[2024-01-25 19:33:21,093] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:21,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:21,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg649b0b85-c618-4a58-8bb9-9cfd42c61557/dqc_reference
[2024-01-25 19:33:22,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:22,236] [INFO] Task started: Prodigal
[2024-01-25 19:33:22,236] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f05b221-6ea1-49d1-a302-977fd7fbc089/GCF_001648595.1_ASM164859v1_genomic.fna.gz | prodigal -d GCF_001648595.1_ASM164859v1_genomic.fna/cds.fna -a GCF_001648595.1_ASM164859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:29,596] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:29,597] [INFO] Task started: HMMsearch
[2024-01-25 19:33:29,597] [INFO] Running command: hmmsearch --tblout GCF_001648595.1_ASM164859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg649b0b85-c618-4a58-8bb9-9cfd42c61557/dqc_reference/reference_markers.hmm GCF_001648595.1_ASM164859v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:29,810] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:29,811] [INFO] Found 6/6 markers.
[2024-01-25 19:33:29,841] [INFO] Query marker FASTA was written to GCF_001648595.1_ASM164859v1_genomic.fna/markers.fasta
[2024-01-25 19:33:29,841] [INFO] Task started: Blastn
[2024-01-25 19:33:29,841] [INFO] Running command: blastn -query GCF_001648595.1_ASM164859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg649b0b85-c618-4a58-8bb9-9cfd42c61557/dqc_reference/reference_markers.fasta -out GCF_001648595.1_ASM164859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:30,442] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:30,444] [INFO] Selected 6 target genomes.
[2024-01-25 19:33:30,444] [INFO] Target genome list was writen to GCF_001648595.1_ASM164859v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:30,458] [INFO] Task started: fastANI
[2024-01-25 19:33:30,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f05b221-6ea1-49d1-a302-977fd7fbc089/GCF_001648595.1_ASM164859v1_genomic.fna.gz --refList GCF_001648595.1_ASM164859v1_genomic.fna/target_genomes.txt --output GCF_001648595.1_ASM164859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:36,530] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:36,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg649b0b85-c618-4a58-8bb9-9cfd42c61557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:36,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg649b0b85-c618-4a58-8bb9-9cfd42c61557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:36,537] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:33:36,537] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:36,537] [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 bozemanae	strain=ATCC 33217	GCA_001648595.1	447	447	type	True	100.0	1326	1327	95	conclusive
Legionella bozemanae	strain=NCTC11368	GCA_900450575.1	447	447	type	True	99.9975	1322	1327	95	conclusive
Legionella bozemanae	strain=WIGA	GCA_900640135.1	447	447	type	True	99.99	1318	1327	95	conclusive
Legionella bozemanae	strain=WIGA	GCA_001467045.1	447	447	type	True	99.9817	1318	1327	95	conclusive
Legionella parisiensis	strain=PF-209-C-C2	GCA_001467945.1	45071	45071	type	True	90.3513	1080	1327	95	below_threshold
Legionella tucsonensis	strain=ATCC 49180	GCA_001468035.1	40335	40335	type	True	89.3375	935	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:36,539] [INFO] DFAST Taxonomy check result was written to GCF_001648595.1_ASM164859v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:36,539] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:36,539] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:36,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg649b0b85-c618-4a58-8bb9-9cfd42c61557/dqc_reference/checkm_data
[2024-01-25 19:33:36,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:36,583] [INFO] Task started: CheckM
[2024-01-25 19:33:36,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001648595.1_ASM164859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001648595.1_ASM164859v1_genomic.fna/checkm_input GCF_001648595.1_ASM164859v1_genomic.fna/checkm_result
[2024-01-25 19:34:02,674] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:02,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:02,695] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:02,695] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:02,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001648595.1_ASM164859v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:02,696] [INFO] Task started: Blastn
[2024-01-25 19:34:02,696] [INFO] Running command: blastn -query GCF_001648595.1_ASM164859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg649b0b85-c618-4a58-8bb9-9cfd42c61557/dqc_reference/reference_markers_gtdb.fasta -out GCF_001648595.1_ASM164859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:03,637] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:03,641] [INFO] Selected 5 target genomes.
[2024-01-25 19:34:03,641] [INFO] Target genome list was writen to GCF_001648595.1_ASM164859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:03,647] [INFO] Task started: fastANI
[2024-01-25 19:34:03,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f05b221-6ea1-49d1-a302-977fd7fbc089/GCF_001648595.1_ASM164859v1_genomic.fna.gz --refList GCF_001648595.1_ASM164859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001648595.1_ASM164859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:34:09,095] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:09,100] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:34:09,100] [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_001648595.1	s__Legionella bozemanae	100.0	1326	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	conclusive
GCF_001467945.1	s__Legionella parisiensis	90.3513	1080	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.98	1.00	1.00	4	-
GCF_001468035.1	s__Legionella tucsonensis	89.3375	935	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001467525.1	s__Legionella anisa	89.1889	1025	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_014109805.1	s__Legionella sp014109805	88.8403	1054	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:34:09,101] [INFO] GTDB search result was written to GCF_001648595.1_ASM164859v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:34:09,102] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:34:09,105] [INFO] DFAST_QC result json was written to GCF_001648595.1_ASM164859v1_genomic.fna/dqc_result.json
[2024-01-25 19:34:09,105] [INFO] DFAST_QC completed!
[2024-01-25 19:34:09,106] [INFO] Total running time: 0h0m48s