[2024-01-25 18:45:20,750] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:20,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:20,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg45954e8e-af0b-44bb-9b5c-54eae1d3ff4c/dqc_reference
[2024-01-25 18:45:21,904] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:21,905] [INFO] Task started: Prodigal
[2024-01-25 18:45:21,905] [INFO] Running command: gunzip -c /var/lib/cwl/stg5526b28b-8263-4e72-9155-cf894056107b/GCF_001643395.1_ASM164339v1_genomic.fna.gz | prodigal -d GCF_001643395.1_ASM164339v1_genomic.fna/cds.fna -a GCF_001643395.1_ASM164339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:32,380] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:32,380] [INFO] Task started: HMMsearch
[2024-01-25 18:45:32,380] [INFO] Running command: hmmsearch --tblout GCF_001643395.1_ASM164339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45954e8e-af0b-44bb-9b5c-54eae1d3ff4c/dqc_reference/reference_markers.hmm GCF_001643395.1_ASM164339v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:32,611] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:32,612] [INFO] Found 6/6 markers.
[2024-01-25 18:45:32,650] [INFO] Query marker FASTA was written to GCF_001643395.1_ASM164339v1_genomic.fna/markers.fasta
[2024-01-25 18:45:32,651] [INFO] Task started: Blastn
[2024-01-25 18:45:32,651] [INFO] Running command: blastn -query GCF_001643395.1_ASM164339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45954e8e-af0b-44bb-9b5c-54eae1d3ff4c/dqc_reference/reference_markers.fasta -out GCF_001643395.1_ASM164339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:33,514] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:33,520] [INFO] Selected 9 target genomes.
[2024-01-25 18:45:33,520] [INFO] Target genome list was writen to GCF_001643395.1_ASM164339v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:33,549] [INFO] Task started: fastANI
[2024-01-25 18:45:33,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg5526b28b-8263-4e72-9155-cf894056107b/GCF_001643395.1_ASM164339v1_genomic.fna.gz --refList GCF_001643395.1_ASM164339v1_genomic.fna/target_genomes.txt --output GCF_001643395.1_ASM164339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:43,942] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:43,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45954e8e-af0b-44bb-9b5c-54eae1d3ff4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:43,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45954e8e-af0b-44bb-9b5c-54eae1d3ff4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:43,951] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 18:45:43,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:43,951] [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
Salmonella enterica	strain=FDAARGOS_768	GCA_006365335.1	28901	28901	type	True	98.8219	1486	1540	95	conclusive
Salmonella enterica subsp. enterica	strain=LT2	GCA_010649825.1	59201	28901	suspected-type	True	98.8199	1464	1540	95	conclusive
Salmonella enterica	strain=FDAARGOS_878	GCA_016028495.1	28901	28901	type	True	98.8179	1486	1540	95	conclusive
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	98.8128	1492	1540	95	conclusive
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	98.8002	1475	1540	95	conclusive
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	83.06	981	1540	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.2323	774	1540	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.1254	759	1540	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.0786	750	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:43,952] [INFO] DFAST Taxonomy check result was written to GCF_001643395.1_ASM164339v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:43,953] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:43,953] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:43,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45954e8e-af0b-44bb-9b5c-54eae1d3ff4c/dqc_reference/checkm_data
[2024-01-25 18:45:43,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:44,002] [INFO] Task started: CheckM
[2024-01-25 18:45:44,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001643395.1_ASM164339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001643395.1_ASM164339v1_genomic.fna/checkm_input GCF_001643395.1_ASM164339v1_genomic.fna/checkm_result
[2024-01-25 18:46:17,208] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:17,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:17,226] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:17,226] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:17,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001643395.1_ASM164339v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:17,228] [INFO] Task started: Blastn
[2024-01-25 18:46:17,228] [INFO] Running command: blastn -query GCF_001643395.1_ASM164339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45954e8e-af0b-44bb-9b5c-54eae1d3ff4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001643395.1_ASM164339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:18,604] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:18,607] [INFO] Selected 5 target genomes.
[2024-01-25 18:46:18,607] [INFO] Target genome list was writen to GCF_001643395.1_ASM164339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:18,612] [INFO] Task started: fastANI
[2024-01-25 18:46:18,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg5526b28b-8263-4e72-9155-cf894056107b/GCF_001643395.1_ASM164339v1_genomic.fna.gz --refList GCF_001643395.1_ASM164339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001643395.1_ASM164339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:25,048] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:25,054] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:25,054] [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_000006945.2	s__Salmonella enterica	98.8097	1487	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.80	95.43	0.94	0.81	12285	conclusive
GCF_008692785.1	s__Salmonella diarizonae	95.0143	1287	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.90	95.36	0.91	0.81	98	-
GCA_900478215.1	s__Salmonella houtenae	94.6658	1293	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.09	96.71	0.94	0.89	62	-
GCF_008692845.1	s__Salmonella arizonae	93.1693	1237	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.33	99.07	0.96	0.94	67	-
GCF_000252995.1	s__Salmonella bongori	90.0271	1243	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.43	98.73	0.97	0.94	32	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:25,055] [INFO] GTDB search result was written to GCF_001643395.1_ASM164339v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:25,056] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:25,058] [INFO] DFAST_QC result json was written to GCF_001643395.1_ASM164339v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:25,058] [INFO] DFAST_QC completed!
[2024-01-25 18:46:25,058] [INFO] Total running time: 0h1m4s