[2023-06-08 12:19:15,466] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:19:15,469] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:19:15,469] [INFO] DQC Reference Directory: /var/lib/cwl/stge3d4a69c-e404-4555-b708-d10ef901e6be/dqc_reference
[2023-06-08 12:19:16,688] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:19:16,689] [INFO] Task started: Prodigal
[2023-06-08 12:19:16,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a771787-1b90-43d2-abc6-c7272ab78d00/GCA_945860385.1_MaE-09apr19-44_genomic.fna.gz | prodigal -d GCA_945860385.1_MaE-09apr19-44_genomic.fna/cds.fna -a GCA_945860385.1_MaE-09apr19-44_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:19:28,894] [INFO] Task succeeded: Prodigal
[2023-06-08 12:19:28,894] [INFO] Task started: HMMsearch
[2023-06-08 12:19:28,895] [INFO] Running command: hmmsearch --tblout GCA_945860385.1_MaE-09apr19-44_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3d4a69c-e404-4555-b708-d10ef901e6be/dqc_reference/reference_markers.hmm GCA_945860385.1_MaE-09apr19-44_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:19:29,134] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:19:29,135] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4a771787-1b90-43d2-abc6-c7272ab78d00/GCA_945860385.1_MaE-09apr19-44_genomic.fna.gz]
[2023-06-08 12:19:29,173] [INFO] Query marker FASTA was written to GCA_945860385.1_MaE-09apr19-44_genomic.fna/markers.fasta
[2023-06-08 12:19:29,173] [INFO] Task started: Blastn
[2023-06-08 12:19:29,173] [INFO] Running command: blastn -query GCA_945860385.1_MaE-09apr19-44_genomic.fna/markers.fasta -db /var/lib/cwl/stge3d4a69c-e404-4555-b708-d10ef901e6be/dqc_reference/reference_markers.fasta -out GCA_945860385.1_MaE-09apr19-44_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:19:29,830] [INFO] Task succeeded: Blastn
[2023-06-08 12:19:29,835] [INFO] Selected 14 target genomes.
[2023-06-08 12:19:29,836] [INFO] Target genome list was writen to GCA_945860385.1_MaE-09apr19-44_genomic.fna/target_genomes.txt
[2023-06-08 12:19:29,843] [INFO] Task started: fastANI
[2023-06-08 12:19:29,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a771787-1b90-43d2-abc6-c7272ab78d00/GCA_945860385.1_MaE-09apr19-44_genomic.fna.gz --refList GCA_945860385.1_MaE-09apr19-44_genomic.fna/target_genomes.txt --output GCA_945860385.1_MaE-09apr19-44_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:19:39,740] [INFO] Task succeeded: fastANI
[2023-06-08 12:19:39,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3d4a69c-e404-4555-b708-d10ef901e6be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:19:39,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3d4a69c-e404-4555-b708-d10ef901e6be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:19:39,756] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:19:39,757] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:19:39,757] [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 franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	85.8183	727	993	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	82.6181	626	993	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	82.312	642	993	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	81.6193	564	993	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	79.8756	492	993	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	78.8946	353	993	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	78.8939	392	993	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	78.8061	361	993	95	below_threshold
Flavobacterium restrictum	strain=LB1R34	GCA_007097245.1	2594428	2594428	type	True	78.7247	364	993	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.575	360	993	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.408	273	993	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.2954	259	993	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.882	152	993	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.6544	54	993	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:19:39,759] [INFO] DFAST Taxonomy check result was written to GCA_945860385.1_MaE-09apr19-44_genomic.fna/tc_result.tsv
[2023-06-08 12:19:39,759] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:19:39,760] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:19:39,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3d4a69c-e404-4555-b708-d10ef901e6be/dqc_reference/checkm_data
[2023-06-08 12:19:39,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:19:39,796] [INFO] Task started: CheckM
[2023-06-08 12:19:39,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945860385.1_MaE-09apr19-44_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945860385.1_MaE-09apr19-44_genomic.fna/checkm_input GCA_945860385.1_MaE-09apr19-44_genomic.fna/checkm_result
[2023-06-08 12:20:18,490] [INFO] Task succeeded: CheckM
[2023-06-08 12:20:18,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:20:18,513] [INFO] ===== Completeness check finished =====
[2023-06-08 12:20:18,514] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:20:18,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945860385.1_MaE-09apr19-44_genomic.fna/markers.fasta)
[2023-06-08 12:20:18,515] [INFO] Task started: Blastn
[2023-06-08 12:20:18,515] [INFO] Running command: blastn -query GCA_945860385.1_MaE-09apr19-44_genomic.fna/markers.fasta -db /var/lib/cwl/stge3d4a69c-e404-4555-b708-d10ef901e6be/dqc_reference/reference_markers_gtdb.fasta -out GCA_945860385.1_MaE-09apr19-44_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:20:19,455] [INFO] Task succeeded: Blastn
[2023-06-08 12:20:19,460] [INFO] Selected 13 target genomes.
[2023-06-08 12:20:19,460] [INFO] Target genome list was writen to GCA_945860385.1_MaE-09apr19-44_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:20:19,467] [INFO] Task started: fastANI
[2023-06-08 12:20:19,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a771787-1b90-43d2-abc6-c7272ab78d00/GCA_945860385.1_MaE-09apr19-44_genomic.fna.gz --refList GCA_945860385.1_MaE-09apr19-44_genomic.fna/target_genomes_gtdb.txt --output GCA_945860385.1_MaE-09apr19-44_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:20:28,636] [INFO] Task succeeded: fastANI
[2023-06-08 12:20:28,656] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:20:28,657] [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_007097365.1	s__Flavobacterium franklandianum	85.8303	726	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCA_010365135.1	s__Flavobacterium sp010365135	82.7914	554	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920895.1	s__Flavobacterium alvei	82.6266	625	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355225.1	s__Flavobacterium nackdongense	82.3242	641	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277675.1	s__Flavobacterium soyangense	82.1108	575	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379405.1	s__Flavobacterium sp014379405	81.9694	491	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129545.1	s__Flavobacterium fluvii	81.6159	564	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861155.1	s__Flavobacterium sp903861155	80.5809	440	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.81	99.81	0.91	0.91	2	-
GCA_002413745.1	s__Flavobacterium sp002413745	80.534	495	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
GCF_004349355.1	s__Flavobacterium cellulosilyticum	79.8809	492	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	79.8568	312	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812945.1	s__Flavobacterium sp000812945	79.1993	403	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842575.1	s__Flavobacterium sp903842575	77.4976	210	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:20:28,659] [INFO] GTDB search result was written to GCA_945860385.1_MaE-09apr19-44_genomic.fna/result_gtdb.tsv
[2023-06-08 12:20:28,660] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:20:28,663] [INFO] DFAST_QC result json was written to GCA_945860385.1_MaE-09apr19-44_genomic.fna/dqc_result.json
[2023-06-08 12:20:28,664] [INFO] DFAST_QC completed!
[2023-06-08 12:20:28,664] [INFO] Total running time: 0h1m13s