[2024-01-24 11:42:20,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg777eea16-5e8b-4bff-8a7f-f1c30f283384/dqc_reference
[2024-01-24 11:42:24,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,522] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg52d5a07e-5ccb-4a44-89c1-e8a315ad3b07/GCF_016028495.1_ASM1602849v1_genomic.fna.gz | prodigal -d GCF_016028495.1_ASM1602849v1_genomic.fna/cds.fna -a GCF_016028495.1_ASM1602849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:37,229] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:37,229] [INFO] Task started: HMMsearch
[2024-01-24 11:42:37,230] [INFO] Running command: hmmsearch --tblout GCF_016028495.1_ASM1602849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg777eea16-5e8b-4bff-8a7f-f1c30f283384/dqc_reference/reference_markers.hmm GCF_016028495.1_ASM1602849v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:37,513] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:37,514] [INFO] Found 6/6 markers.
[2024-01-24 11:42:37,554] [INFO] Query marker FASTA was written to GCF_016028495.1_ASM1602849v1_genomic.fna/markers.fasta
[2024-01-24 11:42:37,554] [INFO] Task started: Blastn
[2024-01-24 11:42:37,554] [INFO] Running command: blastn -query GCF_016028495.1_ASM1602849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg777eea16-5e8b-4bff-8a7f-f1c30f283384/dqc_reference/reference_markers.fasta -out GCF_016028495.1_ASM1602849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:38,431] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:38,435] [INFO] Selected 9 target genomes.
[2024-01-24 11:42:38,436] [INFO] Target genome list was writen to GCF_016028495.1_ASM1602849v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:38,441] [INFO] Task started: fastANI
[2024-01-24 11:42:38,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg52d5a07e-5ccb-4a44-89c1-e8a315ad3b07/GCF_016028495.1_ASM1602849v1_genomic.fna.gz --refList GCF_016028495.1_ASM1602849v1_genomic.fna/target_genomes.txt --output GCF_016028495.1_ASM1602849v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:42:48,714] [INFO] Task succeeded: fastANI
[2024-01-24 11:42:48,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg777eea16-5e8b-4bff-8a7f-f1c30f283384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:42:48,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg777eea16-5e8b-4bff-8a7f-f1c30f283384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:42:48,724] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:42:48,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:42:48,724] [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	strain=FDAARGOS_878	GCA_016028495.1	28901	28901	type	True	100.0	1654	1655	95	conclusive
Salmonella enterica	strain=FDAARGOS_768	GCA_006365335.1	28901	28901	type	True	99.9974	1646	1655	95	conclusive
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	99.9955	1648	1655	95	conclusive
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	99.9777	1600	1655	95	conclusive
Salmonella enterica subsp. enterica	strain=LT2	GCA_010649825.1	59201	28901	suspected-type	True	99.9736	1594	1655	95	conclusive
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	83.1708	978	1655	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.2685	807	1655	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.1922	770	1655	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.906	763	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:42:48,726] [INFO] DFAST Taxonomy check result was written to GCF_016028495.1_ASM1602849v1_genomic.fna/tc_result.tsv
[2024-01-24 11:42:48,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:42:48,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:42:48,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg777eea16-5e8b-4bff-8a7f-f1c30f283384/dqc_reference/checkm_data
[2024-01-24 11:42:48,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:42:48,772] [INFO] Task started: CheckM
[2024-01-24 11:42:48,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016028495.1_ASM1602849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016028495.1_ASM1602849v1_genomic.fna/checkm_input GCF_016028495.1_ASM1602849v1_genomic.fna/checkm_result
[2024-01-24 11:43:29,119] [INFO] Task succeeded: CheckM
[2024-01-24 11:43:29,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:43:29,141] [INFO] ===== Completeness check finished =====
[2024-01-24 11:43:29,141] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:43:29,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016028495.1_ASM1602849v1_genomic.fna/markers.fasta)
[2024-01-24 11:43:29,142] [INFO] Task started: Blastn
[2024-01-24 11:43:29,142] [INFO] Running command: blastn -query GCF_016028495.1_ASM1602849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg777eea16-5e8b-4bff-8a7f-f1c30f283384/dqc_reference/reference_markers_gtdb.fasta -out GCF_016028495.1_ASM1602849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:30,561] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:30,565] [INFO] Selected 5 target genomes.
[2024-01-24 11:43:30,565] [INFO] Target genome list was writen to GCF_016028495.1_ASM1602849v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:43:30,570] [INFO] Task started: fastANI
[2024-01-24 11:43:30,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg52d5a07e-5ccb-4a44-89c1-e8a315ad3b07/GCF_016028495.1_ASM1602849v1_genomic.fna.gz --refList GCF_016028495.1_ASM1602849v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016028495.1_ASM1602849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:43:37,108] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:37,119] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:43:37,120] [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	99.9937	1647	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0604	98.80	95.43	0.94	0.81	12285	conclusive
GCF_008692785.1	s__Salmonella diarizonae	94.9949	1306	1655	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	94.7664	1337	1655	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	93.1857	1257	1655	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	90.0187	1273	1655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Salmonella	95.0	99.43	98.73	0.97	0.94	32	-
--------------------------------------------------------------------------------
[2024-01-24 11:43:37,121] [INFO] GTDB search result was written to GCF_016028495.1_ASM1602849v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:43:37,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:43:37,124] [INFO] DFAST_QC result json was written to GCF_016028495.1_ASM1602849v1_genomic.fna/dqc_result.json
[2024-01-24 11:43:37,125] [INFO] DFAST_QC completed!
[2024-01-24 11:43:37,125] [INFO] Total running time: 0h1m17s