[2023-06-18 17:51:29,009] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:51:29,011] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:51:29,011] [INFO] DQC Reference Directory: /var/lib/cwl/stg706c72c5-dd1a-4615-9245-ab83bfcf4023/dqc_reference
[2023-06-18 17:51:30,262] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:51:30,263] [INFO] Task started: Prodigal
[2023-06-18 17:51:30,263] [INFO] Running command: gunzip -c /var/lib/cwl/stg74c4b1ab-c4c3-4537-bd38-3ec52649e85a/GCA_018376935.1_ASM1837693v1_genomic.fna.gz | prodigal -d GCA_018376935.1_ASM1837693v1_genomic.fna/cds.fna -a GCA_018376935.1_ASM1837693v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:51:44,952] [INFO] Task succeeded: Prodigal
[2023-06-18 17:51:44,953] [INFO] Task started: HMMsearch
[2023-06-18 17:51:44,953] [INFO] Running command: hmmsearch --tblout GCA_018376935.1_ASM1837693v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg706c72c5-dd1a-4615-9245-ab83bfcf4023/dqc_reference/reference_markers.hmm GCA_018376935.1_ASM1837693v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:51:45,279] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:51:45,280] [INFO] Found 6/6 markers.
[2023-06-18 17:51:45,342] [INFO] Query marker FASTA was written to GCA_018376935.1_ASM1837693v1_genomic.fna/markers.fasta
[2023-06-18 17:51:45,342] [INFO] Task started: Blastn
[2023-06-18 17:51:45,342] [INFO] Running command: blastn -query GCA_018376935.1_ASM1837693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg706c72c5-dd1a-4615-9245-ab83bfcf4023/dqc_reference/reference_markers.fasta -out GCA_018376935.1_ASM1837693v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:51:46,258] [INFO] Task succeeded: Blastn
[2023-06-18 17:51:46,263] [INFO] Selected 12 target genomes.
[2023-06-18 17:51:46,264] [INFO] Target genome list was writen to GCA_018376935.1_ASM1837693v1_genomic.fna/target_genomes.txt
[2023-06-18 17:51:46,268] [INFO] Task started: fastANI
[2023-06-18 17:51:46,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg74c4b1ab-c4c3-4537-bd38-3ec52649e85a/GCA_018376935.1_ASM1837693v1_genomic.fna.gz --refList GCA_018376935.1_ASM1837693v1_genomic.fna/target_genomes.txt --output GCA_018376935.1_ASM1837693v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:52:01,654] [INFO] Task succeeded: fastANI
[2023-06-18 17:52:01,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg706c72c5-dd1a-4615-9245-ab83bfcf4023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:52:01,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg706c72c5-dd1a-4615-9245-ab83bfcf4023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:52:01,672] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2023-06-18 17:52:01,672] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 17:52:01,672] [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 oxytoca	strain=NCTC13727	GCA_900636985.1	571	571	type	True	99.5028	1847	1929	95	conclusive
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	99.5021	1838	1929	95	conclusive
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	99.4828	1822	1929	95	conclusive
Klebsiella michiganensis	strain=CCUG 66515	GCA_009173485.1	1134687	1134687	type	True	92.3619	1594	1929	95	below_threshold
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	92.3262	1595	1929	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	91.5889	1603	1929	95	below_threshold
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	91.2311	1636	1929	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	83.7323	1286	1929	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.3252	953	1929	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.3048	907	1929	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.3032	869	1929	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.1019	866	1929	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:52:01,674] [INFO] DFAST Taxonomy check result was written to GCA_018376935.1_ASM1837693v1_genomic.fna/tc_result.tsv
[2023-06-18 17:52:01,675] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:52:01,675] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:52:01,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg706c72c5-dd1a-4615-9245-ab83bfcf4023/dqc_reference/checkm_data
[2023-06-18 17:52:01,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:52:01,746] [INFO] Task started: CheckM
[2023-06-18 17:52:01,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376935.1_ASM1837693v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376935.1_ASM1837693v1_genomic.fna/checkm_input GCA_018376935.1_ASM1837693v1_genomic.fna/checkm_result
[2023-06-18 17:52:47,056] [INFO] Task succeeded: CheckM
[2023-06-18 17:52:47,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.43%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 17:52:47,111] [INFO] ===== Completeness check finished =====
[2023-06-18 17:52:47,111] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:52:47,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376935.1_ASM1837693v1_genomic.fna/markers.fasta)
[2023-06-18 17:52:47,112] [INFO] Task started: Blastn
[2023-06-18 17:52:47,112] [INFO] Running command: blastn -query GCA_018376935.1_ASM1837693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg706c72c5-dd1a-4615-9245-ab83bfcf4023/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376935.1_ASM1837693v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:52:48,398] [INFO] Task succeeded: Blastn
[2023-06-18 17:52:48,421] [INFO] Selected 6 target genomes.
[2023-06-18 17:52:48,421] [INFO] Target genome list was writen to GCA_018376935.1_ASM1837693v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:52:48,427] [INFO] Task started: fastANI
[2023-06-18 17:52:48,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg74c4b1ab-c4c3-4537-bd38-3ec52649e85a/GCA_018376935.1_ASM1837693v1_genomic.fna.gz --refList GCA_018376935.1_ASM1837693v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376935.1_ASM1837693v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:52:57,458] [INFO] Task succeeded: fastANI
[2023-06-18 17:52:57,469] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:52:57,469] [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_001598695.1	s__Klebsiella oxytoca	99.5021	1838	1929	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	conclusive
GCF_002925905.1	s__Klebsiella michiganensis	92.3371	1594	1929	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.53	97.41	0.90	0.83	291	-
GCF_900200035.1	s__Klebsiella grimontii	91.5931	1602	1929	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.56	95.68	0.89	0.83	175	-
GCF_009707385.1	s__Klebsiella oxytoca_C	89.7666	1510	1929	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	88.6587	1534	1929	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	87.6509	1545	1929	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	96.95	95.21	0.89	0.84	9	-
--------------------------------------------------------------------------------
[2023-06-18 17:52:57,472] [INFO] GTDB search result was written to GCA_018376935.1_ASM1837693v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:52:57,473] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:52:57,478] [INFO] DFAST_QC result json was written to GCA_018376935.1_ASM1837693v1_genomic.fna/dqc_result.json
[2023-06-18 17:52:57,478] [INFO] DFAST_QC completed!
[2023-06-18 17:52:57,478] [INFO] Total running time: 0h1m28s