcf770-c5a5-4ed6-a4aa-7da0c2ba34ec/GCF_004571175.1_ASM457117v1_genomic.fna.gz --refList GCF_004571175.1_ASM457117v1_genomic.fna/target_genomes.txt --output GCF_004571175.1_ASM457117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:14,138] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:14,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01c7db7c-dcd2-4f5f-bac7-e435dcb5a8a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:14,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01c7db7c-dcd2-4f5f-bac7-e435dcb5a8a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:14,149] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:14:14,149] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:14,149] [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 israelensis	strain=Bercovier 4	GCA_004571175.1	454	454	type	True	100.0	1084	1087	95	conclusive
Legionella israelensis	strain=NCTC12010	GCA_900452605.1	454	454	type	True	99.9969	1083	1087	95	conclusive
Legionella israelensis	strain=DSM 19235	GCA_900101805.1	454	454	type	True	99.8755	931	1087	95	conclusive
Legionella israelensis	strain=Bercovier 4	GCA_900640145.1	454	454	type	True	99.8656	933	1087	95	conclusive
Legionella israelensis	strain=Bercovier 4	GCA_001467785.1	454	454	type	True	99.786	952	1087	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:14:14,151] [INFO] DFAST Taxonomy check result was written to GCF_004571175.1_ASM457117v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:14,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:14,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:14,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01c7db7c-dcd2-4f5f-bac7-e435dcb5a8a0/dqc_reference/checkm_data
[2024-01-24 12:14:14,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:14,189] [INFO] Task started: CheckM
[2024-01-24 12:14:14,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004571175.1_ASM457117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004571175.1_ASM457117v1_genomic.fna/checkm_input GCF_004571175.1_ASM457117v1_genomic.fna/checkm_result
[2024-01-24 12:14:42,934] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:42,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:42,959] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:42,960] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:42,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004571175.1_ASM457117v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:42,961] [INFO] Task started: Blastn
[2024-01-24 12:14:42,961] [INFO] Running command: blastn -query GCF_004571175.1_ASM457117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c7db7c-dcd2-4f5f-bac7-e435dcb5a8a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004571175.1_ASM457117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:43,982] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:43,988] [INFO] Selected 28 target genomes.
[2024-01-24 12:14:43,988] [INFO] Target genome list was writen to GCF_004571175.1_ASM457117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:44,007] [INFO] Task started: fastANI
[2024-01-24 12:14:44,007] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8dcf770-c5a5-4ed6-a4aa-7da0c2ba34ec/GCF_004571175.1_ASM457117v1_genomic.fna.gz --refList GCF_004571175.1_ASM457117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004571175.1_ASM457117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:59,267] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:59,286] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:59,287] [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_004571175.1	s__Legionella_D israelensis	100.0	1086	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_D	95.0	99.34	97.95	0.96	0.86	7	conclusive
GCF_001467825.1	s__Legionella_A londiniensis	80.5587	79	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	99.98	99.97	0.99	0.99	3	-
GCF_900639915.1	s__Legionella_A nagasakiensis	78.964	86	1087	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_900452385.1	s__Tatlockia donaldsonii	78.4925	68	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512355.1	s__Legionella_A oakridgensis	78.4375	71	1087	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_000953635.1	s__Tatlockia micdadei	78.3569	57	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.75	0.99	0.96	7	-
GCF_900452415.1	s__Legionella cincinnatiensis	78.18	79	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_900637635.1	s__Tatlockia jordanis	78.1617	81	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.59	0.99	0.98	6	-
GCF_001467625.1	s__Tatlockia feeleii	77.6983	68	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.52	98.18	0.97	0.92	5	-
GCF_000953135.1	s__Legionella fallonii	77.6885	75	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468065.1	s__Legionella steigerwaltii	77.5707	60	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001467955.1	s__Legionella quateirensis	77.4428	74	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.97	99.97	0.99	0.99	3	-
GCA_017306715.1	s__Legionella sp001899505	77.4339	50	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.70	99.70	0.88	0.88	2	-
GCA_000586315.1	s__Legionella fraseri	77.4194	68	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.50	96.27	0.94	0.87	43	-
GCF_000008485.1	s__Legionella pneumophila	77.3807	78	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.85	95.56	0.93	0.84	789	-
GCF_900637585.1	s__Legionella pascullei	77.3173	81	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.92	99.72	1.00	0.99	8	-
GCF_000621525.1	s__Tatlockia fairfieldensis	77.284	79	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_016786215.1	s__Legionella sp016786215	76.887	75	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
GCA_013697725.1	s__Tatlockia sp013697725	76.7728	51	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467535.1	s__Legionella worsleiensis	76.7589	67	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000423305.1	s__Legionella moravica	76.697	65	1087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.09	96.46	0.96	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:59,295] [INFO] GTDB search result was written to GCF_004571175.1_ASM457117v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:59,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:59,300] [INFO] DFAST_QC result json was written to GCF_004571175.1_ASM457117v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:59,301] [INFO] DFAST_QC completed!
[2024-01-24 12:14:59,301] [INFO] Total running time: 0h1m6s