[2024-01-24 13:01:52,781] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:52,784] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:52,784] [INFO] DQC Reference Directory: /var/lib/cwl/stg78de3f0c-4187-4485-9234-16181c1f6b77/dqc_reference
[2024-01-24 13:01:54,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,127] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg786edb00-81c6-4124-9f65-d42830fab46b/GCF_008692785.1_ASM869278v1_genomic.fna.gz | prodigal -d GCF_008692785.1_ASM869278v1_genomic.fna/cds.fna -a GCF_008692785.1_ASM869278v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:07,540] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:07,541] [INFO] Task started: HMMsearch
[2024-01-24 13:02:07,541] [INFO] Running command: hmmsearch --tblout GCF_008692785.1_ASM869278v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78de3f0c-4187-4485-9234-16181c1f6b77/dqc_reference/reference_markers.hmm GCF_008692785.1_ASM869278v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:07,895] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:07,896] [INFO] Found 6/6 markers.
[2024-01-24 13:02:07,936] [INFO] Query marker FASTA was written to GCF_008692785.1_ASM869278v1_genomic.fna/markers.fasta
[2024-01-24 13:02:07,937] [INFO] Task started: Blastn
[2024-01-24 13:02:07,937] [INFO] Running command: blastn -query GCF_008692785.1_ASM869278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78de3f0c-4187-4485-9234-16181c1f6b77/dqc_reference/reference_markers.fasta -out GCF_008692785.1_ASM869278v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:08,760] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:08,764] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:08,764] [INFO] Target genome list was writen to GCF_008692785.1_ASM869278v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:08,773] [INFO] Task started: fastANI
[2024-01-24 13:02:08,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg786edb00-81c6-4124-9f65-d42830fab46b/GCF_008692785.1_ASM869278v1_genomic.fna.gz --refList GCF_008692785.1_ASM869278v1_genomic.fna/target_genomes.txt --output GCF_008692785.1_ASM869278v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:24,652] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:24,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78de3f0c-4187-4485-9234-16181c1f6b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:24,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78de3f0c-4187-4485-9234-16181c1f6b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:24,666] [INFO] Found 16 fastANI hits (7 hits with ANI > threshold)
[2024-01-24 13:02:24,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:24,667] [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. diarizonae	strain=CCUG 30040T	GCA_008692785.1	59204	28901	type	True	100.0	1622	1624	95	conclusive
Salmonella enterica subsp. diarizonae	strain=CCUG30040	GCA_016030095.1	59204	28901	type	True	99.9953	1607	1624	95	conclusive
Salmonella enterica subsp. salamae	strain=CCUG 30039T	GCA_008692775.1	59202	28901	type	True	95.8214	1299	1624	95	conclusive
Salmonella enterica subsp. salamae	strain=CCUG30039	GCA_016029065.1	59202	28901	type	True	95.7895	1295	1624	95	conclusive
Salmonella enterica subsp. indica	strain=CCUG30038	GCA_018033035.1	59207	28901	type	True	95.0816	1292	1624	95	conclusive
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	95.0765	1268	1624	95	conclusive
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	95.0378	1292	1624	95	conclusive
Salmonella enterica subsp. houtenae	strain=CCUG 30041T	GCA_008692755.1	59205	28901	type	True	94.8159	1298	1624	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	83.1241	948	1624	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.132	748	1624	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.0298	802	1624	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.0116	753	1624	95	below_threshold
Raoultella ornithinolytica	strain=NBRC 105727	GCA_001598295.1	54291	54291	type	True	80.8877	713	1624	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	78.37	340	1624	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	78.3652	362	1624	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	78.335	361	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:24,670] [INFO] DFAST Taxonomy check result was written to GCF_008692785.1_ASM869278v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:24,671] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:24,671] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:24,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78de3f0c-4187-4485-9234-16181c1f6b77/dqc_reference/checkm_data
[2024-01-24 13:02:24,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:24,722] [INFO] Task started: CheckM
[2024-01-24 13:02:24,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008692785.1_ASM869278v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008692785.1_ASM869278v1_genomic.fna/checkm_input GCF_008692785.1_ASM869278v1_genomic.fna/checkm_result
[2024-01-24 13:03:07,540] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:07,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:07,569] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:07,570] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:07,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008692785.1_ASM869278v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:07,571] [INFO] Task started: Blastn
[2024-01-24 13:03:07,571] [INFO] Running command: blastn -query GCF_008692785.1_ASM869278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78de3f0c-4187-4485-9234-16181c1f6b77/dqc_reference/reference_markers_gtdb.fasta -out GCF_008692785.1_ASM869278v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:08,698] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:08,702] [INFO] Selected 9 target genomes.
[2024-01-24 13:03:08,703] [INFO] Target genome list was writen to GCF_008692785.1_ASM869278v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:08,710] [INFO] Task started: fastANI
[2024-01-24 13:03:08,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg786edb00-81c6-4124-9f65-d42830fab46b/GCF_008692785.1_ASM869278v1_genomic.fna.gz --refList GCF_008692785.1_ASM869278v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008692785.1_ASM869278v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:18,758] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:18,776] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:18,776] [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_008692785.1	s__Salmonella diarizonae	100.0	1622	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.90	95.36	0.91	0.81	98	conclusive
GCF_000006945.2	s__Salmonella enterica	95.0604	1288	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.80	95.43	0.94	0.81	12285	conclusive
GCA_900478215.1	s__Salmonella houtenae	94.8707	1308	1624	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	93.7796	1306	1624	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	90.0017	1230	1624	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	83.1798	922	1624	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	82.8841	995	1624	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	80.2465	712	1624	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	80.1044	682	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.54	98.53	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:18,778] [INFO] GTDB search result was written to GCF_008692785.1_ASM869278v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:18,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:18,789] [INFO] DFAST_QC result json was written to GCF_008692785.1_ASM869278v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:18,790] [INFO] DFAST_QC completed!
[2024-01-24 13:03:18,790] [INFO] Total running time: 0h1m26s