[2024-01-24 13:40:43,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg5691cba9-489d-4a8f-a8d8-8c98b3ff0017/dqc_reference
[2024-01-24 13:40:45,066] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,067] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,068] [INFO] Running command: gunzip -c /var/lib/cwl/stg79f5aac7-0490-4e32-bbb2-58b8ce883b20/GCF_900453045.1_52465_G01_genomic.fna.gz | prodigal -d GCF_900453045.1_52465_G01_genomic.fna/cds.fna -a GCF_900453045.1_52465_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:52,902] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:52,902] [INFO] Task started: HMMsearch
[2024-01-24 13:40:52,902] [INFO] Running command: hmmsearch --tblout GCF_900453045.1_52465_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5691cba9-489d-4a8f-a8d8-8c98b3ff0017/dqc_reference/reference_markers.hmm GCF_900453045.1_52465_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:53,231] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:53,233] [INFO] Found 6/6 markers.
[2024-01-24 13:40:53,272] [INFO] Query marker FASTA was written to GCF_900453045.1_52465_G01_genomic.fna/markers.fasta
[2024-01-24 13:40:53,272] [INFO] Task started: Blastn
[2024-01-24 13:40:53,272] [INFO] Running command: blastn -query GCF_900453045.1_52465_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg5691cba9-489d-4a8f-a8d8-8c98b3ff0017/dqc_reference/reference_markers.fasta -out GCF_900453045.1_52465_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:53,943] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:53,949] [INFO] Selected 10 target genomes.
[2024-01-24 13:40:53,950] [INFO] Target genome list was writen to GCF_900453045.1_52465_G01_genomic.fna/target_genomes.txt
[2024-01-24 13:40:53,953] [INFO] Task started: fastANI
[2024-01-24 13:40:53,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg79f5aac7-0490-4e32-bbb2-58b8ce883b20/GCF_900453045.1_52465_G01_genomic.fna.gz --refList GCF_900453045.1_52465_G01_genomic.fna/target_genomes.txt --output GCF_900453045.1_52465_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:01,973] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:01,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5691cba9-489d-4a8f-a8d8-8c98b3ff0017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:01,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5691cba9-489d-4a8f-a8d8-8c98b3ff0017/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:01,982] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:01,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:01,983] [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 worsleiensis	strain=NCTC12377	GCA_900453045.1	45076	45076	type	True	100.0	1053	1053	95	conclusive
Legionella worsleiensis	strain=ATCC 49508	GCA_001467535.1	45076	45076	type	True	99.9588	991	1053	95	conclusive
Legionella anisa	strain=FDAARGOS_1480	GCA_019930885.1	28082	28082	type	True	80.3192	162	1053	95	below_threshold
Legionella moravica	strain=DSM 19234	GCA_000423305.1	39962	39962	type	True	80.2409	529	1053	95	below_threshold
Legionella quateirensis	strain=NCTC12376	GCA_900452695.1	45072	45072	type	True	80.0407	524	1053	95	below_threshold
Legionella bononiensis	strain=30cs62	GCA_016786415.1	2793102	2793102	type	True	80.0212	493	1053	95	below_threshold
Legionella quateirensis	strain=ATCC 49507	GCA_001467955.1	45072	45072	type	True	80.0008	521	1053	95	below_threshold
Legionella anisa	strain=WA-316-C3	GCA_001467525.1	28082	28082	type	True	79.8592	150	1053	95	below_threshold
Legionella anisa	strain=WA-316-C3	GCA_900639785.1	28082	28082	type	True	79.7169	148	1053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:01,984] [INFO] DFAST Taxonomy check result was written to GCF_900453045.1_52465_G01_genomic.fna/tc_result.tsv
[2024-01-24 13:41:01,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:01,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:01,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5691cba9-489d-4a8f-a8d8-8c98b3ff0017/dqc_reference/checkm_data
[2024-01-24 13:41:01,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:02,027] [INFO] Task started: CheckM
[2024-01-24 13:41:02,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900453045.1_52465_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900453045.1_52465_G01_genomic.fna/checkm_input GCF_900453045.1_52465_G01_genomic.fna/checkm_result
[2024-01-24 13:41:31,228] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:31,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:31,248] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:31,248] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:31,249] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900453045.1_52465_G01_genomic.fna/markers.fasta)
[2024-01-24 13:41:31,249] [INFO] Task started: Blastn
[2024-01-24 13:41:31,249] [INFO] Running command: blastn -query GCF_900453045.1_52465_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg5691cba9-489d-4a8f-a8d8-8c98b3ff0017/dqc_reference/reference_markers_gtdb.fasta -out GCF_900453045.1_52465_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:32,350] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:32,355] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:32,355] [INFO] Target genome list was writen to GCF_900453045.1_52465_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:32,363] [INFO] Task started: fastANI
[2024-01-24 13:41:32,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg79f5aac7-0490-4e32-bbb2-58b8ce883b20/GCF_900453045.1_52465_G01_genomic.fna.gz --refList GCF_900453045.1_52465_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900453045.1_52465_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:42,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:42,178] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:42,179] [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_001467535.1	s__Legionella worsleiensis	99.9588	991	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.98	0.98	2	conclusive
GCF_000423305.1	s__Legionella moravica	80.2267	528	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.09	96.46	0.96	0.86	5	-
GCF_001467955.1	s__Legionella quateirensis	80.0118	520	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.97	99.97	0.99	0.99	3	-
GCF_016786215.1	s__Legionella sp016786215	79.9088	502	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
GCF_001467525.1	s__Legionella anisa	79.901	149	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_000008485.1	s__Legionella pneumophila	79.2467	184	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.85	95.56	0.93	0.84	789	-
GCF_001467945.1	s__Legionella parisiensis	78.7766	140	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.98	1.00	1.00	4	-
GCF_000373765.1	s__Legionella shakespearei	78.6147	213	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.95	0.97	0.97	2	-
GCF_011764505.1	s__Legionella sp011764505	78.3329	216	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637585.1	s__Legionella pascullei	78.2083	178	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.92	99.72	1.00	0.99	8	-
GCF_900452395.1	s__Legionella_C beliardensis	77.9867	64	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.99	99.99	1.00	1.00	2	-
GCA_000586315.1	s__Legionella fraseri	77.7167	188	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.50	96.27	0.94	0.87	43	-
GCA_002786205.1	s__Legionella sp002786205	77.1235	84	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	0.95	0.95	2	-
GCF_900640175.1	s__Tatlockia sp900640175	76.9609	81	1053	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 13:41:42,182] [INFO] GTDB search result was written to GCF_900453045.1_52465_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:42,188] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:42,197] [INFO] DFAST_QC result json was written to GCF_900453045.1_52465_G01_genomic.fna/dqc_result.json
[2024-01-24 13:41:42,197] [INFO] DFAST_QC completed!
[2024-01-24 13:41:42,197] [INFO] Total running time: 0h0m59s