[2024-01-24 12:40:07,999] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:08,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:08,001] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2ffa3d1-d310-418b-9135-7ef735610805/dqc_reference
[2024-01-24 12:40:09,286] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,287] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,287] [INFO] Running command: gunzip -c /var/lib/cwl/stgb730b99b-6c96-4ff1-9d2d-db33b7c24e4f/GCF_000735455.1_GYRE_DRAFTv1_genomic.fna.gz | prodigal -d GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/cds.fna -a GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:22,859] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:22,859] [INFO] Task started: HMMsearch
[2024-01-24 12:40:22,859] [INFO] Running command: hmmsearch --tblout GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2ffa3d1-d310-418b-9135-7ef735610805/dqc_reference/reference_markers.hmm GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:23,187] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:23,188] [INFO] Found 6/6 markers.
[2024-01-24 12:40:23,237] [INFO] Query marker FASTA was written to GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/markers.fasta
[2024-01-24 12:40:23,237] [INFO] Task started: Blastn
[2024-01-24 12:40:23,237] [INFO] Running command: blastn -query GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2ffa3d1-d310-418b-9135-7ef735610805/dqc_reference/reference_markers.fasta -out GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:24,216] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:24,220] [INFO] Selected 20 target genomes.
[2024-01-24 12:40:24,221] [INFO] Target genome list was writen to GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:24,226] [INFO] Task started: fastANI
[2024-01-24 12:40:24,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgb730b99b-6c96-4ff1-9d2d-db33b7c24e4f/GCF_000735455.1_GYRE_DRAFTv1_genomic.fna.gz --refList GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/target_genomes.txt --output GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:45,813] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:45,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2ffa3d1-d310-418b-9135-7ef735610805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:45,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2ffa3d1-d310-418b-9135-7ef735610805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:45,835] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:45,836] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:45,836] [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
Yokenella regensburgei	strain=ATCC 49455	GCA_000735455.1	158877	158877	type	True	100.0	1576	1584	95	conclusive
Yokenella regensburgei	strain=NCTC11966	GCA_900460805.1	158877	158877	type	True	99.9968	1584	1584	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.1315	918	1584	95	below_threshold
Enterobacter hormaechei subsp. steigerwaltii	strain=DSM 16691	GCA_001729725.1	299766	158836	type	True	81.9415	881	1584	95	below_threshold
Kluyvera ascorbata	strain=ATCC 33433	GCA_000735365.1	51288	51288	suspected-type	True	81.9299	849	1584	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.9269	884	1584	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	81.9243	878	1584	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	81.9099	931	1584	95	below_threshold
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_001875655.1	301105	158836	type	True	81.9095	862	1584	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.8608	888	1584	95	below_threshold
Enterobacter oligotrophicus	strain=CCA6	GCA_009176645.1	2478464	2478464	type	True	81.8562	870	1584	95	below_threshold
Kluyvera sichuanensis	strain=090646	GCA_014218705.1	2725494	2725494	type	True	81.8281	915	1584	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.8113	920	1584	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	81.7131	906	1584	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.6715	909	1584	95	below_threshold
Klebsiella oxytoca	strain=NCTC13727	GCA_900636985.1	571	571	type	True	81.2835	890	1584	95	below_threshold
Klebsiella oxytoca	strain=NBRC 105695	GCA_001598695.1	571	571	type	True	81.2434	870	1584	95	below_threshold
Klebsiella oxytoca	strain=DSM 5175	GCA_020115535.1	571	571	type	True	81.1402	879	1584	95	below_threshold
Pluralibacter gergoviae	strain=NBRC 105706	GCA_001598855.1	61647	61647	type	True	80.9893	842	1584	95	below_threshold
Salmonella enterica subsp. enterica	strain=LT2	GCA_002289225.1	59201	28901	type	True	80.7687	721	1584	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:45,838] [INFO] DFAST Taxonomy check result was written to GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:45,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:45,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:45,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2ffa3d1-d310-418b-9135-7ef735610805/dqc_reference/checkm_data
[2024-01-24 12:40:45,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:45,889] [INFO] Task started: CheckM
[2024-01-24 12:40:45,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/checkm_input GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/checkm_result
[2024-01-24 12:41:26,951] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:26,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.98%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:26,979] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:26,979] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:26,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/markers.fasta)
[2024-01-24 12:41:26,980] [INFO] Task started: Blastn
[2024-01-24 12:41:26,980] [INFO] Running command: blastn -query GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2ffa3d1-d310-418b-9135-7ef735610805/dqc_reference/reference_markers_gtdb.fasta -out GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:28,471] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:28,475] [INFO] Selected 20 target genomes.
[2024-01-24 12:41:28,476] [INFO] Target genome list was writen to GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:28,492] [INFO] Task started: fastANI
[2024-01-24 12:41:28,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgb730b99b-6c96-4ff1-9d2d-db33b7c24e4f/GCF_000735455.1_GYRE_DRAFTv1_genomic.fna.gz --refList GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/target_genomes_gtdb.txt --output GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:49,102] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:49,124] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:49,124] [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_000735455.1	s__Yokenella regensburgei	100.0	1576	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yokenella	95.0	99.37	98.92	0.95	0.91	10	conclusive
GCF_001188485.1	s__Trabulsiella odontotermitis_A	83.1201	986	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Trabulsiella	95.0	98.66	98.66	0.88	0.88	2	-
GCF_001297775.1	s__Trabulsiella odontotermitis	83.0656	1003	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Trabulsiella	95.0	99.98	99.97	0.99	0.99	5	-
GCF_000734965.1	s__Trabulsiella guamensis	82.6287	948	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Trabulsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	82.4452	1038	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	98.80	98.80	0.94	0.94	2	-
GCA_019237635.1	s__Enterobacter_B sp019237635	82.2131	912	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014156375.1	s__Scandinavium sp014156375	82.0147	977	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594915.1	s__Enterobacter chuandaensis	81.9613	912	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	98.32	0.92	0.92	3	-
GCF_009755685.1	s__Enterobacter sp000568095	81.9341	926	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_000735365.1	s__Kluyvera ascorbata	81.927	850	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.94	97.70	0.94	0.89	5	-
GCF_013375935.1	s__Enterobacter cloacae_O	81.9176	911	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCA_016939855.1	s__Kluyvera ascorbata_C	81.8701	499	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218705.1	s__Kluyvera sichuanensis	81.8411	913	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176645.1	s__Enterobacter oligotrophicus	81.8361	873	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.55	99.09	0.97	0.94	3	-
GCF_900322725.1	s__Enterobacter quasihormaechei	81.836	892	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_011754535.1	s__Enterobacter cloacae_N	81.8266	929	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCA_002470465.1	s__Scandinavium sp002470465	81.7445	891	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001729765.1	s__Enterobacter kobei	81.7141	881	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_000215745.1	s__Klebsiella aerogenes	81.6453	897	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.40	95.78	0.92	0.85	341	-
GCA_009668205.1	s__Scandinavium sp009668205	81.6257	899	1584	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 12:41:49,126] [INFO] GTDB search result was written to GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:49,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:49,131] [INFO] DFAST_QC result json was written to GCF_000735455.1_GYRE_DRAFTv1_genomic.fna/dqc_result.json
[2024-01-24 12:41:49,131] [INFO] DFAST_QC completed!
[2024-01-24 12:41:49,131] [INFO] Total running time: 0h1m41s