[2024-01-24 12:13:27,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:27,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:27,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bc5e2ed-0079-463c-866a-7c4b0f98de8e/dqc_reference
[2024-01-24 12:13:29,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:29,375] [INFO] Task started: Prodigal
[2024-01-24 12:13:29,375] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2607220-e56d-4e53-9627-107b637f2bb6/GCF_000025565.1_ASM2556v1_genomic.fna.gz | prodigal -d GCF_000025565.1_ASM2556v1_genomic.fna/cds.fna -a GCF_000025565.1_ASM2556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:45,090] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:45,091] [INFO] Task started: HMMsearch
[2024-01-24 12:13:45,091] [INFO] Running command: hmmsearch --tblout GCF_000025565.1_ASM2556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bc5e2ed-0079-463c-866a-7c4b0f98de8e/dqc_reference/reference_markers.hmm GCF_000025565.1_ASM2556v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:45,522] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:45,524] [INFO] Found 6/6 markers.
[2024-01-24 12:13:45,575] [INFO] Query marker FASTA was written to GCF_000025565.1_ASM2556v1_genomic.fna/markers.fasta
[2024-01-24 12:13:45,575] [INFO] Task started: Blastn
[2024-01-24 12:13:45,576] [INFO] Running command: blastn -query GCF_000025565.1_ASM2556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bc5e2ed-0079-463c-866a-7c4b0f98de8e/dqc_reference/reference_markers.fasta -out GCF_000025565.1_ASM2556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:46,499] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:46,502] [INFO] Selected 22 target genomes.
[2024-01-24 12:13:46,503] [INFO] Target genome list was writen to GCF_000025565.1_ASM2556v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:46,511] [INFO] Task started: fastANI
[2024-01-24 12:13:46,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2607220-e56d-4e53-9627-107b637f2bb6/GCF_000025565.1_ASM2556v1_genomic.fna.gz --refList GCF_000025565.1_ASM2556v1_genomic.fna/target_genomes.txt --output GCF_000025565.1_ASM2556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:11,425] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:11,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bc5e2ed-0079-463c-866a-7c4b0f98de8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:11,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bc5e2ed-0079-463c-866a-7c4b0f98de8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:11,440] [INFO] Found 18 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:14:11,440] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:11,441] [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 cloacae subsp. cloacae	strain=ATCC 13047	GCA_000025565.1	336306	550	type	True	100.0	1862	1865	95	conclusive
Enterobacter cloacae	strain=FDAARGOS 1431	GCA_019047105.1	550	550	type	True	99.9915	1859	1865	95	conclusive
Enterobacter cloacae	strain=DSM 30054	GCA_013376815.1	550	550	type	True	99.9908	1859	1865	95	conclusive
Enterobacter cloacae	strain=ATCC 13047	GCA_000755525.1	550	550	type	True	99.9618	1842	1865	95	conclusive
Enterobacter cloacae	strain=ATCC 13047	GCA_001997105.1	550	550	type	True	99.941	1743	1865	95	conclusive
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	99.6177	1615	1865	95	conclusive
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	89.2488	1364	1865	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	89.1827	1291	1865	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	87.827	1298	1865	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	87.6697	1327	1865	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	84.0962	1083	1865	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	84.0826	1075	1865	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	79.6145	50	1865	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	79.0617	553	1865	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	78.8669	535	1865	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	78.7898	515	1865	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	78.7443	476	1865	95	below_threshold
Edwardsiella piscicida	strain=ACC35.1	GCA_001896205.1	1263550	1263550	reftype	True	78.1708	341	1865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:11,442] [INFO] DFAST Taxonomy check result was written to GCF_000025565.1_ASM2556v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:11,443] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:11,443] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:11,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bc5e2ed-0079-463c-866a-7c4b0f98de8e/dqc_reference/checkm_data
[2024-01-24 12:14:11,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:11,502] [INFO] Task started: CheckM
[2024-01-24 12:14:11,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000025565.1_ASM2556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000025565.1_ASM2556v1_genomic.fna/checkm_input GCF_000025565.1_ASM2556v1_genomic.fna/checkm_result
[2024-01-24 12:15:00,737] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:00,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:00,772] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:00,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:00,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000025565.1_ASM2556v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:00,773] [INFO] Task started: Blastn
[2024-01-24 12:15:00,773] [INFO] Running command: blastn -query GCF_000025565.1_ASM2556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bc5e2ed-0079-463c-866a-7c4b0f98de8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000025565.1_ASM2556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:02,147] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:02,152] [INFO] Selected 33 target genomes.
[2024-01-24 12:15:02,153] [INFO] Target genome list was writen to GCF_000025565.1_ASM2556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:02,175] [INFO] Task started: fastANI
[2024-01-24 12:15:02,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2607220-e56d-4e53-9627-107b637f2bb6/GCF_000025565.1_ASM2556v1_genomic.fna.gz --refList GCF_000025565.1_ASM2556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000025565.1_ASM2556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:36,591] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:36,615] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:36,616] [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_000025565.1	s__Enterobacter cloacae	100.0	1863	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	conclusive
GCF_002939185.1	s__Enterobacter sichuanensis	89.2873	1288	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_007035645.1	s__Enterobacter asburiae_B	89.1129	1349	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_001521715.1	s__Enterobacter asburiae	89.1077	1281	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_001729805.1	s__Enterobacter roggenkampii	89.0304	1326	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	-
GCF_009755685.1	s__Enterobacter sp000568095	88.9204	1328	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_003634515.1	s__Enterobacter asburiae_A	88.8581	1334	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_008364625.1	s__Enterobacter dykesii	88.8398	1294	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_011754535.1	s__Enterobacter cloacae_N	88.8244	1341	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_900324475.1	s__Enterobacter bugandensis	88.808	1339	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_008080435.1	s__Enterobacter asburiae_C	88.7535	1334	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_008364555.1	s__Enterobacter vonholyi	88.6963	1283	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_001729765.1	s__Enterobacter kobei	88.5149	1353	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_003046225.1	s__Enterobacter cloacae_I	88.4076	1284	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.61	95.47	0.89	0.86	14	-
GCF_001750725.1	s__Enterobacter ludwigii	88.2801	1347	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.79	98.47	0.93	0.83	88	-
GCF_014169315.1	s__Enterobacter cloacae_P	87.7738	1237	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.13	99.10	0.85	0.85	3	-
GCF_900322725.1	s__Enterobacter quasihormaechei	87.6414	1317	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_019047785.1	s__Enterobacter cancerogenus	86.6526	1254	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.78	98.42	0.93	0.90	16	-
GCF_011290365.1	s__Leclercia sp003024485	84.6198	1133	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.06	98.06	0.90	0.90	2	-
GCF_017348915.1	s__UBA7405 sp000755535	84.1068	1082	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405	95.0	98.56	97.85	0.93	0.89	10	-
GCF_009363175.1	s__Citrobacter_A telavivensis	82.3807	963	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018261615.1	s__Kosakonia sp018261615	81.4375	848	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010231475.1	s__Citrobacter sp010231475	81.3401	838	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095535.1	s__Pantoea cypripedii	79.2575	544	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_014946725.1	s__Pantoea mediterraneensis_A	79.184	371	1865	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:36,617] [INFO] GTDB search result was written to GCF_000025565.1_ASM2556v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:36,618] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:36,622] [INFO] DFAST_QC result json was written to GCF_000025565.1_ASM2556v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:36,622] [INFO] DFAST_QC completed!
[2024-01-24 12:15:36,622] [INFO] Total running time: 0h2m9s