[2024-01-24 13:25:31,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bbd2ca0-89f3-4a46-928d-ceb7ce13915a/dqc_reference
[2024-01-24 13:25:32,537] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,538] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,538] [INFO] Running command: gunzip -c /var/lib/cwl/stgc46e7791-4b06-424b-8ea0-8c01ed67b618/GCF_900461585.1_51485_C01_genomic.fna.gz | prodigal -d GCF_900461585.1_51485_C01_genomic.fna/cds.fna -a GCF_900461585.1_51485_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:41,834] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:41,834] [INFO] Task started: HMMsearch
[2024-01-24 13:25:41,835] [INFO] Running command: hmmsearch --tblout GCF_900461585.1_51485_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bbd2ca0-89f3-4a46-928d-ceb7ce13915a/dqc_reference/reference_markers.hmm GCF_900461585.1_51485_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:42,100] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:42,101] [INFO] Found 6/6 markers.
[2024-01-24 13:25:42,148] [INFO] Query marker FASTA was written to GCF_900461585.1_51485_C01_genomic.fna/markers.fasta
[2024-01-24 13:25:42,149] [INFO] Task started: Blastn
[2024-01-24 13:25:42,149] [INFO] Running command: blastn -query GCF_900461585.1_51485_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bbd2ca0-89f3-4a46-928d-ceb7ce13915a/dqc_reference/reference_markers.fasta -out GCF_900461585.1_51485_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:42,849] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:42,855] [INFO] Selected 9 target genomes.
[2024-01-24 13:25:42,856] [INFO] Target genome list was writen to GCF_900461585.1_51485_C01_genomic.fna/target_genomes.txt
[2024-01-24 13:25:42,860] [INFO] Task started: fastANI
[2024-01-24 13:25:42,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgc46e7791-4b06-424b-8ea0-8c01ed67b618/GCF_900461585.1_51485_C01_genomic.fna.gz --refList GCF_900461585.1_51485_C01_genomic.fna/target_genomes.txt --output GCF_900461585.1_51485_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:50,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:50,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bbd2ca0-89f3-4a46-928d-ceb7ce13915a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:50,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bbd2ca0-89f3-4a46-928d-ceb7ce13915a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:50,936] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:25:50,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:50,936] [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 parisiensis	strain=NCTC11983	GCA_900461585.1	45071	45071	type	True	100.0	1400	1400	95	conclusive
Legionella parisiensis	strain=PF-209-C-C2	GCA_001467945.1	45071	45071	type	True	99.9843	1381	1400	95	conclusive
Legionella parisiensis	strain=PF-209C-C2	GCA_900639925.1	45071	45071	type	True	99.9726	1376	1400	95	conclusive
Legionella parisiensis	strain=DSM 19216	GCA_001736145.1	45071	45071	type	True	99.9166	1331	1400	95	conclusive
Legionella bozemanae	strain=WIGA	GCA_900640135.1	447	447	type	True	90.3724	1083	1400	95	below_threshold
Legionella bozemanae	strain=WIGA	GCA_001467045.1	447	447	type	True	90.3417	1081	1400	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:50,939] [INFO] DFAST Taxonomy check result was written to GCF_900461585.1_51485_C01_genomic.fna/tc_result.tsv
[2024-01-24 13:25:50,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:50,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:50,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bbd2ca0-89f3-4a46-928d-ceb7ce13915a/dqc_reference/checkm_data
[2024-01-24 13:25:50,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:51,017] [INFO] Task started: CheckM
[2024-01-24 13:25:51,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900461585.1_51485_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900461585.1_51485_C01_genomic.fna/checkm_input GCF_900461585.1_51485_C01_genomic.fna/checkm_result
[2024-01-24 13:26:24,599] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:24,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:24,621] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:24,622] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:24,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900461585.1_51485_C01_genomic.fna/markers.fasta)
[2024-01-24 13:26:24,623] [INFO] Task started: Blastn
[2024-01-24 13:26:24,623] [INFO] Running command: blastn -query GCF_900461585.1_51485_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bbd2ca0-89f3-4a46-928d-ceb7ce13915a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900461585.1_51485_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:25,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:25,650] [INFO] Selected 5 target genomes.
[2024-01-24 13:26:25,650] [INFO] Target genome list was writen to GCF_900461585.1_51485_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:25,651] [INFO] Task started: fastANI
[2024-01-24 13:26:25,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgc46e7791-4b06-424b-8ea0-8c01ed67b618/GCF_900461585.1_51485_C01_genomic.fna.gz --refList GCF_900461585.1_51485_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900461585.1_51485_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:30,856] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:30,866] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:30,867] [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_001467945.1	s__Legionella parisiensis	99.9843	1381	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.98	1.00	1.00	4	conclusive
GCF_001648595.1	s__Legionella bozemanae	90.3116	1094	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_001467525.1	s__Legionella anisa	88.3029	1112	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_001468035.1	s__Legionella tucsonensis	87.7468	976	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014109805.1	s__Legionella sp014109805	87.5951	1099	1400	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:30,868] [INFO] GTDB search result was written to GCF_900461585.1_51485_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:30,869] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:30,871] [INFO] DFAST_QC result json was written to GCF_900461585.1_51485_C01_genomic.fna/dqc_result.json
[2024-01-24 13:26:30,872] [INFO] DFAST_QC completed!
[2024-01-24 13:26:30,872] [INFO] Total running time: 0h0m60s