[2024-01-24 14:02:47,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:47,358] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:47,358] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a56f039-8840-494d-b153-f8fb625aa965/dqc_reference
[2024-01-24 14:02:48,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:48,606] [INFO] Task started: Prodigal
[2024-01-24 14:02:48,606] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd87ec8b-079c-4d88-b163-fd0cb52cf41d/GCF_008692755.1_ASM869275v1_genomic.fna.gz | prodigal -d GCF_008692755.1_ASM869275v1_genomic.fna/cds.fna -a GCF_008692755.1_ASM869275v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:00,710] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:00,710] [INFO] Task started: HMMsearch
[2024-01-24 14:03:00,710] [INFO] Running command: hmmsearch --tblout GCF_008692755.1_ASM869275v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a56f039-8840-494d-b153-f8fb625aa965/dqc_reference/reference_markers.hmm GCF_008692755.1_ASM869275v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:00,998] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:01,000] [INFO] Found 6/6 markers.
[2024-01-24 14:03:01,038] [INFO] Query marker FASTA was written to GCF_008692755.1_ASM869275v1_genomic.fna/markers.fasta
[2024-01-24 14:03:01,039] [INFO] Task started: Blastn
[2024-01-24 14:03:01,039] [INFO] Running command: blastn -query GCF_008692755.1_ASM869275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a56f039-8840-494d-b153-f8fb625aa965/dqc_reference/reference_markers.fasta -out GCF_008692755.1_ASM869275v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:01,904] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:01,907] [INFO] Selected 14 target genomes.
[2024-01-24 14:03:01,907] [INFO] Target genome list was writen to GCF_008692755.1_ASM869275v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:01,920] [INFO] Task started: fastANI
[2024-01-24 14:03:01,920] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd87ec8b-079c-4d88-b163-fd0cb52cf41d/GCF_008692755.1_ASM869275v1_genomic.fna.gz --refList GCF_008692755.1_ASM869275v1_genomic.fna/target_genomes.txt --output GCF_008692755.1_ASM869275v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:16,621] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:16,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a56f039-8840-494d-b153-f8fb625aa965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:16,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a56f039-8840-494d-b153-f8fb625aa965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:16,637] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:03:16,637] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:16,638] [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. houtenae	strain=CCUG 30041T	GCA_008692755.1	59205	28901	type	True	100.0	1524	1525	95	conclusive
Salmonella enterica subsp. salamae	strain=CCUG 30039T	GCA_008692775.1	59202	28901	type	True	95.4093	1289	1525	95	conclusive
Salmonella enterica subsp. salamae	strain=CCUG30039	GCA_016029065.1	59202	28901	type	True	95.3456	1282	1525	95	conclusive
Salmonella enterica subsp. diarizonae	strain=CCUG 30040T	GCA_008692785.1	59204	28901	type	True	94.812	1315	1525	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	94.8072	1286	1525	95	below_threshold
Salmonella enterica	strain=FDAARGOS_768	GCA_006365335.1	28901	28901	type	True	94.7958	1291	1525	95	below_threshold
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	94.7924	1275	1525	95	below_threshold
Salmonella enterica subsp. diarizonae	strain=CCUG30040	GCA_016030095.1	59204	28901	type	True	94.7867	1316	1525	95	below_threshold
Salmonella enterica	strain=FDAARGOS_878	GCA_016028495.1	28901	28901	type	True	94.7808	1296	1525	95	below_threshold
Salmonella enterica subsp. indica	strain=CCUG30038	GCA_018033035.1	59207	28901	type	True	94.6706	1266	1525	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.8752	960	1525	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.1716	749	1525	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.9916	724	1525	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.9731	757	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:16,641] [INFO] DFAST Taxonomy check result was written to GCF_008692755.1_ASM869275v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:16,642] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:16,642] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:16,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a56f039-8840-494d-b153-f8fb625aa965/dqc_reference/checkm_data
[2024-01-24 14:03:16,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:16,691] [INFO] Task started: CheckM
[2024-01-24 14:03:16,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008692755.1_ASM869275v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008692755.1_ASM869275v1_genomic.fna/checkm_input GCF_008692755.1_ASM869275v1_genomic.fna/checkm_result
[2024-01-24 14:03:55,541] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:55,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:55,569] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:55,569] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:55,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008692755.1_ASM869275v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:55,570] [INFO] Task started: Blastn
[2024-01-24 14:03:55,570] [INFO] Running command: blastn -query GCF_008692755.1_ASM869275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a56f039-8840-494d-b153-f8fb625aa965/dqc_reference/reference_markers_gtdb.fasta -out GCF_008692755.1_ASM869275v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:56,718] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:56,721] [INFO] Selected 8 target genomes.
[2024-01-24 14:03:56,722] [INFO] Target genome list was writen to GCF_008692755.1_ASM869275v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:56,731] [INFO] Task started: fastANI
[2024-01-24 14:03:56,732] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd87ec8b-079c-4d88-b163-fd0cb52cf41d/GCF_008692755.1_ASM869275v1_genomic.fna.gz --refList GCF_008692755.1_ASM869275v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008692755.1_ASM869275v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:05,539] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:05,552] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:05,552] [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
GCA_900478215.1	s__Salmonella houtenae	99.2866	1438	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.09	96.71	0.94	0.89	62	conclusive
GCF_008692785.1	s__Salmonella diarizonae	94.812	1315	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.90	95.36	0.91	0.81	98	-
GCF_000006945.2	s__Salmonella enterica	94.8034	1293	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.80	95.43	0.94	0.81	12285	-
GCF_008692845.1	s__Salmonella arizonae	93.1902	1268	1525	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	89.7329	1239	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.43	98.73	0.97	0.94	32	-
GCF_015672735.1	s__Citrobacter sp015672735	82.535	910	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900365.1	s__Escherichia marmotae	81.8043	838	1525	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	77.9408	218	1525	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 14:04:05,554] [INFO] GTDB search result was written to GCF_008692755.1_ASM869275v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:05,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:05,560] [INFO] DFAST_QC result json was written to GCF_008692755.1_ASM869275v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:05,560] [INFO] DFAST_QC completed!
[2024-01-24 14:04:05,560] [INFO] Total running time: 0h1m18s