[2024-01-25 17:41:35,601] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:35,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:35,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg531c1c9f-b58c-4d76-ac17-bb3a1d7771d6/dqc_reference
[2024-01-25 17:41:36,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:36,740] [INFO] Task started: Prodigal
[2024-01-25 17:41:36,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg66257b12-b163-4499-b003-153c8845f9f5/GCF_001467585.1_ASM146758v1_genomic.fna.gz | prodigal -d GCF_001467585.1_ASM146758v1_genomic.fna/cds.fna -a GCF_001467585.1_ASM146758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:43,137] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:43,137] [INFO] Task started: HMMsearch
[2024-01-25 17:41:43,137] [INFO] Running command: hmmsearch --tblout GCF_001467585.1_ASM146758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg531c1c9f-b58c-4d76-ac17-bb3a1d7771d6/dqc_reference/reference_markers.hmm GCF_001467585.1_ASM146758v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:43,358] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:43,359] [INFO] Found 6/6 markers.
[2024-01-25 17:41:43,389] [INFO] Query marker FASTA was written to GCF_001467585.1_ASM146758v1_genomic.fna/markers.fasta
[2024-01-25 17:41:43,389] [INFO] Task started: Blastn
[2024-01-25 17:41:43,389] [INFO] Running command: blastn -query GCF_001467585.1_ASM146758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg531c1c9f-b58c-4d76-ac17-bb3a1d7771d6/dqc_reference/reference_markers.fasta -out GCF_001467585.1_ASM146758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:43,987] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:43,992] [INFO] Selected 10 target genomes.
[2024-01-25 17:41:43,992] [INFO] Target genome list was writen to GCF_001467585.1_ASM146758v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:44,000] [INFO] Task started: fastANI
[2024-01-25 17:41:44,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg66257b12-b163-4499-b003-153c8845f9f5/GCF_001467585.1_ASM146758v1_genomic.fna.gz --refList GCF_001467585.1_ASM146758v1_genomic.fna/target_genomes.txt --output GCF_001467585.1_ASM146758v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:52,283] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:52,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg531c1c9f-b58c-4d76-ac17-bb3a1d7771d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:52,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg531c1c9f-b58c-4d76-ac17-bb3a1d7771d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:52,290] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:41:52,290] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:52,290] [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 drozanskii	strain=ATCC 700990	GCA_001467585.1	96228	96228	type	True	100.0	1172	1172	95	conclusive
Legionella drozanskii	strain=LLAP-1	GCA_900640075.1	96228	96228	type	True	99.9571	1146	1172	95	conclusive
Legionella nautarum	strain=ATCC 49506	GCA_001467895.1	45070	45070	type	True	86.57	907	1172	95	below_threshold
Legionella nautarum	strain=1224	GCA_900639935.1	45070	45070	type	True	86.5378	898	1172	95	below_threshold
Legionella maceachernii	strain=PX-1-G2-E2	GCA_001467845.1	466	466	type	True	78.2525	353	1172	95	below_threshold
Tatlockia micdadei	strain=ATCC 33218	GCA_900102325.1	451	451	type	True	78.1971	361	1172	95	below_threshold
Legionella massiliensis	strain=LegA	GCA_000756815.1	1034943	1034943	type	True	78.1205	200	1172	95	below_threshold
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	77.7132	73	1172	95	below_threshold
Legionella rowbothamii	strain=LLAP6	GCA_900639985.1	96229	96229	type	True	77.2599	87	1172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:52,291] [INFO] DFAST Taxonomy check result was written to GCF_001467585.1_ASM146758v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:52,292] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:52,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:52,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg531c1c9f-b58c-4d76-ac17-bb3a1d7771d6/dqc_reference/checkm_data
[2024-01-25 17:41:52,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:52,330] [INFO] Task started: CheckM
[2024-01-25 17:41:52,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001467585.1_ASM146758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001467585.1_ASM146758v1_genomic.fna/checkm_input GCF_001467585.1_ASM146758v1_genomic.fna/checkm_result
[2024-01-25 17:42:15,829] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:15,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:15,847] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:15,848] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:15,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001467585.1_ASM146758v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:15,848] [INFO] Task started: Blastn
[2024-01-25 17:42:15,848] [INFO] Running command: blastn -query GCF_001467585.1_ASM146758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg531c1c9f-b58c-4d76-ac17-bb3a1d7771d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001467585.1_ASM146758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:16,835] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:16,838] [INFO] Selected 12 target genomes.
[2024-01-25 17:42:16,838] [INFO] Target genome list was writen to GCF_001467585.1_ASM146758v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:16,846] [INFO] Task started: fastANI
[2024-01-25 17:42:16,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg66257b12-b163-4499-b003-153c8845f9f5/GCF_001467585.1_ASM146758v1_genomic.fna.gz --refList GCF_001467585.1_ASM146758v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001467585.1_ASM146758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:25,224] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:25,232] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:25,233] [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_001467585.1	s__Tatlockia drozanskii	100.0	1172	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.88	99.79	0.97	0.95	3	conclusive
GCF_001467895.1	s__Tatlockia nautarum	86.57	907	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000953635.1	s__Tatlockia micdadei	78.3605	368	1172	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	78.2714	106	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.98	1.00	1.00	4	-
GCF_900167045.1	s__Tatlockia maceachernii	78.1587	366	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.96	0.99	0.99	4	-
GCF_000756815.1	s__Tatlockia massiliensis	78.1205	200	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013812775.1	s__Tatlockia sp013812775	77.8457	170	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900452385.1	s__Tatlockia donaldsonii	77.7148	178	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014109805.1	s__Legionella sp014109805	77.5602	92	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467525.1	s__Legionella anisa	77.0979	105	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_001648595.1	s__Legionella bozemanae	77.0423	104	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_016786215.1	s__Legionella sp016786215	76.9839	104	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:25,234] [INFO] GTDB search result was written to GCF_001467585.1_ASM146758v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:25,235] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:25,239] [INFO] DFAST_QC result json was written to GCF_001467585.1_ASM146758v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:25,239] [INFO] DFAST_QC completed!
[2024-01-25 17:42:25,239] [INFO] Total running time: 0h0m50s