[2024-01-24 15:18:37,281] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:37,288] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:37,288] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf3c4bb6-95d7-4a91-b085-4104082eb3b1/dqc_reference
[2024-01-24 15:18:38,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:38,686] [INFO] Task started: Prodigal
[2024-01-24 15:18:38,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg23c56b1e-e7e0-4e65-80a8-5070f795c894/GCF_002939185.1_ASM293918v1_genomic.fna.gz | prodigal -d GCF_002939185.1_ASM293918v1_genomic.fna/cds.fna -a GCF_002939185.1_ASM293918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:51,498] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:51,498] [INFO] Task started: HMMsearch
[2024-01-24 15:18:51,498] [INFO] Running command: hmmsearch --tblout GCF_002939185.1_ASM293918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf3c4bb6-95d7-4a91-b085-4104082eb3b1/dqc_reference/reference_markers.hmm GCF_002939185.1_ASM293918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:51,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:51,855] [INFO] Found 6/6 markers.
[2024-01-24 15:18:51,897] [INFO] Query marker FASTA was written to GCF_002939185.1_ASM293918v1_genomic.fna/markers.fasta
[2024-01-24 15:18:51,898] [INFO] Task started: Blastn
[2024-01-24 15:18:51,898] [INFO] Running command: blastn -query GCF_002939185.1_ASM293918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf3c4bb6-95d7-4a91-b085-4104082eb3b1/dqc_reference/reference_markers.fasta -out GCF_002939185.1_ASM293918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:52,798] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:52,805] [INFO] Selected 24 target genomes.
[2024-01-24 15:18:52,806] [INFO] Target genome list was writen to GCF_002939185.1_ASM293918v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:52,822] [INFO] Task started: fastANI
[2024-01-24 15:18:52,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c56b1e-e7e0-4e65-80a8-5070f795c894/GCF_002939185.1_ASM293918v1_genomic.fna.gz --refList GCF_002939185.1_ASM293918v1_genomic.fna/target_genomes.txt --output GCF_002939185.1_ASM293918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:16,846] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:16,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf3c4bb6-95d7-4a91-b085-4104082eb3b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:16,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf3c4bb6-95d7-4a91-b085-4104082eb3b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:16,861] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:16,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:16,861] [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 sichuanensis	strain=WCHECL1597	GCA_002939185.1	2071710	2071710	type	True	100.0	1536	1542	95	conclusive
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	98.136	1394	1542	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	92.0194	1236	1542	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	91.9496	1295	1542	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	91.9325	1294	1542	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	91.7475	1263	1542	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	91.7419	1261	1542	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	91.0212	1280	1542	95	below_threshold
Enterobacter bugandensis		GCA_900324475.1	881260	881260	type	True	90.332	1275	1542	95	below_threshold
Enterobacter bugandensis	strain=FDAARGOS 1427	GCA_019046905.1	881260	881260	type	True	90.3306	1255	1542	95	below_threshold
Enterobacter quasimori	strain=090044	GCA_003964905.1	2838947	2838947	type	True	89.3513	1251	1542	95	below_threshold
Enterobacter cloacae	strain=ATCC 13047	GCA_000755525.1	550	550	type	True	89.2684	1314	1542	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_013376815.1	550	550	type	True	89.2654	1307	1542	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	89.257	1305	1542	95	below_threshold
Enterobacter cloacae	strain=FDAARGOS 1431	GCA_019047105.1	550	550	type	True	89.2491	1312	1542	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	88.9293	1246	1542	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	88.3523	1201	1542	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	87.5533	1202	1542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:16,864] [INFO] DFAST Taxonomy check result was written to GCF_002939185.1_ASM293918v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:16,865] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:16,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:16,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf3c4bb6-95d7-4a91-b085-4104082eb3b1/dqc_reference/checkm_data
[2024-01-24 15:19:16,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:16,921] [INFO] Task started: CheckM
[2024-01-24 15:19:16,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002939185.1_ASM293918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002939185.1_ASM293918v1_genomic.fna/checkm_input GCF_002939185.1_ASM293918v1_genomic.fna/checkm_result
[2024-01-24 15:19:58,240] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:58,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:58,265] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:58,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:58,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002939185.1_ASM293918v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:58,266] [INFO] Task started: Blastn
[2024-01-24 15:19:58,266] [INFO] Running command: blastn -query GCF_002939185.1_ASM293918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf3c4bb6-95d7-4a91-b085-4104082eb3b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002939185.1_ASM293918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:59,485] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:59,488] [INFO] Selected 23 target genomes.
[2024-01-24 15:19:59,489] [INFO] Target genome list was writen to GCF_002939185.1_ASM293918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:59,505] [INFO] Task started: fastANI
[2024-01-24 15:19:59,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c56b1e-e7e0-4e65-80a8-5070f795c894/GCF_002939185.1_ASM293918v1_genomic.fna.gz --refList GCF_002939185.1_ASM293918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002939185.1_ASM293918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:22,679] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:22,696] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:22,696] [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_002939185.1	s__Enterobacter sichuanensis	100.0	1536	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	conclusive
GCF_001022965.1	s__Enterobacter cloacae_L	92.5744	1354	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.51	97.16	0.91	0.90	5	-
GCF_001729805.1	s__Enterobacter roggenkampii	91.9325	1294	1542	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	91.7545	1311	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_001521715.1	s__Enterobacter asburiae	91.7419	1261	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_003634515.1	s__Enterobacter asburiae_A	91.7298	1297	1542	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	91.6559	1264	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_007035645.1	s__Enterobacter asburiae_B	91.6318	1272	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_002208095.1	s__Enterobacter cloacae_M	91.5278	1295	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.7528	98.28	96.89	0.91	0.85	84	-
GCF_008364555.1	s__Enterobacter vonholyi	91.5049	1281	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_001984825.2	s__Enterobacter chengduensis	91.0212	1280	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.11	95.58	0.88	0.79	24	-
GCF_011754535.1	s__Enterobacter cloacae_N	90.4737	1288	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_003594915.1	s__Enterobacter chuandaensis	90.3523	1260	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	98.32	0.92	0.92	3	-
GCF_900324475.1	s__Enterobacter bugandensis	90.332	1275	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_003046225.1	s__Enterobacter cloacae_I	89.9495	1272	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.61	95.47	0.89	0.86	14	-
GCF_001729765.1	s__Enterobacter kobei	89.9039	1249	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_000025565.1	s__Enterobacter cloacae	89.2325	1307	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	-
GCF_000211415.1	s__Enterobacter mori	88.9251	1246	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.59	96.13	0.88	0.85	23	-
GCF_000280495.2	s__Kosakonia radicincitans	81.3698	908	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.7299	99.26	99.13	0.95	0.93	14	-
GCF_011395035.1	s__Pantoea cypripedii_A	78.7133	513	1542	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 15:20:22,698] [INFO] GTDB search result was written to GCF_002939185.1_ASM293918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:22,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:22,703] [INFO] DFAST_QC result json was written to GCF_002939185.1_ASM293918v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:22,703] [INFO] DFAST_QC completed!
[2024-01-24 15:20:22,703] [INFO] Total running time: 0h1m45s