[2024-01-24 11:13:04,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg409b3730-c705-4ae4-b71b-f793fca22a79/dqc_reference
[2024-01-24 11:13:05,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,769] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a2988e8-61a4-4541-b289-6c119f0b2d0e/GCF_019702945.1_ASM1970294v1_genomic.fna.gz | prodigal -d GCF_019702945.1_ASM1970294v1_genomic.fna/cds.fna -a GCF_019702945.1_ASM1970294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:14,022] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:14,023] [INFO] Task started: HMMsearch
[2024-01-24 11:13:14,023] [INFO] Running command: hmmsearch --tblout GCF_019702945.1_ASM1970294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg409b3730-c705-4ae4-b71b-f793fca22a79/dqc_reference/reference_markers.hmm GCF_019702945.1_ASM1970294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:14,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:14,297] [INFO] Found 6/6 markers.
[2024-01-24 11:13:14,323] [INFO] Query marker FASTA was written to GCF_019702945.1_ASM1970294v1_genomic.fna/markers.fasta
[2024-01-24 11:13:14,324] [INFO] Task started: Blastn
[2024-01-24 11:13:14,324] [INFO] Running command: blastn -query GCF_019702945.1_ASM1970294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg409b3730-c705-4ae4-b71b-f793fca22a79/dqc_reference/reference_markers.fasta -out GCF_019702945.1_ASM1970294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:15,050] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:15,054] [INFO] Selected 16 target genomes.
[2024-01-24 11:13:15,055] [INFO] Target genome list was writen to GCF_019702945.1_ASM1970294v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:15,162] [INFO] Task started: fastANI
[2024-01-24 11:13:15,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a2988e8-61a4-4541-b289-6c119f0b2d0e/GCF_019702945.1_ASM1970294v1_genomic.fna.gz --refList GCF_019702945.1_ASM1970294v1_genomic.fna/target_genomes.txt --output GCF_019702945.1_ASM1970294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:24,834] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:24,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg409b3730-c705-4ae4-b71b-f793fca22a79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:24,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg409b3730-c705-4ae4-b71b-f793fca22a79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:24,851] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:24,851] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:24,851] [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 haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	83.3724	614	927	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	83.217	605	927	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	79.4415	438	927	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	79.3744	422	927	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	79.2152	399	927	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	79.1929	396	927	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	79.1064	412	927	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	79.0416	382	927	95	below_threshold
Flavobacterium sediminis	strain=MEBiC07310	GCA_003148385.1	2201181	2201181	type	True	78.8766	332	927	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	78.6389	378	927	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.6389	378	927	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.5398	416	927	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	78.402	305	927	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	78.0633	225	927	95	below_threshold
Flavobacterium columnare	strain=NBRC 100251	GCA_007990835.1	996	996	type	True	77.6402	190	927	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.3854	193	927	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:24,853] [INFO] DFAST Taxonomy check result was written to GCF_019702945.1_ASM1970294v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:24,854] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:24,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:24,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg409b3730-c705-4ae4-b71b-f793fca22a79/dqc_reference/checkm_data
[2024-01-24 11:13:24,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:24,888] [INFO] Task started: CheckM
[2024-01-24 11:13:24,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019702945.1_ASM1970294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019702945.1_ASM1970294v1_genomic.fna/checkm_input GCF_019702945.1_ASM1970294v1_genomic.fna/checkm_result
[2024-01-24 11:13:54,603] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:54,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:54,626] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:54,626] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:54,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019702945.1_ASM1970294v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:54,627] [INFO] Task started: Blastn
[2024-01-24 11:13:54,627] [INFO] Running command: blastn -query GCF_019702945.1_ASM1970294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg409b3730-c705-4ae4-b71b-f793fca22a79/dqc_reference/reference_markers_gtdb.fasta -out GCF_019702945.1_ASM1970294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:55,631] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:55,643] [INFO] Selected 20 target genomes.
[2024-01-24 11:13:55,644] [INFO] Target genome list was writen to GCF_019702945.1_ASM1970294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:55,662] [INFO] Task started: fastANI
[2024-01-24 11:13:55,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a2988e8-61a4-4541-b289-6c119f0b2d0e/GCF_019702945.1_ASM1970294v1_genomic.fna.gz --refList GCF_019702945.1_ASM1970294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019702945.1_ASM1970294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:07,816] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:07,839] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:14:07,839] [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_009363055.1	s__Flavobacterium haoranii	83.3942	612	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_014763515.1	s__Flavobacterium sp014763515	82.5342	359	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	79.2	396	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003246205.1	s__Flavobacterium haoranii_A	79.1916	312	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009495755.1	s__Flavobacterium sp009495755	79.0534	407	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293845.1	s__Flavobacterium tibetense	79.003	381	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019105125.1	s__Flavobacterium sp019105125	78.8907	219	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148385.1	s__Flavobacterium sediminis	78.8367	331	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483315.1	s__Flavobacterium sp002483315	78.8289	393	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862805.1	s__Flavobacterium sp002862805	78.6806	396	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293165.1	s__Flavobacterium sp004293165	78.6583	360	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.30	97.30	0.81	0.81	2	-
GCF_006491645.1	s__Flavobacterium sp006491645	78.6428	379	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000455605.1	s__Flavobacterium indicum	78.5213	305	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	78.4996	415	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110615.1	s__Flavobacterium urocaniciphilum	78.4846	333	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004303025.1	s__Flavobacterium sp004303025	78.4397	375	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715085.1	s__Flavobacterium sp002715085	78.402	371	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862755.1	s__Flavobacterium sp002862755	78.3802	354	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032075.1	s__Flavobacterium sp012032075	78.34	308	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002204895.1	s__Flavobacterium columnare_C	77.8538	210	927	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.67	99.21	0.94	0.90	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:07,843] [INFO] GTDB search result was written to GCF_019702945.1_ASM1970294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:07,844] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:07,849] [INFO] DFAST_QC result json was written to GCF_019702945.1_ASM1970294v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:07,849] [INFO] DFAST_QC completed!
[2024-01-24 11:14:07,850] [INFO] Total running time: 0h1m3s