[2024-01-24 14:05:31,618] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,621] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2129950-fdf4-416f-8077-3ce390299dbb/dqc_reference
[2024-01-24 14:05:32,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:32,818] [INFO] Task started: Prodigal
[2024-01-24 14:05:32,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d08f936-d448-4a71-b263-643e89bad564/GCF_008993375.1_PDT000158283.2_genomic.fna.gz | prodigal -d GCF_008993375.1_PDT000158283.2_genomic.fna/cds.fna -a GCF_008993375.1_PDT000158283.2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:44,522] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:44,523] [INFO] Task started: HMMsearch
[2024-01-24 14:05:44,523] [INFO] Running command: hmmsearch --tblout GCF_008993375.1_PDT000158283.2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2129950-fdf4-416f-8077-3ce390299dbb/dqc_reference/reference_markers.hmm GCF_008993375.1_PDT000158283.2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:44,814] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:44,816] [INFO] Found 6/6 markers.
[2024-01-24 14:05:44,856] [INFO] Query marker FASTA was written to GCF_008993375.1_PDT000158283.2_genomic.fna/markers.fasta
[2024-01-24 14:05:44,857] [INFO] Task started: Blastn
[2024-01-24 14:05:44,857] [INFO] Running command: blastn -query GCF_008993375.1_PDT000158283.2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2129950-fdf4-416f-8077-3ce390299dbb/dqc_reference/reference_markers.fasta -out GCF_008993375.1_PDT000158283.2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:45,794] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:45,798] [INFO] Selected 9 target genomes.
[2024-01-24 14:05:45,798] [INFO] Target genome list was writen to GCF_008993375.1_PDT000158283.2_genomic.fna/target_genomes.txt
[2024-01-24 14:05:45,801] [INFO] Task started: fastANI
[2024-01-24 14:05:45,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d08f936-d448-4a71-b263-643e89bad564/GCF_008993375.1_PDT000158283.2_genomic.fna.gz --refList GCF_008993375.1_PDT000158283.2_genomic.fna/target_genomes.txt --output GCF_008993375.1_PDT000158283.2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:56,091] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:56,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2129950-fdf4-416f-8077-3ce390299dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:56,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2129950-fdf4-416f-8077-3ce390299dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:56,102] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:05:56,103] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:56,103] [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	98.8529	1476	1530	95	conclusive
Salmonella enterica	strain=FDAARGOS_768	GCA_006365335.1	28901	28901	type	True	98.8314	1478	1530	95	conclusive
Salmonella enterica subsp. enterica	strain=LT2	GCA_010649825.1	59201	28901	suspected-type	True	98.8308	1456	1530	95	conclusive
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	98.8222	1480	1530	95	conclusive
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	98.8166	1473	1530	95	conclusive
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	83.1113	953	1530	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.336	762	1530	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.2296	766	1530	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.0646	748	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:56,108] [INFO] DFAST Taxonomy check result was written to GCF_008993375.1_PDT000158283.2_genomic.fna/tc_result.tsv
[2024-01-24 14:05:56,111] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:56,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:56,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2129950-fdf4-416f-8077-3ce390299dbb/dqc_reference/checkm_data
[2024-01-24 14:05:56,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:56,167] [INFO] Task started: CheckM
[2024-01-24 14:05:56,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008993375.1_PDT000158283.2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008993375.1_PDT000158283.2_genomic.fna/checkm_input GCF_008993375.1_PDT000158283.2_genomic.fna/checkm_result
[2024-01-24 14:06:35,993] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:35,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:36,014] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:36,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:36,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008993375.1_PDT000158283.2_genomic.fna/markers.fasta)
[2024-01-24 14:06:36,015] [INFO] Task started: Blastn
[2024-01-24 14:06:36,015] [INFO] Running command: blastn -query GCF_008993375.1_PDT000158283.2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2129950-fdf4-416f-8077-3ce390299dbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_008993375.1_PDT000158283.2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:37,557] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:37,560] [INFO] Selected 5 target genomes.
[2024-01-24 14:06:37,560] [INFO] Target genome list was writen to GCF_008993375.1_PDT000158283.2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:37,561] [INFO] Task started: fastANI
[2024-01-24 14:06:37,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d08f936-d448-4a71-b263-643e89bad564/GCF_008993375.1_PDT000158283.2_genomic.fna.gz --refList GCF_008993375.1_PDT000158283.2_genomic.fna/target_genomes_gtdb.txt --output GCF_008993375.1_PDT000158283.2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:43,663] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:43,672] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:43,673] [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	98.8261	1478	1530	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	95.0377	1279	1530	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	94.708	1276	1530	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	93.1697	1237	1530	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	90.1377	1233	1530	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 14:06:43,674] [INFO] GTDB search result was written to GCF_008993375.1_PDT000158283.2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:43,675] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:43,678] [INFO] DFAST_QC result json was written to GCF_008993375.1_PDT000158283.2_genomic.fna/dqc_result.json
[2024-01-24 14:06:43,678] [INFO] DFAST_QC completed!
[2024-01-24 14:06:43,678] [INFO] Total running time: 0h1m12s