[2024-01-25 19:04:05,807] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:05,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:05,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg77f3abd5-2610-4b87-89ff-6cc3d4ead62b/dqc_reference
[2024-01-25 19:04:06,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:06,981] [INFO] Task started: Prodigal
[2024-01-25 19:04:06,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a2301cc-18db-4c1e-8d4e-48b392ad0e6c/GCF_001598855.1_ASM159885v1_genomic.fna.gz | prodigal -d GCF_001598855.1_ASM159885v1_genomic.fna/cds.fna -a GCF_001598855.1_ASM159885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:19,808] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:19,808] [INFO] Task started: HMMsearch
[2024-01-25 19:04:19,808] [INFO] Running command: hmmsearch --tblout GCF_001598855.1_ASM159885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77f3abd5-2610-4b87-89ff-6cc3d4ead62b/dqc_reference/reference_markers.hmm GCF_001598855.1_ASM159885v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:20,106] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:20,107] [INFO] Found 6/6 markers.
[2024-01-25 19:04:20,156] [INFO] Query marker FASTA was written to GCF_001598855.1_ASM159885v1_genomic.fna/markers.fasta
[2024-01-25 19:04:20,156] [INFO] Task started: Blastn
[2024-01-25 19:04:20,156] [INFO] Running command: blastn -query GCF_001598855.1_ASM159885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f3abd5-2610-4b87-89ff-6cc3d4ead62b/dqc_reference/reference_markers.fasta -out GCF_001598855.1_ASM159885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:21,060] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:21,063] [INFO] Selected 24 target genomes.
[2024-01-25 19:04:21,063] [INFO] Target genome list was writen to GCF_001598855.1_ASM159885v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:21,072] [INFO] Task started: fastANI
[2024-01-25 19:04:21,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a2301cc-18db-4c1e-8d4e-48b392ad0e6c/GCF_001598855.1_ASM159885v1_genomic.fna.gz --refList GCF_001598855.1_ASM159885v1_genomic.fna/target_genomes.txt --output GCF_001598855.1_ASM159885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:44,428] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:44,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77f3abd5-2610-4b87-89ff-6cc3d4ead62b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:44,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77f3abd5-2610-4b87-89ff-6cc3d4ead62b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:44,443] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:44,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:44,444] [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
Pluralibacter gergoviae	strain=NBRC 105706	GCA_001598855.1	61647	61647	type	True	100.0	1830	1836	95	conclusive
Klebsiella quasipneumoniae	strain=DSM 28211	GCA_020115515.1	1463165	1463165	type	True	82.1983	987	1836	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	82.1885	1007	1836	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030	GCA_000751755.1	1667327	1463165	type	True	82.1374	999	1836	95	below_threshold
Klebsiella quasipneumoniae	strain=FDAARGOS_1503	GCA_020099175.1	1463165	1463165	type	True	82.1045	1006	1836	95	below_threshold
Klebsiella quasipneumoniae subsp. quasipneumoniae	strain=01A030T	GCA_020525925.1	1667327	1463165	type	True	82.1023	1018	1836	95	below_threshold
Klebsiella quasipneumoniae subsp. similipneumoniae	strain=07A044T	GCA_020525685.1	1463164	1463165	type	True	82.04	966	1836	95	below_threshold
Klebsiella quasipneumoniae subsp. similipneumoniae	strain=07A044	GCA_000613225.1	1463164	1463165	type	True	82.0303	960	1836	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.9272	883	1836	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	81.8568	916	1836	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	81.8489	976	1836	95	below_threshold
Klebsiella pneumoniae	strain=ATCC 13883	GCA_000742135.1	573	573	type	True	81.8147	982	1836	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=NBRC 14940	GCA_001590945.1	72407	573	type	True	81.7784	946	1836	95	below_threshold
Klebsiella pneumoniae subsp. rhinoscleromatis	strain=ATCC 13884	GCA_000163455.1	39831	573	type	True	81.7783	940	1836	95	below_threshold
Enterobacter bugandensis	strain=FDAARGOS 1427	GCA_019046905.1	881260	881260	type	True	81.5683	905	1836	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.5487	870	1836	95	below_threshold
Enterobacter bugandensis		GCA_900324475.1	881260	881260	type	True	81.5002	890	1836	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	81.4684	901	1836	95	below_threshold
Kluyvera georgiana	strain=ATCC 51603	GCA_001654985.1	73098	73098	type	True	81.345	837	1836	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.3015	846	1836	95	below_threshold
Yokenella regensburgei	strain=ATCC 49455	GCA_000735455.1	158877	158877	type	True	81.1968	809	1836	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.0829	866	1836	95	below_threshold
Yokenella regensburgei	strain=NCTC11966	GCA_900460805.1	158877	158877	type	True	81.0286	859	1836	95	below_threshold
Pseudocitrobacter vendiensis	strain=type strain: CPO20170097	GCA_943590815.1	2488306	2488306	type	True	80.893	778	1836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:44,445] [INFO] DFAST Taxonomy check result was written to GCF_001598855.1_ASM159885v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:44,446] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:44,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:44,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77f3abd5-2610-4b87-89ff-6cc3d4ead62b/dqc_reference/checkm_data
[2024-01-25 19:04:44,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:44,499] [INFO] Task started: CheckM
[2024-01-25 19:04:44,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001598855.1_ASM159885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001598855.1_ASM159885v1_genomic.fna/checkm_input GCF_001598855.1_ASM159885v1_genomic.fna/checkm_result
[2024-01-25 19:05:23,792] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:23,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:23,810] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:23,810] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:23,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001598855.1_ASM159885v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:23,811] [INFO] Task started: Blastn
[2024-01-25 19:05:23,811] [INFO] Running command: blastn -query GCF_001598855.1_ASM159885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f3abd5-2610-4b87-89ff-6cc3d4ead62b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001598855.1_ASM159885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:25,335] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:25,338] [INFO] Selected 21 target genomes.
[2024-01-25 19:05:25,338] [INFO] Target genome list was writen to GCF_001598855.1_ASM159885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:25,355] [INFO] Task started: fastANI
[2024-01-25 19:05:25,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a2301cc-18db-4c1e-8d4e-48b392ad0e6c/GCF_001598855.1_ASM159885v1_genomic.fna.gz --refList GCF_001598855.1_ASM159885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001598855.1_ASM159885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:48,092] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:48,106] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:48,106] [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_001598855.1	s__Pluralibacter gergoviae	100.0	1830	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pluralibacter	95.0	98.81	98.03	0.90	0.85	23	conclusive
GCF_000164865.1	s__Enterobacter_B lignolyticus	82.7151	974	1836	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	82.1507	842	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	82.1307	999	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_003057745.1	s__Enterobacter sp003057745	81.8758	913	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984825.2	s__Enterobacter chengduensis	81.8757	914	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.11	95.58	0.88	0.79	24	-
GCA_014156375.1	s__Scandinavium sp014156375	81.8506	915	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000742135.1	s__Klebsiella pneumoniae	81.8185	983	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_006539725.1	s__Klebsiella terrigena	81.8052	982	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.25	96.63	0.88	0.85	68	-
GCF_000828055.2	s__Klebsiella variicola	81.7558	966	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	-
GCF_900978845.1	s__Klebsiella africana	81.5852	949	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_004331265.1	s__Enterobacter wuhouensis	81.5454	870	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900324475.1	s__Enterobacter bugandensis	81.4855	891	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_001729805.1	s__Enterobacter roggenkampii	81.4046	901	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	-
GCF_000463155.2	s__Siccibacter turicensis	81.291	798	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	98.74	97.87	0.95	0.92	6	-
GCF_000215745.1	s__Klebsiella aerogenes	81.2215	925	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.40	95.78	0.92	0.85	341	-
GCF_000735455.1	s__Yokenella regensburgei	81.1941	809	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yokenella	95.0	99.37	98.92	0.95	0.91	10	-
GCF_000759815.1	s__Citrobacter_A rodentium	81.1907	848	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.98	99.96	0.98	0.96	4	-
GCF_000321045.1	s__Phytobacter massiliensis	81.121	834	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002939185.1	s__Enterobacter sichuanensis	81.1017	876	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCA_002211745.1	s__Kluyvera georgiana_A	80.9793	872	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:48,112] [INFO] GTDB search result was written to GCF_001598855.1_ASM159885v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:48,114] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:48,120] [INFO] DFAST_QC result json was written to GCF_001598855.1_ASM159885v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:48,120] [INFO] DFAST_QC completed!
[2024-01-25 19:05:48,120] [INFO] Total running time: 0h1m42s