[2024-01-24 14:03:05,169] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:05,171] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:05,171] [INFO] DQC Reference Directory: /var/lib/cwl/stg84e01657-ca04-475f-9465-34410f0921c3/dqc_reference
[2024-01-24 14:03:06,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:06,484] [INFO] Task started: Prodigal
[2024-01-24 14:03:06,484] [INFO] Running command: gunzip -c /var/lib/cwl/stge672707e-6df7-4e2c-acc8-c0041169f4cd/GCF_018033035.1_PDT000909609.1_genomic.fna.gz | prodigal -d GCF_018033035.1_PDT000909609.1_genomic.fna/cds.fna -a GCF_018033035.1_PDT000909609.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:19,575] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:19,575] [INFO] Task started: HMMsearch
[2024-01-24 14:03:19,575] [INFO] Running command: hmmsearch --tblout GCF_018033035.1_PDT000909609.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84e01657-ca04-475f-9465-34410f0921c3/dqc_reference/reference_markers.hmm GCF_018033035.1_PDT000909609.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:19,932] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:19,934] [INFO] Found 6/6 markers.
[2024-01-24 14:03:19,987] [INFO] Query marker FASTA was written to GCF_018033035.1_PDT000909609.1_genomic.fna/markers.fasta
[2024-01-24 14:03:19,988] [INFO] Task started: Blastn
[2024-01-24 14:03:19,988] [INFO] Running command: blastn -query GCF_018033035.1_PDT000909609.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84e01657-ca04-475f-9465-34410f0921c3/dqc_reference/reference_markers.fasta -out GCF_018033035.1_PDT000909609.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:20,833] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:20,836] [INFO] Selected 13 target genomes.
[2024-01-24 14:03:20,837] [INFO] Target genome list was writen to GCF_018033035.1_PDT000909609.1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:20,845] [INFO] Task started: fastANI
[2024-01-24 14:03:20,846] [INFO] Running command: fastANI --query /var/lib/cwl/stge672707e-6df7-4e2c-acc8-c0041169f4cd/GCF_018033035.1_PDT000909609.1_genomic.fna.gz --refList GCF_018033035.1_PDT000909609.1_genomic.fna/target_genomes.txt --output GCF_018033035.1_PDT000909609.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:36,466] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:36,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84e01657-ca04-475f-9465-34410f0921c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:36,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84e01657-ca04-475f-9465-34410f0921c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:36,478] [INFO] Found 13 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 14:03:36,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:36,478] [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. indica	strain=CCUG30038	GCA_018033035.1	59207	28901	type	True	100.0	1597	1648	95	conclusive
Salmonella enterica subsp. salamae	strain=CCUG 30039T	GCA_008692775.1	59202	28901	type	True	95.898	1325	1648	95	conclusive
Salmonella enterica subsp. salamae	strain=CCUG30039	GCA_016029065.1	59202	28901	type	True	95.8534	1338	1648	95	conclusive
Salmonella enterica	strain=FDAARGOS_768	GCA_006365335.1	28901	28901	type	True	95.4862	1340	1648	95	conclusive
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	95.4392	1339	1648	95	conclusive
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	95.4371	1342	1648	95	conclusive
Salmonella enterica subsp. diarizonae	strain=CCUG 30040T	GCA_008692785.1	59204	28901	type	True	95.0905	1301	1648	95	conclusive
Salmonella enterica subsp. diarizonae	strain=CCUG30040	GCA_016030095.1	59204	28901	type	True	95.0578	1313	1648	95	conclusive
Salmonella enterica subsp. houtenae	strain=CCUG 30041T	GCA_008692755.1	59205	28901	type	True	94.7082	1277	1648	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.9286	957	1648	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.114	740	1648	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.1021	740	1648	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.9056	746	1648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:36,480] [INFO] DFAST Taxonomy check result was written to GCF_018033035.1_PDT000909609.1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:36,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:36,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:36,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84e01657-ca04-475f-9465-34410f0921c3/dqc_reference/checkm_data
[2024-01-24 14:03:36,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:36,534] [INFO] Task started: CheckM
[2024-01-24 14:03:36,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018033035.1_PDT000909609.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018033035.1_PDT000909609.1_genomic.fna/checkm_input GCF_018033035.1_PDT000909609.1_genomic.fna/checkm_result
[2024-01-24 14:04:17,609] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:17,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:17,635] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:17,635] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:17,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018033035.1_PDT000909609.1_genomic.fna/markers.fasta)
[2024-01-24 14:04:17,636] [INFO] Task started: Blastn
[2024-01-24 14:04:17,636] [INFO] Running command: blastn -query GCF_018033035.1_PDT000909609.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84e01657-ca04-475f-9465-34410f0921c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_018033035.1_PDT000909609.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:18,749] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:18,753] [INFO] Selected 7 target genomes.
[2024-01-24 14:04:18,753] [INFO] Target genome list was writen to GCF_018033035.1_PDT000909609.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:18,769] [INFO] Task started: fastANI
[2024-01-24 14:04:18,769] [INFO] Running command: fastANI --query /var/lib/cwl/stge672707e-6df7-4e2c-acc8-c0041169f4cd/GCF_018033035.1_PDT000909609.1_genomic.fna.gz --refList GCF_018033035.1_PDT000909609.1_genomic.fna/target_genomes_gtdb.txt --output GCF_018033035.1_PDT000909609.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:26,429] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:26,438] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:04:26,438] [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	95.468	1340	1648	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	95.0905	1301	1648	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	94.7852	1268	1648	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	93.054	1262	1648	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	89.7581	1261	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.43	98.73	0.97	0.94	32	-
GCF_002900365.1	s__Escherichia marmotae	81.731	846	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	-
GCF_000474215.1	s__Edwardsiella hoshinae	78.0236	226	1648	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.58	0.98	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:26,441] [INFO] GTDB search result was written to GCF_018033035.1_PDT000909609.1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:26,441] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:26,446] [INFO] DFAST_QC result json was written to GCF_018033035.1_PDT000909609.1_genomic.fna/dqc_result.json
[2024-01-24 14:04:26,446] [INFO] DFAST_QC completed!
[2024-01-24 14:04:26,446] [INFO] Total running time: 0h1m21s