[2024-01-25 17:42:20,497] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:20,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:20,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a3e7809-70b5-47f2-b545-8f91b3abe72a/dqc_reference
[2024-01-25 17:42:21,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:21,650] [INFO] Task started: Prodigal
[2024-01-25 17:42:21,651] [INFO] Running command: gunzip -c /var/lib/cwl/stge98db8c7-8092-4a02-a1f0-40cbe734b768/GCF_009173485.1_ASM917348v1_genomic.fna.gz | prodigal -d GCF_009173485.1_ASM917348v1_genomic.fna/cds.fna -a GCF_009173485.1_ASM917348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:35,166] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:35,166] [INFO] Task started: HMMsearch
[2024-01-25 17:42:35,166] [INFO] Running command: hmmsearch --tblout GCF_009173485.1_ASM917348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a3e7809-70b5-47f2-b545-8f91b3abe72a/dqc_reference/reference_markers.hmm GCF_009173485.1_ASM917348v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:35,455] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:35,456] [INFO] Found 6/6 markers.
[2024-01-25 17:42:35,505] [INFO] Query marker FASTA was written to GCF_009173485.1_ASM917348v1_genomic.fna/markers.fasta
[2024-01-25 17:42:35,506] [INFO] Task started: Blastn
[2024-01-25 17:42:35,506] [INFO] Running command: blastn -query GCF_009173485.1_ASM917348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a3e7809-70b5-47f2-b545-8f91b3abe72a/dqc_reference/reference_markers.fasta -out GCF_009173485.1_ASM917348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:36,379] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:36,382] [INFO] Selected 12 target genomes.
[2024-01-25 17:42:36,382] [INFO] Target genome list was writen to GCF_009173485.1_ASM917348v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:36,387] [INFO] Task started: fastANI
[2024-01-25 17:42:36,387] [INFO] Running command: fastANI --query /var/lib/cwl/stge98db8c7-8092-4a02-a1f0-40cbe734b768/GCF_009173485.1_ASM917348v1_genomic.fna.gz --refList GCF_009173485.1_ASM917348v1_genomic.fna/target_genomes.txt --output GCF_009173485.1_ASM917348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:52,381] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:52,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a3e7809-70b5-47f2-b545-8f91b3abe72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:52,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a3e7809-70b5-47f2-b545-8f91b3abe72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:52,390] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:42:52,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:52,391] [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
Klebsiella michiganensis	strain=CCUG 66515	GCA_009173485.1	1134687	1134687	type	True	100.0	1983	1988	95	conclusive
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	99.9865	1976	1988	95	conclusive
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	94.0238	1729	1988	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	93.8614	1704	1988	95	below_threshold
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	92.5332	1603	1988	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	92.4726	1625	1988	95	below_threshold
Klebsiella oxytoca	strain=NCTC13727	GCA_900636985.1	571	571	type	True	92.4636	1628	1988	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	84.4425	1320	1988	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.1822	963	1988	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.9159	955	1988	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.8749	975	1988	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.6339	961	1988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:52,392] [INFO] DFAST Taxonomy check result was written to GCF_009173485.1_ASM917348v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:52,394] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:52,394] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:52,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a3e7809-70b5-47f2-b545-8f91b3abe72a/dqc_reference/checkm_data
[2024-01-25 17:42:52,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:52,457] [INFO] Task started: CheckM
[2024-01-25 17:42:52,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009173485.1_ASM917348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009173485.1_ASM917348v1_genomic.fna/checkm_input GCF_009173485.1_ASM917348v1_genomic.fna/checkm_result
[2024-01-25 17:43:32,693] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:32,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:32,714] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:32,714] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:32,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009173485.1_ASM917348v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:32,715] [INFO] Task started: Blastn
[2024-01-25 17:43:32,715] [INFO] Running command: blastn -query GCF_009173485.1_ASM917348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a3e7809-70b5-47f2-b545-8f91b3abe72a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009173485.1_ASM917348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:34,161] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:34,164] [INFO] Selected 7 target genomes.
[2024-01-25 17:43:34,164] [INFO] Target genome list was writen to GCF_009173485.1_ASM917348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:34,176] [INFO] Task started: fastANI
[2024-01-25 17:43:34,177] [INFO] Running command: fastANI --query /var/lib/cwl/stge98db8c7-8092-4a02-a1f0-40cbe734b768/GCF_009173485.1_ASM917348v1_genomic.fna.gz --refList GCF_009173485.1_ASM917348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009173485.1_ASM917348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:45,298] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:45,304] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:45,304] [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_002925905.1	s__Klebsiella michiganensis	99.9865	1976	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.53	97.41	0.90	0.83	291	conclusive
GCF_900200035.1	s__Klebsiella grimontii	93.8614	1704	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.56	95.68	0.89	0.83	175	-
GCF_001598695.1	s__Klebsiella oxytoca	92.4726	1625	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCF_009707385.1	s__Klebsiella oxytoca_C	90.233	1510	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902158555.1	s__Klebsiella spallanzanii	89.3423	1519	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.75	98.01	0.91	0.88	4	-
GCF_003261575.2	s__Klebsiella huaxiensis	88.1559	1548	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	96.95	95.21	0.89	0.84	9	-
GCF_005860775.1	s__Klebsiella indica	86.4393	1296	1988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.34	99.34	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:45,306] [INFO] GTDB search result was written to GCF_009173485.1_ASM917348v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:45,306] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:45,308] [INFO] DFAST_QC result json was written to GCF_009173485.1_ASM917348v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:45,309] [INFO] DFAST_QC completed!
[2024-01-25 17:43:45,309] [INFO] Total running time: 0h1m25s