[2024-01-24 15:18:38,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ad4e9ce-8fa6-4588-95a2-e5dad123b410/dqc_reference
[2024-01-24 15:18:40,233] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,234] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,235] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0bbf5da-0dd1-4f82-bf12-471fab3c034b/GCF_900021175.1_Enterobacter_timonensis_genomic.fna.gz | prodigal -d GCF_900021175.1_Enterobacter_timonensis_genomic.fna/cds.fna -a GCF_900021175.1_Enterobacter_timonensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:51,858] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:51,858] [INFO] Task started: HMMsearch
[2024-01-24 15:18:51,859] [INFO] Running command: hmmsearch --tblout GCF_900021175.1_Enterobacter_timonensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ad4e9ce-8fa6-4588-95a2-e5dad123b410/dqc_reference/reference_markers.hmm GCF_900021175.1_Enterobacter_timonensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:52,218] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:52,221] [INFO] Found 6/6 markers.
[2024-01-24 15:18:52,302] [INFO] Query marker FASTA was written to GCF_900021175.1_Enterobacter_timonensis_genomic.fna/markers.fasta
[2024-01-24 15:18:52,303] [INFO] Task started: Blastn
[2024-01-24 15:18:52,303] [INFO] Running command: blastn -query GCF_900021175.1_Enterobacter_timonensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ad4e9ce-8fa6-4588-95a2-e5dad123b410/dqc_reference/reference_markers.fasta -out GCF_900021175.1_Enterobacter_timonensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:53,382] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:53,385] [INFO] Selected 25 target genomes.
[2024-01-24 15:18:53,385] [INFO] Target genome list was writen to GCF_900021175.1_Enterobacter_timonensis_genomic.fna/target_genomes.txt
[2024-01-24 15:18:53,391] [INFO] Task started: fastANI
[2024-01-24 15:18:53,391] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0bbf5da-0dd1-4f82-bf12-471fab3c034b/GCF_900021175.1_Enterobacter_timonensis_genomic.fna.gz --refList GCF_900021175.1_Enterobacter_timonensis_genomic.fna/target_genomes.txt --output GCF_900021175.1_Enterobacter_timonensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:20,341] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:20,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ad4e9ce-8fa6-4588-95a2-e5dad123b410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:20,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ad4e9ce-8fa6-4588-95a2-e5dad123b410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:20,360] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:20,361] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:20,361] [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
Enterobacter bugandensis	strain=FDAARGOS 1427	GCA_019046905.1	881260	881260	type	True	84.2909	1066	1394	95	below_threshold
Enterobacter bugandensis		GCA_900324475.1	881260	881260	type	True	84.2523	1063	1394	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	84.204	1067	1394	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	84.1878	1013	1394	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=DSM 16687	GCA_001729705.1	301102	158836	type	True	84.187	1069	1394	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	84.1742	1056	1394	95	below_threshold
Enterobacter hormaechei subsp. xiangfangensis	strain=LMG27195	GCA_001729785.1	1296536	158836	type	True	84.1389	1074	1394	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	84.1225	1082	1394	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	84.1128	1072	1394	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	84.0981	1083	1394	95	below_threshold
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_001875655.1	301105	158836	type	True	84.0687	1073	1394	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	84.0416	1078	1394	95	below_threshold
Enterobacter hormaechei subsp. steigerwaltii	strain=DSM 16691	GCA_001729725.1	299766	158836	type	True	84.0183	1089	1394	95	below_threshold
Enterobacter hormaechei subsp. hormaechei	strain=ATCC 49162	GCA_000213995.1	301105	158836	type	True	83.9354	1067	1394	95	below_threshold
Enterobacter vonholyi	strain=E13	GCA_008364555.1	2797505	2797505	type	True	83.911	1026	1394	95	below_threshold
Enterobacter oligotrophicus	strain=CCA6	GCA_009176645.1	2478464	2478464	type	True	83.817	1044	1394	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	83.7391	1036	1394	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	83.689	1029	1394	95	below_threshold
Enterobacter kobei	strain=DSM 13645	GCA_001729765.1	208224	208224	type	True	83.6321	1034	1394	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	83.55	1060	1394	95	below_threshold
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	81.2175	710	1394	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	81.1424	727	1394	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	81.1041	723	1394	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	80.9233	733	1394	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	80.84	732	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:20,363] [INFO] DFAST Taxonomy check result was written to GCF_900021175.1_Enterobacter_timonensis_genomic.fna/tc_result.tsv
[2024-01-24 15:19:20,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:20,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:20,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ad4e9ce-8fa6-4588-95a2-e5dad123b410/dqc_reference/checkm_data
[2024-01-24 15:19:20,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:20,413] [INFO] Task started: CheckM
[2024-01-24 15:19:20,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900021175.1_Enterobacter_timonensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900021175.1_Enterobacter_timonensis_genomic.fna/checkm_input GCF_900021175.1_Enterobacter_timonensis_genomic.fna/checkm_result
[2024-01-24 15:19:55,993] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:55,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:56,014] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:56,015] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:56,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900021175.1_Enterobacter_timonensis_genomic.fna/markers.fasta)
[2024-01-24 15:19:56,016] [INFO] Task started: Blastn
[2024-01-24 15:19:56,016] [INFO] Running command: blastn -query GCF_900021175.1_Enterobacter_timonensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ad4e9ce-8fa6-4588-95a2-e5dad123b410/dqc_reference/reference_markers_gtdb.fasta -out GCF_900021175.1_Enterobacter_timonensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:57,518] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:57,523] [INFO] Selected 21 target genomes.
[2024-01-24 15:19:57,523] [INFO] Target genome list was writen to GCF_900021175.1_Enterobacter_timonensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:57,541] [INFO] Task started: fastANI
[2024-01-24 15:19:57,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0bbf5da-0dd1-4f82-bf12-471fab3c034b/GCF_900021175.1_Enterobacter_timonensis_genomic.fna.gz --refList GCF_900021175.1_Enterobacter_timonensis_genomic.fna/target_genomes_gtdb.txt --output GCF_900021175.1_Enterobacter_timonensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:19,682] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:19,704] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:19,704] [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_900021175.1	s__Enterobacter_A timonensis	100.0	1394	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900322725.1	s__Enterobacter quasihormaechei	84.2641	1063	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_900324475.1	s__Enterobacter bugandensis	84.2479	1063	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_011754535.1	s__Enterobacter cloacae_N	84.189	1059	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_001729805.1	s__Enterobacter roggenkampii	84.1778	1067	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	-
GCF_007035645.1	s__Enterobacter asburiae_B	84.1562	1047	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_013375935.1	s__Enterobacter cloacae_O	84.1517	1088	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_003594915.1	s__Enterobacter chuandaensis	84.0806	1055	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	98.32	0.92	0.92	3	-
GCF_001875655.1	s__Enterobacter hormaechei	84.072	1072	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	98.52	0.92	0.86	32	-
GCF_004331265.1	s__Enterobacter wuhouensis	84.0444	1077	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000493015.1	s__Enterobacter sp000493015	84.033	1045	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.7595	98.68	98.68	0.92	0.92	2	-
GCF_001729745.1	s__Enterobacter hormaechei_A	84.006	1064	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	96.63	95.22	0.89	0.83	1867	-
GCF_008364555.1	s__Enterobacter vonholyi	83.9074	1027	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_002902985.1	s__Leclercia sp002902985	83.7828	1035	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.13	96.37	0.93	0.86	16	-
GCF_006874705.1	s__Leclercia adecarboxylata_C	83.7814	1048	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.71	98.25	0.93	0.90	13	-
GCF_000211415.1	s__Enterobacter mori	83.6849	1027	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.59	96.13	0.88	0.85	23	-
GCF_000321045.1	s__Phytobacter massiliensis	82.0251	881	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000759835.1	s__Citrobacter_A sedlakii	81.7419	859	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.16	99.00	0.95	0.93	10	-
GCF_003697165.2	s__Escherichia coli	81.1424	720	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	-
GCF_005843885.1	s__Escherichia sp005843885	81.0406	728	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_902498915.1	s__Escherichia ruysiae	80.9971	721	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:19,706] [INFO] GTDB search result was written to GCF_900021175.1_Enterobacter_timonensis_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:19,707] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:19,711] [INFO] DFAST_QC result json was written to GCF_900021175.1_Enterobacter_timonensis_genomic.fna/dqc_result.json
[2024-01-24 15:20:19,712] [INFO] DFAST_QC completed!
[2024-01-24 15:20:19,712] [INFO] Total running time: 0h1m41s