[2024-01-24 14:47:27,294] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:27,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:27,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a06b17d-f5cd-4c96-9ebd-6d87d6feecb8/dqc_reference
[2024-01-24 14:47:28,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:28,838] [INFO] Task started: Prodigal
[2024-01-24 14:47:28,839] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f52eadb-ab42-42d9-b23b-0c4f79de9132/GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna.gz | prodigal -d GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/cds.fna -a GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:37,685] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:37,686] [INFO] Task started: HMMsearch
[2024-01-24 14:47:37,686] [INFO] Running command: hmmsearch --tblout GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a06b17d-f5cd-4c96-9ebd-6d87d6feecb8/dqc_reference/reference_markers.hmm GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:37,986] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:37,987] [INFO] Found 6/6 markers.
[2024-01-24 14:47:38,047] [INFO] Query marker FASTA was written to GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/markers.fasta
[2024-01-24 14:47:38,048] [INFO] Task started: Blastn
[2024-01-24 14:47:38,048] [INFO] Running command: blastn -query GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a06b17d-f5cd-4c96-9ebd-6d87d6feecb8/dqc_reference/reference_markers.fasta -out GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:38,873] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:38,876] [INFO] Selected 6 target genomes.
[2024-01-24 14:47:38,877] [INFO] Target genome list was writen to GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:38,885] [INFO] Task started: fastANI
[2024-01-24 14:47:38,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f52eadb-ab42-42d9-b23b-0c4f79de9132/GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna.gz --refList GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/target_genomes.txt --output GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:43,423] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:43,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a06b17d-f5cd-4c96-9ebd-6d87d6feecb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:43,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a06b17d-f5cd-4c96-9ebd-6d87d6feecb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:43,430] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:43,430] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:43,430] [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 rubrilucens	strain=WA-270A-C2	GCA_900640015.1	458	458	type	True	100.0	1045	1047	95	conclusive
Legionella rubrilucens	strain=WA-270A-C2	GCA_001468125.1	458	458	type	True	99.9931	1026	1047	95	conclusive
Legionella taurinensis	strain=NCTC13314	GCA_900452865.1	70611	70611	type	True	92.0578	919	1047	95	below_threshold
Legionella erythra	strain=SE-32A-C8	GCA_900639845.1	448	448	type	True	84.5352	833	1047	95	below_threshold
Legionella erythra	strain=SE-32A-C8	GCA_001467615.1	448	448	type	True	84.2278	829	1047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:43,437] [INFO] DFAST Taxonomy check result was written to GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:43,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:43,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:43,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a06b17d-f5cd-4c96-9ebd-6d87d6feecb8/dqc_reference/checkm_data
[2024-01-24 14:47:43,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:43,478] [INFO] Task started: CheckM
[2024-01-24 14:47:43,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/checkm_input GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/checkm_result
[2024-01-24 14:48:17,211] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:17,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:17,236] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:17,236] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:17,237] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:17,237] [INFO] Task started: Blastn
[2024-01-24 14:48:17,237] [INFO] Running command: blastn -query GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a06b17d-f5cd-4c96-9ebd-6d87d6feecb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:18,472] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:18,475] [INFO] Selected 10 target genomes.
[2024-01-24 14:48:18,475] [INFO] Target genome list was writen to GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:18,485] [INFO] Task started: fastANI
[2024-01-24 14:48:18,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f52eadb-ab42-42d9-b23b-0c4f79de9132/GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna.gz --refList GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:25,597] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:25,614] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:25,615] [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_001468125.1	s__Legionella_C rubrilucens	99.9931	1026	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_900452865.1	s__Legionella_C taurinensis	92.0616	918	1047	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_016864235.1	s__Legionella_C sp016864235	91.0436	934	1047	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_001467615.1	s__Legionella_C erythra	84.2278	829	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.95	99.95	0.98	0.98	2	-
GCF_000621525.1	s__Tatlockia fairfieldensis	82.4581	101	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900637635.1	s__Tatlockia jordanis	80.1602	102	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.59	0.99	0.98	6	-
GCF_900452385.1	s__Tatlockia donaldsonii	77.6839	83	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900461555.1	s__Legionella_C quinlivanii	77.3532	98	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.97	99.95	0.99	0.98	4	-
GCF_000373765.1	s__Legionella shakespearei	77.2175	70	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:25,617] [INFO] GTDB search result was written to GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:25,618] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:25,622] [INFO] DFAST_QC result json was written to GCF_900640015.1_Leg_rubrilucens_WA-270A-C2.v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:25,622] [INFO] DFAST_QC completed!
[2024-01-24 14:48:25,622] [INFO] Total running time: 0h0m58s