[2024-01-24 12:29:19,199] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:19,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:19,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg77b1ae95-f59e-455f-a8d6-a060c88eec62/dqc_reference
[2024-01-24 12:29:20,379] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:20,380] [INFO] Task started: Prodigal
[2024-01-24 12:29:20,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg33b31979-8f6e-4c13-9d90-7f0fc3a76fb8/GCF_009915155.1_ASM991515v1_genomic.fna.gz | prodigal -d GCF_009915155.1_ASM991515v1_genomic.fna/cds.fna -a GCF_009915155.1_ASM991515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:32,312] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:32,313] [INFO] Task started: HMMsearch
[2024-01-24 12:29:32,313] [INFO] Running command: hmmsearch --tblout GCF_009915155.1_ASM991515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77b1ae95-f59e-455f-a8d6-a060c88eec62/dqc_reference/reference_markers.hmm GCF_009915155.1_ASM991515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:32,569] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:32,571] [INFO] Found 6/6 markers.
[2024-01-24 12:29:32,602] [INFO] Query marker FASTA was written to GCF_009915155.1_ASM991515v1_genomic.fna/markers.fasta
[2024-01-24 12:29:32,603] [INFO] Task started: Blastn
[2024-01-24 12:29:32,603] [INFO] Running command: blastn -query GCF_009915155.1_ASM991515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77b1ae95-f59e-455f-a8d6-a060c88eec62/dqc_reference/reference_markers.fasta -out GCF_009915155.1_ASM991515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:33,283] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:33,289] [INFO] Selected 22 target genomes.
[2024-01-24 12:29:33,290] [INFO] Target genome list was writen to GCF_009915155.1_ASM991515v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:33,353] [INFO] Task started: fastANI
[2024-01-24 12:29:33,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg33b31979-8f6e-4c13-9d90-7f0fc3a76fb8/GCF_009915155.1_ASM991515v1_genomic.fna.gz --refList GCF_009915155.1_ASM991515v1_genomic.fna/target_genomes.txt --output GCF_009915155.1_ASM991515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:45,700] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:45,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77b1ae95-f59e-455f-a8d6-a060c88eec62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:45,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77b1ae95-f59e-455f-a8d6-a060c88eec62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:45,721] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:45,721] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:45,721] [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 ichthyis	strain=NST-5	GCA_009915155.1	2698827	2698827	type	True	100.0	937	938	95	conclusive
Flavobacterium macacae	strain=YIM 102600	GCA_003865365.1	2488993	2488993	type	True	78.7524	339	938	95	below_threshold
Flavobacterium gossypii	strain=DSM 100397	GCA_014138495.1	1646119	1646119	type	True	78.3053	260	938	95	below_threshold
Flavobacterium endophyticum	strain=DSM 29537	GCA_003634455.1	1540163	1540163	type	True	78.2068	271	938	95	below_threshold
Flavobacterium lindanitolerans	strain=IP-10	GCA_002846575.1	428988	428988	type	True	77.8828	262	938	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	77.8637	247	938	95	below_threshold
Flavobacterium orientale	strain=CGMCC 1.12506	GCA_014638005.1	1756020	1756020	type	True	77.7315	181	938	95	below_threshold
Flavobacterium flevense	strain=DSM 1076	GCA_900142775.1	983	983	type	True	77.6209	179	938	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.5245	166	938	95	below_threshold
Flavobacterium piscinae	strain=ICH-30	GCA_004122145.1	2506424	2506424	type	True	77.5121	201	938	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	77.5012	171	938	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	77.4482	201	938	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	77.4436	203	938	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.4297	206	938	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	77.4185	182	938	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	77.3994	201	938	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.3886	198	938	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.3821	186	938	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.3562	182	938	95	below_threshold
Flavobacterium cucumis	strain=DSM 18830	GCA_900148835.1	416016	416016	type	True	77.3273	186	938	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	77.0565	109	938	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.8703	144	938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:45,723] [INFO] DFAST Taxonomy check result was written to GCF_009915155.1_ASM991515v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:45,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:45,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:45,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77b1ae95-f59e-455f-a8d6-a060c88eec62/dqc_reference/checkm_data
[2024-01-24 12:29:45,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:45,758] [INFO] Task started: CheckM
[2024-01-24 12:29:45,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009915155.1_ASM991515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009915155.1_ASM991515v1_genomic.fna/checkm_input GCF_009915155.1_ASM991515v1_genomic.fna/checkm_result
[2024-01-24 12:30:23,650] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:23,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:23,674] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:23,674] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:23,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009915155.1_ASM991515v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:23,675] [INFO] Task started: Blastn
[2024-01-24 12:30:23,675] [INFO] Running command: blastn -query GCF_009915155.1_ASM991515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77b1ae95-f59e-455f-a8d6-a060c88eec62/dqc_reference/reference_markers_gtdb.fasta -out GCF_009915155.1_ASM991515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:24,604] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:24,609] [INFO] Selected 25 target genomes.
[2024-01-24 12:30:24,609] [INFO] Target genome list was writen to GCF_009915155.1_ASM991515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:24,639] [INFO] Task started: fastANI
[2024-01-24 12:30:24,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg33b31979-8f6e-4c13-9d90-7f0fc3a76fb8/GCF_009915155.1_ASM991515v1_genomic.fna.gz --refList GCF_009915155.1_ASM991515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009915155.1_ASM991515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:37,906] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:37,937] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:37,937] [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_009915155.1	s__Flavobacterium sp009915155	100.0	937	938	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_003865365.1	s__Flavobacterium macacae	78.731	341	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634455.1	s__Flavobacterium endophyticum	78.2246	269	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.19	97.19	0.95	0.95	2	-
GCF_006385255.1	s__Flavobacterium microcysteis	78.1037	264	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846575.1	s__Flavobacterium lindanitolerans	77.8954	261	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.86	97.14	0.91	0.85	11	-
GCF_012911605.1	s__Flavobacterium sp012911605	77.8505	248	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638005.1	s__Flavobacterium orientale	77.7134	182	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497625.1	s__Flavobacterium sp003497625	77.5884	184	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_009495755.1	s__Flavobacterium sp009495755	77.5425	201	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122145.1	s__Flavobacterium piscinae	77.5277	200	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.76	99.76	1.00	1.00	2	-
GCF_014642275.1	s__Flavobacterium lutivivi	77.495	174	938	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	77.4891	172	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	77.4448	204	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282055.1	s__Flavobacterium sp000282055	77.4428	168	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	77.4402	205	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004797125.1	s__Flavobacterium sangjuense	77.4206	181	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454195.1	s__Flavobacterium sp002454195	77.3993	113	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119235.1	s__Flavobacterium phycosphaerae	77.3589	154	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352205.1	s__Flavobacterium sp002352205	77.2774	235	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
GCF_003312425.1	s__Flavobacterium psychrolimnae	77.2575	199	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920835.1	s__Flavobacterium sp903920835	77.1469	72	938	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	77.1374	182	938	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	77.0049	187	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422095.1	s__Flavobacterium sp002422095	76.9589	164	938	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888655.1	s__Flavobacterium sp903888655	76.9015	117	938	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 12:30:37,939] [INFO] GTDB search result was written to GCF_009915155.1_ASM991515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:37,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:37,945] [INFO] DFAST_QC result json was written to GCF_009915155.1_ASM991515v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:37,945] [INFO] DFAST_QC completed!
[2024-01-24 12:30:37,945] [INFO] Total running time: 0h1m19s