[2023-06-04 22:24:16,473] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:24:16,475] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:24:16,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a599e01-62e1-4709-8dcc-64e9f4b2f42b/dqc_reference
[2023-06-04 22:24:17,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:24:17,646] [INFO] Task started: Prodigal
[2023-06-04 22:24:17,646] [INFO] Running command: gunzip -c /var/lib/cwl/stgc277b69d-95b5-4255-af54-5a6b05bf9173/GCA_934270975.1_ERR7745903_bin.38_genomic.fna.gz | prodigal -d GCA_934270975.1_ERR7745903_bin.38_genomic.fna/cds.fna -a GCA_934270975.1_ERR7745903_bin.38_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:24:26,682] [INFO] Task succeeded: Prodigal
[2023-06-04 22:24:26,682] [INFO] Task started: HMMsearch
[2023-06-04 22:24:26,682] [INFO] Running command: hmmsearch --tblout GCA_934270975.1_ERR7745903_bin.38_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a599e01-62e1-4709-8dcc-64e9f4b2f42b/dqc_reference/reference_markers.hmm GCA_934270975.1_ERR7745903_bin.38_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:24:26,881] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:24:26,882] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc277b69d-95b5-4255-af54-5a6b05bf9173/GCA_934270975.1_ERR7745903_bin.38_genomic.fna.gz]
[2023-06-04 22:24:26,915] [INFO] Query marker FASTA was written to GCA_934270975.1_ERR7745903_bin.38_genomic.fna/markers.fasta
[2023-06-04 22:24:26,915] [INFO] Task started: Blastn
[2023-06-04 22:24:26,916] [INFO] Running command: blastn -query GCA_934270975.1_ERR7745903_bin.38_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a599e01-62e1-4709-8dcc-64e9f4b2f42b/dqc_reference/reference_markers.fasta -out GCA_934270975.1_ERR7745903_bin.38_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:24:27,637] [INFO] Task succeeded: Blastn
[2023-06-04 22:24:27,642] [INFO] Selected 13 target genomes.
[2023-06-04 22:24:27,642] [INFO] Target genome list was writen to GCA_934270975.1_ERR7745903_bin.38_genomic.fna/target_genomes.txt
[2023-06-04 22:24:27,697] [INFO] Task started: fastANI
[2023-06-04 22:24:27,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgc277b69d-95b5-4255-af54-5a6b05bf9173/GCA_934270975.1_ERR7745903_bin.38_genomic.fna.gz --refList GCA_934270975.1_ERR7745903_bin.38_genomic.fna/target_genomes.txt --output GCA_934270975.1_ERR7745903_bin.38_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:24:40,275] [INFO] Task succeeded: fastANI
[2023-06-04 22:24:40,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a599e01-62e1-4709-8dcc-64e9f4b2f42b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:24:40,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a599e01-62e1-4709-8dcc-64e9f4b2f42b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:24:40,286] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2023-06-04 22:24:40,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-04 22:24:40,287] [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 aerogenes	strain=KCTC 2190	GCA_000215745.1	548	548	type	True	98.6126	1079	1133	95	conclusive
Klebsiella aerogenes	strain=FDAARGOS 1442	GCA_019048125.1	548	548	type	True	98.6086	1077	1133	95	conclusive
Klebsiella variicola	strain=type strain: F2R9	GCA_900978195.1	244366	244366	type	True	84.9603	826	1133	95	below_threshold
Klebsiella variicola	strain=F2R9	GCA_017638945.1	244366	244366	type	True	84.8875	841	1133	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	84.8588	834	1133	95	below_threshold
Klebsiella variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	84.8267	847	1133	95	below_threshold
Klebsiella grimontii	strain=06D021	GCA_900200035.1	2058152	2058152	type	True	83.2647	809	1133	95	below_threshold
Klebsiella pasteurii		GCA_902158725.1	2587529	2587529	type	True	83.2254	821	1133	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	83.1504	810	1133	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.5492	595	1133	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	80.5046	589	1133	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	80.3138	589	1133	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.1988	592	1133	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 22:24:40,289] [INFO] DFAST Taxonomy check result was written to GCA_934270975.1_ERR7745903_bin.38_genomic.fna/tc_result.tsv
[2023-06-04 22:24:40,289] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:24:40,289] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:24:40,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a599e01-62e1-4709-8dcc-64e9f4b2f42b/dqc_reference/checkm_data
[2023-06-04 22:24:40,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:24:40,331] [INFO] Task started: CheckM
[2023-06-04 22:24:40,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934270975.1_ERR7745903_bin.38_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934270975.1_ERR7745903_bin.38_genomic.fna/checkm_input GCA_934270975.1_ERR7745903_bin.38_genomic.fna/checkm_result
[2023-06-04 22:25:11,044] [INFO] Task succeeded: CheckM
[2023-06-04 22:25:11,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:25:11,063] [INFO] ===== Completeness check finished =====
[2023-06-04 22:25:11,064] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:25:11,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934270975.1_ERR7745903_bin.38_genomic.fna/markers.fasta)
[2023-06-04 22:25:11,064] [INFO] Task started: Blastn
[2023-06-04 22:25:11,064] [INFO] Running command: blastn -query GCA_934270975.1_ERR7745903_bin.38_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a599e01-62e1-4709-8dcc-64e9f4b2f42b/dqc_reference/reference_markers_gtdb.fasta -out GCA_934270975.1_ERR7745903_bin.38_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:25:12,153] [INFO] Task succeeded: Blastn
[2023-06-04 22:25:12,157] [INFO] Selected 12 target genomes.
[2023-06-04 22:25:12,157] [INFO] Target genome list was writen to GCA_934270975.1_ERR7745903_bin.38_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:25:12,418] [INFO] Task started: fastANI
[2023-06-04 22:25:12,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgc277b69d-95b5-4255-af54-5a6b05bf9173/GCA_934270975.1_ERR7745903_bin.38_genomic.fna.gz --refList GCA_934270975.1_ERR7745903_bin.38_genomic.fna/target_genomes_gtdb.txt --output GCA_934270975.1_ERR7745903_bin.38_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:25:25,136] [INFO] Task succeeded: fastANI
[2023-06-04 22:25:25,147] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:25:25,147] [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_000215745.1	s__Klebsiella aerogenes	98.6126	1079	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.40	95.78	0.92	0.85	341	conclusive
GCF_000828055.2	s__Klebsiella variicola	84.8512	845	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_000742135.1	s__Klebsiella pneumoniae	84.8028	840	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_900978845.1	s__Klebsiella africana	84.5878	820	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	84.584	837	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_900200035.1	s__Klebsiella grimontii	83.2641	810	1133	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	83.161	809	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.31	98.97	0.94	0.89	181	-
GCF_902158555.1	s__Klebsiella spallanzanii	82.7726	784	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.75	98.01	0.91	0.88	4	-
GCF_014298075.1	s__Klebsiella sp003752615	82.6868	790	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	99.02	98.38	0.93	0.91	5	-
GCF_000735435.1	s__Klebsiella planticola	82.6758	814	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.7194	99.21	98.49	0.93	0.89	44	-
GCF_009707385.1	s__Klebsiella oxytoca_C	82.662	794	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759445.1	s__Klebsiella sp900759445	82.4067	481	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 22:25:25,149] [INFO] GTDB search result was written to GCA_934270975.1_ERR7745903_bin.38_genomic.fna/result_gtdb.tsv
[2023-06-04 22:25:25,150] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:25:25,153] [INFO] DFAST_QC result json was written to GCA_934270975.1_ERR7745903_bin.38_genomic.fna/dqc_result.json
[2023-06-04 22:25:25,154] [INFO] DFAST_QC completed!
[2023-06-04 22:25:25,154] [INFO] Total running time: 0h1m9s