[2024-01-24 11:05:03,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,929] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3580c62-b862-4d76-bd10-38ba994da1d5/dqc_reference
[2024-01-24 11:05:05,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,765] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fc37345-865e-4880-b61b-854d808b3706/GCF_016029385.1_PDT000910268.1_genomic.fna.gz | prodigal -d GCF_016029385.1_PDT000910268.1_genomic.fna/cds.fna -a GCF_016029385.1_PDT000910268.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:15,939] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:15,939] [INFO] Task started: HMMsearch
[2024-01-24 11:05:15,940] [INFO] Running command: hmmsearch --tblout GCF_016029385.1_PDT000910268.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3580c62-b862-4d76-bd10-38ba994da1d5/dqc_reference/reference_markers.hmm GCF_016029385.1_PDT000910268.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:16,248] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:16,249] [INFO] Found 6/6 markers.
[2024-01-24 11:05:16,296] [INFO] Query marker FASTA was written to GCF_016029385.1_PDT000910268.1_genomic.fna/markers.fasta
[2024-01-24 11:05:16,296] [INFO] Task started: Blastn
[2024-01-24 11:05:16,297] [INFO] Running command: blastn -query GCF_016029385.1_PDT000910268.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3580c62-b862-4d76-bd10-38ba994da1d5/dqc_reference/reference_markers.fasta -out GCF_016029385.1_PDT000910268.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:17,113] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:17,115] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:17,116] [INFO] Target genome list was writen to GCF_016029385.1_PDT000910268.1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:17,121] [INFO] Task started: fastANI
[2024-01-24 11:05:17,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fc37345-865e-4880-b61b-854d808b3706/GCF_016029385.1_PDT000910268.1_genomic.fna.gz --refList GCF_016029385.1_PDT000910268.1_genomic.fna/target_genomes.txt --output GCF_016029385.1_PDT000910268.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:34,267] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:34,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3580c62-b862-4d76-bd10-38ba994da1d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:34,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3580c62-b862-4d76-bd10-38ba994da1d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:34,277] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:34,277] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:34,277] [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 subsp. arizonae	strain=CCUG6322	GCA_016029385.1	59203	28901	type	True	100.0	1493	1520	95	conclusive
Salmonella enterica subsp. arizonae	strain=CCUG 6322T	GCA_008692845.1	59203	28901	type	True	99.9977	1466	1520	95	conclusive
Salmonella enterica subsp. diarizonae	strain=CCUG 30040T	GCA_008692785.1	59204	28901	type	True	93.8276	1310	1520	95	below_threshold
Salmonella enterica subsp. diarizonae	strain=CCUG30040	GCA_016030095.1	59204	28901	type	True	93.8084	1324	1520	95	below_threshold
Salmonella enterica subsp. salamae	strain=CCUG30039	GCA_016029065.1	59202	28901	type	True	93.7171	1262	1520	95	below_threshold
Salmonella enterica subsp. salamae	strain=CCUG 30039T	GCA_008692775.1	59202	28901	type	True	93.6736	1277	1520	95	below_threshold
Salmonella enterica subsp. houtenae	strain=CCUG 30041T	GCA_008692755.1	59205	28901	type	True	93.2735	1266	1520	95	below_threshold
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	93.1973	1263	1520	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	93.1835	1259	1520	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.8098	953	1520	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.115	736	1520	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.0193	753	1520	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.9089	705	1520	95	below_threshold
Chimaeribacter coloradensis	strain=2016-Iso4	GCA_002858715.1	2060068	2060068	type	True	78.4552	340	1520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:34,278] [INFO] DFAST Taxonomy check result was written to GCF_016029385.1_PDT000910268.1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:34,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:34,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:34,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3580c62-b862-4d76-bd10-38ba994da1d5/dqc_reference/checkm_data
[2024-01-24 11:05:34,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:34,324] [INFO] Task started: CheckM
[2024-01-24 11:05:34,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016029385.1_PDT000910268.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016029385.1_PDT000910268.1_genomic.fna/checkm_input GCF_016029385.1_PDT000910268.1_genomic.fna/checkm_result
[2024-01-24 11:06:06,575] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:06,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:06,596] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:06,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:06,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016029385.1_PDT000910268.1_genomic.fna/markers.fasta)
[2024-01-24 11:06:06,597] [INFO] Task started: Blastn
[2024-01-24 11:06:06,597] [INFO] Running command: blastn -query GCF_016029385.1_PDT000910268.1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3580c62-b862-4d76-bd10-38ba994da1d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_016029385.1_PDT000910268.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:07,773] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:07,775] [INFO] Selected 10 target genomes.
[2024-01-24 11:06:07,775] [INFO] Target genome list was writen to GCF_016029385.1_PDT000910268.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:07,781] [INFO] Task started: fastANI
[2024-01-24 11:06:07,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fc37345-865e-4880-b61b-854d808b3706/GCF_016029385.1_PDT000910268.1_genomic.fna.gz --refList GCF_016029385.1_PDT000910268.1_genomic.fna/target_genomes_gtdb.txt --output GCF_016029385.1_PDT000910268.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:18,935] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:18,943] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:18,943] [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_008692845.1	s__Salmonella arizonae	99.9977	1466	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.33	99.07	0.96	0.94	67	conclusive
GCF_008692785.1	s__Salmonella diarizonae	93.8128	1311	1520	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	93.3336	1274	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.09	96.71	0.94	0.89	62	-
GCF_000006945.2	s__Salmonella enterica	93.2178	1257	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.80	95.43	0.94	0.81	12285	-
GCF_000252995.1	s__Salmonella bongori	89.407	1191	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.43	98.73	0.97	0.94	32	-
GCF_000759815.1	s__Citrobacter_A rodentium	82.8444	927	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.98	99.96	0.98	0.96	4	-
GCF_000155975.1	s__Citrobacter portucalensis_A	82.7912	953	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902706235.1	s__Scandinavium sp902706235	80.3752	684	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193285.1	s__Atlantibacter sp002345315	80.0915	672	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.54	98.53	0.93	0.90	4	-
GCF_003818135.1	s__Buttiauxella warmboldiae	79.6002	524	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:18,944] [INFO] GTDB search result was written to GCF_016029385.1_PDT000910268.1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:18,945] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:18,948] [INFO] DFAST_QC result json was written to GCF_016029385.1_PDT000910268.1_genomic.fna/dqc_result.json
[2024-01-24 11:06:18,948] [INFO] DFAST_QC completed!
[2024-01-24 11:06:18,948] [INFO] Total running time: 0h1m15s