[2024-01-24 14:19:31,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:31,928] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:31,928] [INFO] DQC Reference Directory: /var/lib/cwl/stgca905692-619d-46c2-b776-7baf49d4439d/dqc_reference
[2024-01-24 14:19:33,426] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:33,427] [INFO] Task started: Prodigal
[2024-01-24 14:19:33,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg232175b5-826f-4345-9029-3f81c07f6aeb/GCF_001571285.1_ASM157128v1_genomic.fna.gz | prodigal -d GCF_001571285.1_ASM157128v1_genomic.fna/cds.fna -a GCF_001571285.1_ASM157128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:47,408] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:47,408] [INFO] Task started: HMMsearch
[2024-01-24 14:19:47,408] [INFO] Running command: hmmsearch --tblout GCF_001571285.1_ASM157128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca905692-619d-46c2-b776-7baf49d4439d/dqc_reference/reference_markers.hmm GCF_001571285.1_ASM157128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:47,779] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:47,781] [INFO] Found 6/6 markers.
[2024-01-24 14:19:47,850] [INFO] Query marker FASTA was written to GCF_001571285.1_ASM157128v1_genomic.fna/markers.fasta
[2024-01-24 14:19:47,851] [INFO] Task started: Blastn
[2024-01-24 14:19:47,851] [INFO] Running command: blastn -query GCF_001571285.1_ASM157128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca905692-619d-46c2-b776-7baf49d4439d/dqc_reference/reference_markers.fasta -out GCF_001571285.1_ASM157128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:48,850] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:48,853] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:48,853] [INFO] Target genome list was writen to GCF_001571285.1_ASM157128v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:48,858] [INFO] Task started: fastANI
[2024-01-24 14:19:48,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg232175b5-826f-4345-9029-3f81c07f6aeb/GCF_001571285.1_ASM157128v1_genomic.fna.gz --refList GCF_001571285.1_ASM157128v1_genomic.fna/target_genomes.txt --output GCF_001571285.1_ASM157128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:04,180] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:04,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca905692-619d-46c2-b776-7baf49d4439d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:04,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca905692-619d-46c2-b776-7baf49d4439d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:04,192] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:04,192] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:04,193] [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
Kluyvera cryocrescens	strain=NBRC 102467	GCA_001571285.1	580	580	type	True	100.0	1635	1636	95	conclusive
Kluyvera intermedia	strain=NBRC 102594	GCA_001598315.1	61648	61648	suspected-type	True	86.1046	1186	1636	95	below_threshold
Kluyvera intermedia	strain=NCTC12125	GCA_900635475.1	61648	61648	suspected-type	True	86.0865	1219	1636	95	below_threshold
Kluyvera sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	85.8335	1230	1636	95	below_threshold
Kluyvera ascorbata	strain=ATCC 33433	GCA_000735365.1	51288	51288	suspected-type	True	85.7851	1160	1636	95	below_threshold
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	85.692	1146	1636	95	below_threshold
Pseudocitrobacter vendiensis	strain=type strain: CPO20170097	GCA_943590815.1	2488306	2488306	type	True	82.625	990	1636	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	82.5335	1021	1636	95	below_threshold
Citrobacter youngae	strain=NCTC13709	GCA_900638065.1	133448	133448	type	True	81.3842	810	1636	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.3706	903	1636	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	81.3309	925	1636	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	81.2768	838	1636	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	80.8391	721	1636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:04,195] [INFO] DFAST Taxonomy check result was written to GCF_001571285.1_ASM157128v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:04,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:04,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:04,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca905692-619d-46c2-b776-7baf49d4439d/dqc_reference/checkm_data
[2024-01-24 14:20:04,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:04,251] [INFO] Task started: CheckM
[2024-01-24 14:20:04,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001571285.1_ASM157128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001571285.1_ASM157128v1_genomic.fna/checkm_input GCF_001571285.1_ASM157128v1_genomic.fna/checkm_result
[2024-01-24 14:20:47,616] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:47,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:47,640] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:47,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:47,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001571285.1_ASM157128v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:47,641] [INFO] Task started: Blastn
[2024-01-24 14:20:47,641] [INFO] Running command: blastn -query GCF_001571285.1_ASM157128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca905692-619d-46c2-b776-7baf49d4439d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001571285.1_ASM157128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:49,048] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:49,053] [INFO] Selected 11 target genomes.
[2024-01-24 14:20:49,053] [INFO] Target genome list was writen to GCF_001571285.1_ASM157128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:49,074] [INFO] Task started: fastANI
[2024-01-24 14:20:49,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg232175b5-826f-4345-9029-3f81c07f6aeb/GCF_001571285.1_ASM157128v1_genomic.fna.gz --refList GCF_001571285.1_ASM157128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001571285.1_ASM157128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:01,339] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:01,359] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:01,359] [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_001571285.1	s__Kluyvera cryocrescens	100.0	1635	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.35	99.12	0.95	0.93	4	conclusive
GCF_001266615.1	s__Kluyvera cryocrescens_A	89.9169	1362	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635475.1	s__Kluyvera intermedia	86.0872	1221	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.24	98.87	0.94	0.90	4	-
GCF_014218705.1	s__Kluyvera sichuanensis	85.8394	1229	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363335.1	s__Kluyvera sp902363335	85.832	1144	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735365.1	s__Kluyvera ascorbata	85.7851	1161	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.94	97.70	0.94	0.89	5	-
GCF_001654985.1	s__Kluyvera georgiana	85.7096	1144	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.06	98.06	0.84	0.84	2	-
GCA_016939855.1	s__Kluyvera ascorbata_C	85.6141	673	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002211745.1	s__Kluyvera georgiana_A	85.3749	1231	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
GCF_014168815.1	s__Kluyvera ascorbata_B	85.2626	1246	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	99.36	99.08	0.90	0.88	9	-
GCA_009668205.1	s__Scandinavium sp009668205	80.9339	834	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:01,361] [INFO] GTDB search result was written to GCF_001571285.1_ASM157128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:01,362] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:01,366] [INFO] DFAST_QC result json was written to GCF_001571285.1_ASM157128v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:01,366] [INFO] DFAST_QC completed!
[2024-01-24 14:21:01,366] [INFO] Total running time: 0h1m29s