[2024-01-24 12:14:10,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,086] [INFO] DQC Reference Directory: /var/lib/cwl/stge51b8ea1-baa6-4942-8138-987856140fb6/dqc_reference
[2024-01-24 12:14:11,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,424] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,424] [INFO] Running command: gunzip -c /var/lib/cwl/stga10d9bd4-a25b-49c1-a7bd-55fe36c0513b/GCF_001736145.1_ASM173614v1_genomic.fna.gz | prodigal -d GCF_001736145.1_ASM173614v1_genomic.fna/cds.fna -a GCF_001736145.1_ASM173614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:19,853] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:19,854] [INFO] Task started: HMMsearch
[2024-01-24 12:14:19,854] [INFO] Running command: hmmsearch --tblout GCF_001736145.1_ASM173614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge51b8ea1-baa6-4942-8138-987856140fb6/dqc_reference/reference_markers.hmm GCF_001736145.1_ASM173614v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:20,187] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:20,188] [INFO] Found 6/6 markers.
[2024-01-24 12:14:20,238] [INFO] Query marker FASTA was written to GCF_001736145.1_ASM173614v1_genomic.fna/markers.fasta
[2024-01-24 12:14:20,238] [INFO] Task started: Blastn
[2024-01-24 12:14:20,238] [INFO] Running command: blastn -query GCF_001736145.1_ASM173614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge51b8ea1-baa6-4942-8138-987856140fb6/dqc_reference/reference_markers.fasta -out GCF_001736145.1_ASM173614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:20,952] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:20,955] [INFO] Selected 8 target genomes.
[2024-01-24 12:14:20,956] [INFO] Target genome list was writen to GCF_001736145.1_ASM173614v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:20,959] [INFO] Task started: fastANI
[2024-01-24 12:14:20,960] [INFO] Running command: fastANI --query /var/lib/cwl/stga10d9bd4-a25b-49c1-a7bd-55fe36c0513b/GCF_001736145.1_ASM173614v1_genomic.fna.gz --refList GCF_001736145.1_ASM173614v1_genomic.fna/target_genomes.txt --output GCF_001736145.1_ASM173614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:28,800] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:28,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge51b8ea1-baa6-4942-8138-987856140fb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:28,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge51b8ea1-baa6-4942-8138-987856140fb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:28,808] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:14:28,808] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:28,808] [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=DSM 19216	GCA_001736145.1	45071	45071	type	True	100.0	1332	1339	95	conclusive
Legionella parisiensis	strain=NCTC11983	GCA_900461585.1	45071	45071	type	True	99.9846	1339	1339	95	conclusive
Legionella parisiensis	strain=PF-209-C-C2	GCA_001467945.1	45071	45071	type	True	99.9804	1333	1339	95	conclusive
Legionella parisiensis	strain=PF-209C-C2	GCA_900639925.1	45071	45071	type	True	99.9793	1329	1339	95	conclusive
Legionella bozemanae	strain=WIGA	GCA_001467045.1	447	447	type	True	90.4539	1043	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:28,810] [INFO] DFAST Taxonomy check result was written to GCF_001736145.1_ASM173614v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:28,811] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:28,811] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:28,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge51b8ea1-baa6-4942-8138-987856140fb6/dqc_reference/checkm_data
[2024-01-24 12:14:28,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:28,861] [INFO] Task started: CheckM
[2024-01-24 12:14:28,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001736145.1_ASM173614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001736145.1_ASM173614v1_genomic.fna/checkm_input GCF_001736145.1_ASM173614v1_genomic.fna/checkm_result
[2024-01-24 12:15:01,446] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:01,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:01,623] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:01,624] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:01,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001736145.1_ASM173614v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:01,624] [INFO] Task started: Blastn
[2024-01-24 12:15:01,625] [INFO] Running command: blastn -query GCF_001736145.1_ASM173614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge51b8ea1-baa6-4942-8138-987856140fb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001736145.1_ASM173614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:02,565] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:02,569] [INFO] Selected 5 target genomes.
[2024-01-24 12:15:02,569] [INFO] Target genome list was writen to GCF_001736145.1_ASM173614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:02,574] [INFO] Task started: fastANI
[2024-01-24 12:15:02,575] [INFO] Running command: fastANI --query /var/lib/cwl/stga10d9bd4-a25b-49c1-a7bd-55fe36c0513b/GCF_001736145.1_ASM173614v1_genomic.fna.gz --refList GCF_001736145.1_ASM173614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001736145.1_ASM173614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:07,719] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:07,730] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:07,731] [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	99.9804	1333	1339	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	90.3852	1047	1339	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	88.232	1086	1339	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	87.8086	947	1339	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	87.6785	1062	1339	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 12:15:07,732] [INFO] GTDB search result was written to GCF_001736145.1_ASM173614v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:07,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:07,738] [INFO] DFAST_QC result json was written to GCF_001736145.1_ASM173614v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:07,739] [INFO] DFAST_QC completed!
[2024-01-24 12:15:07,739] [INFO] Total running time: 0h0m58s