[2024-01-24 13:48:59,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg093347ac-0030-4dd0-bb9e-0b1e943fa21a/dqc_reference
[2024-01-24 13:49:01,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,038] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg694bf4bd-d822-4ffa-9e9c-9ef9c4879ec3/GCF_001039365.2_ASM103936v2_genomic.fna.gz | prodigal -d GCF_001039365.2_ASM103936v2_genomic.fna/cds.fna -a GCF_001039365.2_ASM103936v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:14,497] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:14,498] [INFO] Task started: HMMsearch
[2024-01-24 13:49:14,498] [INFO] Running command: hmmsearch --tblout GCF_001039365.2_ASM103936v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg093347ac-0030-4dd0-bb9e-0b1e943fa21a/dqc_reference/reference_markers.hmm GCF_001039365.2_ASM103936v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:14,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:14,784] [INFO] Found 6/6 markers.
[2024-01-24 13:49:14,829] [INFO] Query marker FASTA was written to GCF_001039365.2_ASM103936v2_genomic.fna/markers.fasta
[2024-01-24 13:49:14,830] [INFO] Task started: Blastn
[2024-01-24 13:49:14,830] [INFO] Running command: blastn -query GCF_001039365.2_ASM103936v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg093347ac-0030-4dd0-bb9e-0b1e943fa21a/dqc_reference/reference_markers.fasta -out GCF_001039365.2_ASM103936v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:15,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:15,769] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:15,770] [INFO] Target genome list was writen to GCF_001039365.2_ASM103936v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:15,786] [INFO] Task started: fastANI
[2024-01-24 13:49:15,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg694bf4bd-d822-4ffa-9e9c-9ef9c4879ec3/GCF_001039365.2_ASM103936v2_genomic.fna.gz --refList GCF_001039365.2_ASM103936v2_genomic.fna/target_genomes.txt --output GCF_001039365.2_ASM103936v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:30,648] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:30,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg093347ac-0030-4dd0-bb9e-0b1e943fa21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:30,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg093347ac-0030-4dd0-bb9e-0b1e943fa21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:30,659] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:30,659] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:30,659] [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 roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	95.8066	1422	1593	95	conclusive
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	95.7871	1421	1593	95	conclusive
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	95.6766	1320	1593	95	conclusive
Enterobacter vonholyi	strain=E13	GCA_008364555.1	2797505	2797505	type	True	94.3665	1386	1593	95	below_threshold
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	93.2748	1339	1593	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	93.2463	1347	1593	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	92.8732	1375	1593	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_002939185.1	2071710	2071710	type	True	91.6871	1298	1593	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	91.6867	1355	1593	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	89.003	1290	1593	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	88.8204	1303	1593	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	88.0167	1228	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:30,662] [INFO] DFAST Taxonomy check result was written to GCF_001039365.2_ASM103936v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:30,663] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:30,663] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:30,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg093347ac-0030-4dd0-bb9e-0b1e943fa21a/dqc_reference/checkm_data
[2024-01-24 13:49:30,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:30,714] [INFO] Task started: CheckM
[2024-01-24 13:49:30,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001039365.2_ASM103936v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001039365.2_ASM103936v2_genomic.fna/checkm_input GCF_001039365.2_ASM103936v2_genomic.fna/checkm_result
[2024-01-24 13:50:15,481] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:15,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:15,503] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:15,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:15,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001039365.2_ASM103936v2_genomic.fna/markers.fasta)
[2024-01-24 13:50:15,504] [INFO] Task started: Blastn
[2024-01-24 13:50:15,504] [INFO] Running command: blastn -query GCF_001039365.2_ASM103936v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg093347ac-0030-4dd0-bb9e-0b1e943fa21a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001039365.2_ASM103936v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:16,961] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:16,965] [INFO] Selected 14 target genomes.
[2024-01-24 13:50:16,965] [INFO] Target genome list was writen to GCF_001039365.2_ASM103936v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:16,975] [INFO] Task started: fastANI
[2024-01-24 13:50:16,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg694bf4bd-d822-4ffa-9e9c-9ef9c4879ec3/GCF_001039365.2_ASM103936v2_genomic.fna.gz --refList GCF_001039365.2_ASM103936v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001039365.2_ASM103936v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:33,296] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:33,310] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:33,310] [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_001729805.1	s__Enterobacter roggenkampii	95.8066	1422	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	conclusive
GCF_009755685.1	s__Enterobacter sp000568095	94.9604	1413	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_008364555.1	s__Enterobacter vonholyi	94.3665	1386	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_008364625.1	s__Enterobacter dykesii	93.4347	1361	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_003634515.1	s__Enterobacter asburiae_A	93.3742	1391	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_007035645.1	s__Enterobacter asburiae_B	93.3028	1384	1593	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	93.2948	1377	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.7528	98.28	96.89	0.91	0.85	84	-
GCF_001521715.1	s__Enterobacter asburiae	93.2463	1347	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_000493015.1	s__Enterobacter sp000493015	93.1891	1394	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.7595	98.68	98.68	0.92	0.92	2	-
GCF_008080435.1	s__Enterobacter asburiae_C	93.1445	1371	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_001984825.2	s__Enterobacter chengduensis	92.8871	1373	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.11	95.58	0.88	0.79	24	-
GCF_001022965.1	s__Enterobacter cloacae_L	92.355	1400	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.51	97.16	0.91	0.90	5	-
GCF_004402045.1	s__Enterobacter nimipressuralis_A	92.2543	1362	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939185.1	s__Enterobacter sichuanensis	91.6871	1298	1593	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:33,312] [INFO] GTDB search result was written to GCF_001039365.2_ASM103936v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:33,313] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:33,316] [INFO] DFAST_QC result json was written to GCF_001039365.2_ASM103936v2_genomic.fna/dqc_result.json
[2024-01-24 13:50:33,317] [INFO] DFAST_QC completed!
[2024-01-24 13:50:33,317] [INFO] Total running time: 0h1m34s