[2024-01-24 13:36:57,067] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:57,069] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:57,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg769291ea-d61b-4855-b85d-b55c1e13b2b7/dqc_reference
[2024-01-24 13:36:58,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:58,412] [INFO] Task started: Prodigal
[2024-01-24 13:36:58,413] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc89aeb7-af0f-4bc2-ad6e-862a449b3946/GCF_016029065.1_PDT000910284.1_genomic.fna.gz | prodigal -d GCF_016029065.1_PDT000910284.1_genomic.fna/cds.fna -a GCF_016029065.1_PDT000910284.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:10,863] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:10,864] [INFO] Task started: HMMsearch
[2024-01-24 13:37:10,864] [INFO] Running command: hmmsearch --tblout GCF_016029065.1_PDT000910284.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg769291ea-d61b-4855-b85d-b55c1e13b2b7/dqc_reference/reference_markers.hmm GCF_016029065.1_PDT000910284.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:11,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:11,231] [INFO] Found 6/6 markers.
[2024-01-24 13:37:11,282] [INFO] Query marker FASTA was written to GCF_016029065.1_PDT000910284.1_genomic.fna/markers.fasta
[2024-01-24 13:37:11,283] [INFO] Task started: Blastn
[2024-01-24 13:37:11,283] [INFO] Running command: blastn -query GCF_016029065.1_PDT000910284.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769291ea-d61b-4855-b85d-b55c1e13b2b7/dqc_reference/reference_markers.fasta -out GCF_016029065.1_PDT000910284.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:12,157] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:12,161] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:12,161] [INFO] Target genome list was writen to GCF_016029065.1_PDT000910284.1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:12,176] [INFO] Task started: fastANI
[2024-01-24 13:37:12,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc89aeb7-af0f-4bc2-ad6e-862a449b3946/GCF_016029065.1_PDT000910284.1_genomic.fna.gz --refList GCF_016029065.1_PDT000910284.1_genomic.fna/target_genomes.txt --output GCF_016029065.1_PDT000910284.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:30,473] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:30,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg769291ea-d61b-4855-b85d-b55c1e13b2b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:30,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg769291ea-d61b-4855-b85d-b55c1e13b2b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:30,489] [INFO] Found 16 fastANI hits (9 hits with ANI > threshold)
[2024-01-24 13:37:30,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:30,490] [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. salamae	strain=CCUG30039	GCA_016029065.1	59202	28901	type	True	100.0	1566	1590	95	conclusive
Salmonella enterica subsp. salamae	strain=CCUG 30039T	GCA_008692775.1	59202	28901	type	True	99.9985	1533	1590	95	conclusive
Salmonella enterica	strain=FDAARGOS_768	GCA_006365335.1	28901	28901	type	True	96.0673	1353	1590	95	conclusive
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	96.0462	1341	1590	95	conclusive
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	96.0195	1361	1590	95	conclusive
Salmonella enterica subsp. indica	strain=CCUG30038	GCA_018033035.1	59207	28901	type	True	95.8333	1346	1590	95	conclusive
Salmonella enterica subsp. diarizonae	strain=CCUG30040	GCA_016030095.1	59204	28901	type	True	95.7543	1331	1590	95	conclusive
Salmonella enterica subsp. diarizonae	strain=CCUG 30040T	GCA_008692785.1	59204	28901	type	True	95.7505	1310	1590	95	conclusive
Salmonella enterica subsp. houtenae	strain=CCUG 30041T	GCA_008692755.1	59205	28901	type	True	95.2791	1297	1590	95	conclusive
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.9645	993	1590	95	below_threshold
Citrobacter farmeri	strain=FDAARGOS 1423	GCA_019048065.1	67824	67824	type	True	82.7266	952	1590	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.1903	762	1590	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.0236	805	1590	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.893	753	1590	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	77.9045	302	1590	95	below_threshold
Leminorella richardii	strain=NCTC12151	GCA_900478135.1	158841	158841	type	True	77.2844	191	1590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:30,492] [INFO] DFAST Taxonomy check result was written to GCF_016029065.1_PDT000910284.1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:30,493] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:30,493] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:30,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg769291ea-d61b-4855-b85d-b55c1e13b2b7/dqc_reference/checkm_data
[2024-01-24 13:37:30,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:30,549] [INFO] Task started: CheckM
[2024-01-24 13:37:30,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016029065.1_PDT000910284.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016029065.1_PDT000910284.1_genomic.fna/checkm_input GCF_016029065.1_PDT000910284.1_genomic.fna/checkm_result
[2024-01-24 13:38:10,009] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:10,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:10,034] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:10,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:10,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016029065.1_PDT000910284.1_genomic.fna/markers.fasta)
[2024-01-24 13:38:10,035] [INFO] Task started: Blastn
[2024-01-24 13:38:10,035] [INFO] Running command: blastn -query GCF_016029065.1_PDT000910284.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769291ea-d61b-4855-b85d-b55c1e13b2b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_016029065.1_PDT000910284.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:11,142] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:11,147] [INFO] Selected 10 target genomes.
[2024-01-24 13:38:11,147] [INFO] Target genome list was writen to GCF_016029065.1_PDT000910284.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:11,161] [INFO] Task started: fastANI
[2024-01-24 13:38:11,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc89aeb7-af0f-4bc2-ad6e-862a449b3946/GCF_016029065.1_PDT000910284.1_genomic.fna.gz --refList GCF_016029065.1_PDT000910284.1_genomic.fna/target_genomes_gtdb.txt --output GCF_016029065.1_PDT000910284.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:22,118] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:22,134] [INFO] Found 10 fastANI hits (3 hits with ANI > circumscription radius)
[2024-01-24 13:38:22,134] [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	96.0503	1360	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.80	95.43	0.94	0.81	12285	inconclusive
GCF_008692785.1	s__Salmonella diarizonae	95.7505	1310	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.90	95.36	0.91	0.81	98	inconclusive
GCA_900478215.1	s__Salmonella houtenae	95.3256	1315	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.09	96.71	0.94	0.89	62	inconclusive
GCF_008692845.1	s__Salmonella arizonae	93.5402	1275	1590	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	90.0903	1274	1590	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	83.0891	964	1590	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	82.8914	1037	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005281345.1	s__Citrobacter sp005281345	82.6393	966	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.53	97.53	0.86	0.86	2	-
GCF_902706235.1	s__Scandinavium sp902706235	80.4857	704	1590	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003818135.1	s__Buttiauxella warmboldiae	79.5779	539	1590	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 13:38:22,136] [INFO] GTDB search result was written to GCF_016029065.1_PDT000910284.1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:22,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:22,140] [INFO] DFAST_QC result json was written to GCF_016029065.1_PDT000910284.1_genomic.fna/dqc_result.json
[2024-01-24 13:38:22,140] [INFO] DFAST_QC completed!
[2024-01-24 13:38:22,140] [INFO] Total running time: 0h1m25s