[2024-01-24 12:45:20,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,804] [INFO] DQC Reference Directory: /var/lib/cwl/stge7f9e0e4-9498-4abc-9cc8-87624c43971e/dqc_reference
[2024-01-24 12:45:22,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:22,085] [INFO] Task started: Prodigal
[2024-01-24 12:45:22,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg310fee6d-9e6e-41b0-a01d-6bdd502920b2/GCF_020026925.1_ASM2002692v1_genomic.fna.gz | prodigal -d GCF_020026925.1_ASM2002692v1_genomic.fna/cds.fna -a GCF_020026925.1_ASM2002692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:38,720] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:38,721] [INFO] Task started: HMMsearch
[2024-01-24 12:45:38,721] [INFO] Running command: hmmsearch --tblout GCF_020026925.1_ASM2002692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7f9e0e4-9498-4abc-9cc8-87624c43971e/dqc_reference/reference_markers.hmm GCF_020026925.1_ASM2002692v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:39,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:39,012] [INFO] Found 6/6 markers.
[2024-01-24 12:45:39,054] [INFO] Query marker FASTA was written to GCF_020026925.1_ASM2002692v1_genomic.fna/markers.fasta
[2024-01-24 12:45:39,054] [INFO] Task started: Blastn
[2024-01-24 12:45:39,055] [INFO] Running command: blastn -query GCF_020026925.1_ASM2002692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7f9e0e4-9498-4abc-9cc8-87624c43971e/dqc_reference/reference_markers.fasta -out GCF_020026925.1_ASM2002692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:39,725] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:39,728] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:39,729] [INFO] Target genome list was writen to GCF_020026925.1_ASM2002692v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:39,743] [INFO] Task started: fastANI
[2024-01-24 12:45:39,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg310fee6d-9e6e-41b0-a01d-6bdd502920b2/GCF_020026925.1_ASM2002692v1_genomic.fna.gz --refList GCF_020026925.1_ASM2002692v1_genomic.fna/target_genomes.txt --output GCF_020026925.1_ASM2002692v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:57,007] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:57,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7f9e0e4-9498-4abc-9cc8-87624c43971e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:57,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7f9e0e4-9498-4abc-9cc8-87624c43971e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:57,026] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:57,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:57,026] [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 hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	100.0	1618	1620	95	conclusive
Flavobacterium limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	87.055	1256	1620	95	below_threshold
Flavobacterium limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	86.963	1264	1620	95	below_threshold
Flavobacterium fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	86.3168	1083	1620	95	below_threshold
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	86.0577	1256	1620	95	below_threshold
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	85.288	1178	1620	95	below_threshold
Flavobacterium ajazii	strain=SSM4.2	GCA_010614725.1	2692318	2692318	type	True	85.0085	1126	1620	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	82.2581	885	1620	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	82.1533	866	1620	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	82.1324	843	1620	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	82.0231	904	1620	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	81.9573	819	1620	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.7521	826	1620	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	81.4949	885	1620	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.6793	177	1620	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:57,028] [INFO] DFAST Taxonomy check result was written to GCF_020026925.1_ASM2002692v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:57,028] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:57,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:57,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7f9e0e4-9498-4abc-9cc8-87624c43971e/dqc_reference/checkm_data
[2024-01-24 12:45:57,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:57,082] [INFO] Task started: CheckM
[2024-01-24 12:45:57,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020026925.1_ASM2002692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020026925.1_ASM2002692v1_genomic.fna/checkm_input GCF_020026925.1_ASM2002692v1_genomic.fna/checkm_result
[2024-01-24 12:46:47,178] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:47,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:47,196] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:47,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:47,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020026925.1_ASM2002692v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:47,197] [INFO] Task started: Blastn
[2024-01-24 12:46:47,197] [INFO] Running command: blastn -query GCF_020026925.1_ASM2002692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7f9e0e4-9498-4abc-9cc8-87624c43971e/dqc_reference/reference_markers_gtdb.fasta -out GCF_020026925.1_ASM2002692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:48,141] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:48,146] [INFO] Selected 17 target genomes.
[2024-01-24 12:46:48,146] [INFO] Target genome list was writen to GCF_020026925.1_ASM2002692v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:48,175] [INFO] Task started: fastANI
[2024-01-24 12:46:48,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg310fee6d-9e6e-41b0-a01d-6bdd502920b2/GCF_020026925.1_ASM2002692v1_genomic.fna.gz --refList GCF_020026925.1_ASM2002692v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020026925.1_ASM2002692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:07,336] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:07,357] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:47:07,358] [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_010645075.1	s__Flavobacterium limi	87.0605	1255	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010645065.1	s__Flavobacterium fluviatile	86.2968	1085	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202405.1	s__Flavobacterium hydrophilum	86.0634	1255	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735715.2	s__Flavobacterium chungangense	85.4498	1177	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_010614725.1	s__Flavobacterium ajazii	85.0089	1126	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202435.1	s__Flavobacterium cheongpyeongense	84.2171	1098	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	82.8621	849	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352115.1	s__Flavobacterium sp017352115	82.1742	864	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182645.1	s__Flavobacterium resistens	82.1356	841	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000745775.1	s__Flavobacterium sp000745775	81.9706	860	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	81.9524	819	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900142715.1	s__Flavobacterium pectinovorum	81.8797	931	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.60	0.94	0.89	3	-
GCF_016735615.1	s__Flavobacterium sp016735615	81.8484	799	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688345.1	s__Flavobacterium sp003688345	81.7592	928	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003946915.1	s__Flavobacterium sp003946915	81.7484	810	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405855.1	s__Flavobacterium sp002399805	81.63	849	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	-
GCF_900112575.1	s__Flavobacterium phragmitis	81.5042	883	1620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:07,360] [INFO] GTDB search result was written to GCF_020026925.1_ASM2002692v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:07,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:07,367] [INFO] DFAST_QC result json was written to GCF_020026925.1_ASM2002692v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:07,367] [INFO] DFAST_QC completed!
[2024-01-24 12:47:07,367] [INFO] Total running time: 0h1m47s