[2024-01-24 13:17:05,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,263] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,263] [INFO] DQC Reference Directory: /var/lib/cwl/stge97d1d6b-2240-4a1b-94e4-829b7ee5ff9d/dqc_reference
[2024-01-24 13:17:06,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,815] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d168436-fbb1-4927-90ca-89d6674bc39c/GCF_000252995.1_ASM25299v1_genomic.fna.gz | prodigal -d GCF_000252995.1_ASM25299v1_genomic.fna/cds.fna -a GCF_000252995.1_ASM25299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:18,894] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:18,894] [INFO] Task started: HMMsearch
[2024-01-24 13:17:18,894] [INFO] Running command: hmmsearch --tblout GCF_000252995.1_ASM25299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge97d1d6b-2240-4a1b-94e4-829b7ee5ff9d/dqc_reference/reference_markers.hmm GCF_000252995.1_ASM25299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:19,192] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:19,193] [INFO] Found 6/6 markers.
[2024-01-24 13:17:19,244] [INFO] Query marker FASTA was written to GCF_000252995.1_ASM25299v1_genomic.fna/markers.fasta
[2024-01-24 13:17:19,245] [INFO] Task started: Blastn
[2024-01-24 13:17:19,245] [INFO] Running command: blastn -query GCF_000252995.1_ASM25299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge97d1d6b-2240-4a1b-94e4-829b7ee5ff9d/dqc_reference/reference_markers.fasta -out GCF_000252995.1_ASM25299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:20,120] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:20,124] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:20,124] [INFO] Target genome list was writen to GCF_000252995.1_ASM25299v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:20,129] [INFO] Task started: fastANI
[2024-01-24 13:17:20,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d168436-fbb1-4927-90ca-89d6674bc39c/GCF_000252995.1_ASM25299v1_genomic.fna.gz --refList GCF_000252995.1_ASM25299v1_genomic.fna/target_genomes.txt --output GCF_000252995.1_ASM25299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:35,330] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:35,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge97d1d6b-2240-4a1b-94e4-829b7ee5ff9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:35,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge97d1d6b-2240-4a1b-94e4-829b7ee5ff9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:35,343] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:35,343] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:35,343] [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 bongori	strain=NCTC 12419	GCA_000252995.1	54736	54736	type	True	100.0	1486	1486	95	conclusive
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	90.1434	1249	1486	95	below_threshold
Salmonella enterica subsp. salamae	strain=CCUG 30039T	GCA_008692775.1	59202	28901	type	True	90.1332	1282	1486	95	below_threshold
Salmonella enterica	strain=FDAARGOS_768	GCA_006365335.1	28901	28901	type	True	90.132	1258	1486	95	below_threshold
Salmonella enterica subsp. salamae	strain=CCUG30039	GCA_016029065.1	59202	28901	type	True	90.1244	1266	1486	95	below_threshold
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	90.0535	1231	1486	95	below_threshold
Salmonella enterica subsp. diarizonae	strain=CCUG 30040T	GCA_008692785.1	59204	28901	type	True	89.975	1235	1486	95	below_threshold
Salmonella enterica subsp. diarizonae	strain=CCUG30040	GCA_016030095.1	59204	28901	type	True	89.9309	1241	1486	95	below_threshold
Salmonella enterica subsp. houtenae	strain=CCUG 30041T	GCA_008692755.1	59205	28901	type	True	89.7067	1236	1486	95	below_threshold
Salmonella enterica subsp. indica	strain=CCUG30038	GCA_018033035.1	59207	28901	type	True	89.6862	1242	1486	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.71	928	1486	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	80.7697	709	1486	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.6551	712	1486	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.5906	714	1486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:35,354] [INFO] DFAST Taxonomy check result was written to GCF_000252995.1_ASM25299v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:35,355] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:35,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:35,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge97d1d6b-2240-4a1b-94e4-829b7ee5ff9d/dqc_reference/checkm_data
[2024-01-24 13:17:35,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:35,404] [INFO] Task started: CheckM
[2024-01-24 13:17:35,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000252995.1_ASM25299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000252995.1_ASM25299v1_genomic.fna/checkm_input GCF_000252995.1_ASM25299v1_genomic.fna/checkm_result
[2024-01-24 13:18:13,071] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:13,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:13,094] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:13,094] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:13,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000252995.1_ASM25299v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:13,095] [INFO] Task started: Blastn
[2024-01-24 13:18:13,095] [INFO] Running command: blastn -query GCF_000252995.1_ASM25299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge97d1d6b-2240-4a1b-94e4-829b7ee5ff9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000252995.1_ASM25299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:14,446] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:14,451] [INFO] Selected 5 target genomes.
[2024-01-24 13:18:14,452] [INFO] Target genome list was writen to GCF_000252995.1_ASM25299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:14,459] [INFO] Task started: fastANI
[2024-01-24 13:18:14,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d168436-fbb1-4927-90ca-89d6674bc39c/GCF_000252995.1_ASM25299v1_genomic.fna.gz --refList GCF_000252995.1_ASM25299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000252995.1_ASM25299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:20,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:20,312] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:20,313] [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_000252995.1	s__Salmonella bongori	100.0	1485	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.43	98.73	0.97	0.94	32	conclusive
GCF_000006945.2	s__Salmonella enterica	90.0648	1267	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.80	95.43	0.94	0.81	12285	-
GCF_008692785.1	s__Salmonella diarizonae	89.974	1235	1486	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	89.7552	1255	1486	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	89.3501	1197	1486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.33	99.07	0.96	0.94	67	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:20,314] [INFO] GTDB search result was written to GCF_000252995.1_ASM25299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:20,315] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:20,318] [INFO] DFAST_QC result json was written to GCF_000252995.1_ASM25299v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:20,318] [INFO] DFAST_QC completed!
[2024-01-24 13:18:20,318] [INFO] Total running time: 0h1m15s