[2024-01-24 12:47:49,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:49,073] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:49,073] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8358d6e-3f70-424a-a10d-3f779dc26cc1/dqc_reference
[2024-01-24 12:47:50,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,426] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,427] [INFO] Running command: gunzip -c /var/lib/cwl/stg9132f606-675d-4272-97ba-e0425fd054d1/GCF_900452375.1_54424_F01_genomic.fna.gz | prodigal -d GCF_900452375.1_54424_F01_genomic.fna/cds.fna -a GCF_900452375.1_54424_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:58,569] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:58,569] [INFO] Task started: HMMsearch
[2024-01-24 12:47:58,569] [INFO] Running command: hmmsearch --tblout GCF_900452375.1_54424_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8358d6e-3f70-424a-a10d-3f779dc26cc1/dqc_reference/reference_markers.hmm GCF_900452375.1_54424_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:58,811] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:58,813] [INFO] Found 6/6 markers.
[2024-01-24 12:47:58,843] [INFO] Query marker FASTA was written to GCF_900452375.1_54424_F01_genomic.fna/markers.fasta
[2024-01-24 12:47:58,844] [INFO] Task started: Blastn
[2024-01-24 12:47:58,844] [INFO] Running command: blastn -query GCF_900452375.1_54424_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8358d6e-3f70-424a-a10d-3f779dc26cc1/dqc_reference/reference_markers.fasta -out GCF_900452375.1_54424_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:59,538] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:59,542] [INFO] Selected 10 target genomes.
[2024-01-24 12:47:59,543] [INFO] Target genome list was writen to GCF_900452375.1_54424_F01_genomic.fna/target_genomes.txt
[2024-01-24 12:47:59,562] [INFO] Task started: fastANI
[2024-01-24 12:47:59,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg9132f606-675d-4272-97ba-e0425fd054d1/GCF_900452375.1_54424_F01_genomic.fna.gz --refList GCF_900452375.1_54424_F01_genomic.fna/target_genomes.txt --output GCF_900452375.1_54424_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:07,438] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:07,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8358d6e-3f70-424a-a10d-3f779dc26cc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:07,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8358d6e-3f70-424a-a10d-3f779dc26cc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:07,444] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:48:07,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:07,444] [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 geestiana	strain=NCTC12373	GCA_900452375.1	45065	45065	type	True	100.0	891	892	95	conclusive
Legionella geestiana	strain=1308	GCA_004571195.1	45065	45065	type	True	99.9967	887	892	95	conclusive
Legionella geestiana	strain=1308	GCA_900639805.1	45065	45065	type	True	99.936	848	892	95	conclusive
Legionella geestiana	strain=DSM 21217	GCA_000621365.1	45065	45065	type	True	99.9344	807	892	95	conclusive
Legionella geestiana	strain=ATCC 49504	GCA_001467645.1	45065	45065	type	True	99.913	809	892	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:48:07,446] [INFO] DFAST Taxonomy check result was written to GCF_900452375.1_54424_F01_genomic.fna/tc_result.tsv
[2024-01-24 12:48:07,446] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:07,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:07,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8358d6e-3f70-424a-a10d-3f779dc26cc1/dqc_reference/checkm_data
[2024-01-24 12:48:07,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:07,477] [INFO] Task started: CheckM
[2024-01-24 12:48:07,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900452375.1_54424_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900452375.1_54424_F01_genomic.fna/checkm_input GCF_900452375.1_54424_F01_genomic.fna/checkm_result
[2024-01-24 12:48:36,946] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:36,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:36,971] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:36,971] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:36,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900452375.1_54424_F01_genomic.fna/markers.fasta)
[2024-01-24 12:48:36,972] [INFO] Task started: Blastn
[2024-01-24 12:48:36,972] [INFO] Running command: blastn -query GCF_900452375.1_54424_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8358d6e-3f70-424a-a10d-3f779dc26cc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900452375.1_54424_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:38,066] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:38,071] [INFO] Selected 29 target genomes.
[2024-01-24 12:48:38,071] [INFO] Target genome list was writen to GCF_900452375.1_54424_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:38,093] [INFO] Task started: fastANI
[2024-01-24 12:48:38,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg9132f606-675d-4272-97ba-e0425fd054d1/GCF_900452375.1_54424_F01_genomic.fna.gz --refList GCF_900452375.1_54424_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900452375.1_54424_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:52,963] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:52,972] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:52,972] [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_004571195.1	s__Legionella_B geestiana	99.9967	887	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_B	95.0	99.84	99.28	0.98	0.92	6	conclusive
GCF_016864235.1	s__Legionella_C sp016864235	79.0178	61	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900452865.1	s__Legionella_C taurinensis	78.6215	56	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.63	99.52	0.96	0.95	16	-
GCF_001467615.1	s__Legionella_C erythra	77.8284	55	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.95	99.95	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:52,974] [INFO] GTDB search result was written to GCF_900452375.1_54424_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:52,975] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:52,978] [INFO] DFAST_QC result json was written to GCF_900452375.1_54424_F01_genomic.fna/dqc_result.json
[2024-01-24 12:48:52,978] [INFO] DFAST_QC completed!
[2024-01-24 12:48:52,978] [INFO] Total running time: 0h1m4s