[2023-06-18 17:35:09,835] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:35:09,837] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:35:09,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg0da477f1-9047-456d-b292-7c1abc359ef5/dqc_reference
[2023-06-18 17:35:10,980] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:35:10,981] [INFO] Task started: Prodigal
[2023-06-18 17:35:10,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg8446efff-2af6-485b-a03f-e9f126d58bae/GCA_018267095.1_ASM1826709v1_genomic.fna.gz | prodigal -d GCA_018267095.1_ASM1826709v1_genomic.fna/cds.fna -a GCA_018267095.1_ASM1826709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:35:27,015] [INFO] Task succeeded: Prodigal
[2023-06-18 17:35:27,016] [INFO] Task started: HMMsearch
[2023-06-18 17:35:27,016] [INFO] Running command: hmmsearch --tblout GCA_018267095.1_ASM1826709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0da477f1-9047-456d-b292-7c1abc359ef5/dqc_reference/reference_markers.hmm GCA_018267095.1_ASM1826709v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:35:27,217] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:35:27,218] [INFO] Found 6/6 markers.
[2023-06-18 17:35:27,255] [INFO] Query marker FASTA was written to GCA_018267095.1_ASM1826709v1_genomic.fna/markers.fasta
[2023-06-18 17:35:27,256] [INFO] Task started: Blastn
[2023-06-18 17:35:27,256] [INFO] Running command: blastn -query GCA_018267095.1_ASM1826709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0da477f1-9047-456d-b292-7c1abc359ef5/dqc_reference/reference_markers.fasta -out GCA_018267095.1_ASM1826709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:35:27,914] [INFO] Task succeeded: Blastn
[2023-06-18 17:35:27,917] [INFO] Selected 29 target genomes.
[2023-06-18 17:35:27,918] [INFO] Target genome list was writen to GCA_018267095.1_ASM1826709v1_genomic.fna/target_genomes.txt
[2023-06-18 17:35:27,950] [INFO] Task started: fastANI
[2023-06-18 17:35:27,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg8446efff-2af6-485b-a03f-e9f126d58bae/GCA_018267095.1_ASM1826709v1_genomic.fna.gz --refList GCA_018267095.1_ASM1826709v1_genomic.fna/target_genomes.txt --output GCA_018267095.1_ASM1826709v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:35:43,512] [INFO] Task succeeded: fastANI
[2023-06-18 17:35:43,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0da477f1-9047-456d-b292-7c1abc359ef5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:35:43,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0da477f1-9047-456d-b292-7c1abc359ef5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:35:43,531] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:35:43,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:35:43,532] [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
Flavobacterium lotistagni	strain=CYK-4	GCA_011392125.1	2709660	2709660	type	True	78.4344	366	1033	95	below_threshold
Flavobacterium phycosphaerae	strain=MK012	GCA_010119235.1	2697515	2697515	type	True	77.4757	216	1033	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	77.3958	148	1033	95	below_threshold
Flavobacterium fontis	strain=DSM 25660	GCA_900129405.1	1124188	1124188	type	True	77.3554	146	1033	95	below_threshold
Flavobacterium ichthyis	strain=NST-5	GCA_009915155.1	2698827	2698827	type	True	77.3346	117	1033	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	77.3157	63	1033	95	below_threshold
Flavobacterium silvisoli	strain=RD-2-33	GCA_004329815.1	2529433	2529433	type	True	77.298	211	1033	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	77.0308	102	1033	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	77.0281	165	1033	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	76.9954	172	1033	95	below_threshold
Flavobacterium suncheonense	strain=DSM 17707	GCA_000430025.1	350894	350894	type	True	76.9925	134	1033	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	76.9552	109	1033	95	below_threshold
Flavobacterium soli	strain=DSM 19725	GCA_000422705.1	344881	344881	type	True	76.9412	130	1033	95	below_threshold
Flavobacterium noncentrifugens	strain=CGMCC 1.10076	GCA_900100375.1	1128970	1128970	type	True	76.9182	187	1033	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	76.8735	85	1033	95	below_threshold
Flavobacterium agrisoli	strain=SE-1-e	GCA_016522065.1	2793066	2793066	type	True	76.8642	145	1033	95	below_threshold
Flavobacterium suncheonense	strain=GH29-5	GCA_000769835.1	350894	350894	type	True	76.858	133	1033	95	below_threshold
Flavobacterium caeni	strain=CGMCC 1.7031	GCA_900101895.1	490189	490189	type	True	76.8487	169	1033	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	76.8441	93	1033	95	below_threshold
Flavobacterium orientale	strain=CGMCC 1.12506	GCA_014638005.1	1756020	1756020	type	True	76.8085	124	1033	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	76.8008	100	1033	95	below_threshold
Flavobacterium supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	76.7656	106	1033	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	76.7014	119	1033	95	below_threshold
Flavobacterium psychrotolerans	strain=RB1R5	GCA_003097635.1	2169410	2169410	type	True	76.5331	140	1033	95	below_threshold
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	76.464	110	1033	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:35:43,536] [INFO] DFAST Taxonomy check result was written to GCA_018267095.1_ASM1826709v1_genomic.fna/tc_result.tsv
[2023-06-18 17:35:43,536] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:35:43,536] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:35:43,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0da477f1-9047-456d-b292-7c1abc359ef5/dqc_reference/checkm_data
[2023-06-18 17:35:43,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:35:43,568] [INFO] Task started: CheckM
[2023-06-18 17:35:43,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018267095.1_ASM1826709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018267095.1_ASM1826709v1_genomic.fna/checkm_input GCA_018267095.1_ASM1826709v1_genomic.fna/checkm_result
[2023-06-18 17:36:31,796] [INFO] Task succeeded: CheckM
[2023-06-18 17:36:31,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:36:31,820] [INFO] ===== Completeness check finished =====
[2023-06-18 17:36:31,820] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:36:31,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018267095.1_ASM1826709v1_genomic.fna/markers.fasta)
[2023-06-18 17:36:31,821] [INFO] Task started: Blastn
[2023-06-18 17:36:31,821] [INFO] Running command: blastn -query GCA_018267095.1_ASM1826709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0da477f1-9047-456d-b292-7c1abc359ef5/dqc_reference/reference_markers_gtdb.fasta -out GCA_018267095.1_ASM1826709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:36:32,703] [INFO] Task succeeded: Blastn
[2023-06-18 17:36:32,725] [INFO] Selected 14 target genomes.
[2023-06-18 17:36:32,725] [INFO] Target genome list was writen to GCA_018267095.1_ASM1826709v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:36:32,746] [INFO] Task started: fastANI
[2023-06-18 17:36:32,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg8446efff-2af6-485b-a03f-e9f126d58bae/GCA_018267095.1_ASM1826709v1_genomic.fna.gz --refList GCA_018267095.1_ASM1826709v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018267095.1_ASM1826709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:36:41,333] [INFO] Task succeeded: fastANI
[2023-06-18 17:36:41,345] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:36:41,345] [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
GCA_018267095.1	s__Flavobacterium sp018267095	100.0	1033	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018413465.1	s__Flavobacterium sp018413465	84.1242	779	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011392125.1	s__Flavobacterium lotistagni	78.4036	372	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122105.1	s__Flavobacterium sp004122105	77.5067	163	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786385.1	s__Flavobacterium sp002786385	77.49	224	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.88	0.88	2	-
GCF_900129405.1	s__Flavobacterium fontis	77.3348	148	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004329815.1	s__Flavobacterium silvisoli	77.2975	211	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787805.1	s__Flavobacterium sp016787805	77.2838	200	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742145.1	s__Flavobacterium sp011742145	77.1789	204	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016714905.1	s__Flavobacterium sp016714905	77.1011	219	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017987725.1	s__Flavobacterium sp017987725	76.9166	137	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101895.1	s__Flavobacterium caeni	76.8591	170	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097265.1	s__Flavobacterium gawalongense	76.6998	118	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCA_002352205.1	s__Flavobacterium sp002352205	76.6491	141	1033	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-18 17:36:41,350] [INFO] GTDB search result was written to GCA_018267095.1_ASM1826709v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:36:41,350] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:36:41,355] [INFO] DFAST_QC result json was written to GCA_018267095.1_ASM1826709v1_genomic.fna/dqc_result.json
[2023-06-18 17:36:41,355] [INFO] DFAST_QC completed!
[2023-06-18 17:36:41,355] [INFO] Total running time: 0h1m32s