[2024-01-24 12:30:51,911] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:51,914] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:51,914] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a3ccbd1-0dcc-4c73-8b05-5a82f6fccf70/dqc_reference
[2024-01-24 12:30:53,231] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,231] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,232] [INFO] Running command: gunzip -c /var/lib/cwl/stge7537a2c-f2a4-4c24-806e-bff457c93e50/GCF_020115535.1_ASM2011553v1_genomic.fna.gz | prodigal -d GCF_020115535.1_ASM2011553v1_genomic.fna/cds.fna -a GCF_020115535.1_ASM2011553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:07,592] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:07,592] [INFO] Task started: HMMsearch
[2024-01-24 12:31:07,592] [INFO] Running command: hmmsearch --tblout GCF_020115535.1_ASM2011553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a3ccbd1-0dcc-4c73-8b05-5a82f6fccf70/dqc_reference/reference_markers.hmm GCF_020115535.1_ASM2011553v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:07,919] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:07,920] [INFO] Found 6/6 markers.
[2024-01-24 12:31:07,975] [INFO] Query marker FASTA was written to GCF_020115535.1_ASM2011553v1_genomic.fna/markers.fasta
[2024-01-24 12:31:07,976] [INFO] Task started: Blastn
[2024-01-24 12:31:07,976] [INFO] Running command: blastn -query GCF_020115535.1_ASM2011553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a3ccbd1-0dcc-4c73-8b05-5a82f6fccf70/dqc_reference/reference_markers.fasta -out GCF_020115535.1_ASM2011553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:08,826] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:08,829] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:08,830] [INFO] Target genome list was writen to GCF_020115535.1_ASM2011553v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:08,836] [INFO] Task started: fastANI
[2024-01-24 12:31:08,836] [INFO] Running command: fastANI --query /var/lib/cwl/stge7537a2c-f2a4-4c24-806e-bff457c93e50/GCF_020115535.1_ASM2011553v1_genomic.fna.gz --refList GCF_020115535.1_ASM2011553v1_genomic.fna/target_genomes.txt --output GCF_020115535.1_ASM2011553v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:25,004] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:25,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a3ccbd1-0dcc-4c73-8b05-5a82f6fccf70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:25,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a3ccbd1-0dcc-4c73-8b05-5a82f6fccf70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:25,027] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:31:25,027] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:25,028] [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=DSM 5175	GCA_020115535.1	571	571	type	True	100.0	1896	1898	95	conclusive
Klebsiella oxytoca	strain=NCTC13727	GCA_900636985.1	571	571	type	True	99.9993	1898	1898	95	conclusive
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	99.9948	1885	1898	95	conclusive
Klebsiella michiganensis	strain=CCUG 66515	GCA_009173485.1	1134687	1134687	type	True	92.4762	1620	1898	95	below_threshold
Klebsiella michiganensis	strain=DSM 25444	GCA_002925905.1	1134687	1134687	type	True	92.4286	1629	1898	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	91.6725	1602	1898	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	83.9275	1295	1898	95	below_threshold
Klebsiella africana	strain=SB5857	GCA_900978845.1	2489010	2489010	type	True	83.7882	1270	1898	95	below_threshold
Klebsiella africana	strain=200023	GCA_020526085.1	2489010	2489010	type	True	83.7554	1269	1898	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.6671	917	1898	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.53	883	1898	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.318	884	1898	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.3027	873	1898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:25,030] [INFO] DFAST Taxonomy check result was written to GCF_020115535.1_ASM2011553v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:25,030] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:25,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:25,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a3ccbd1-0dcc-4c73-8b05-5a82f6fccf70/dqc_reference/checkm_data
[2024-01-24 12:31:25,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:25,084] [INFO] Task started: CheckM
[2024-01-24 12:31:25,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020115535.1_ASM2011553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020115535.1_ASM2011553v1_genomic.fna/checkm_input GCF_020115535.1_ASM2011553v1_genomic.fna/checkm_result
[2024-01-24 12:32:09,499] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:09,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:09,528] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:09,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:09,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020115535.1_ASM2011553v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:09,529] [INFO] Task started: Blastn
[2024-01-24 12:32:09,529] [INFO] Running command: blastn -query GCF_020115535.1_ASM2011553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a3ccbd1-0dcc-4c73-8b05-5a82f6fccf70/dqc_reference/reference_markers_gtdb.fasta -out GCF_020115535.1_ASM2011553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:10,585] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:10,589] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:10,589] [INFO] Target genome list was writen to GCF_020115535.1_ASM2011553v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:10,596] [INFO] Task started: fastANI
[2024-01-24 12:32:10,597] [INFO] Running command: fastANI --query /var/lib/cwl/stge7537a2c-f2a4-4c24-806e-bff457c93e50/GCF_020115535.1_ASM2011553v1_genomic.fna.gz --refList GCF_020115535.1_ASM2011553v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020115535.1_ASM2011553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:23,516] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:23,525] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:23,526] [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	99.9948	1885	1898	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	92.4397	1628	1898	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	91.6925	1600	1898	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	89.8191	1533	1898	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	88.817	1523	1898	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	87.7259	1541	1898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	96.95	95.21	0.89	0.84	9	-
GCF_002042885.1	s__Citrobacter portucalensis	81.2342	823	1898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.01	95.95	0.89	0.83	128	-
GCF_005843885.1	s__Escherichia sp005843885	80.644	754	1898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCA_901456055.1	s__Phytobacter ursingii	80.5478	812	1898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	97.10	96.01	0.86	0.80	7	-
GCF_900111105.1	s__Rosenbergiella nectarea	78.7066	102	1898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.23	96.23	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:23,528] [INFO] GTDB search result was written to GCF_020115535.1_ASM2011553v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:23,529] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:23,533] [INFO] DFAST_QC result json was written to GCF_020115535.1_ASM2011553v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:23,534] [INFO] DFAST_QC completed!
[2024-01-24 12:32:23,534] [INFO] Total running time: 0h1m32s