[2023-06-29 23:47:53,410] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:47:53,415] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:47:53,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg251af6b0-8d6d-42c5-91b1-739ff3708fce/dqc_reference
[2023-06-29 23:47:54,655] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:47:54,656] [INFO] Task started: Prodigal
[2023-06-29 23:47:54,657] [INFO] Running command: gunzip -c /var/lib/cwl/stgb02a7e50-cc3e-4656-bfe5-8613697cb50e/GCA_024644655.1_ASM2464465v1_genomic.fna.gz | prodigal -d GCA_024644655.1_ASM2464465v1_genomic.fna/cds.fna -a GCA_024644655.1_ASM2464465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:48:06,041] [INFO] Task succeeded: Prodigal
[2023-06-29 23:48:06,041] [INFO] Task started: HMMsearch
[2023-06-29 23:48:06,041] [INFO] Running command: hmmsearch --tblout GCA_024644655.1_ASM2464465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg251af6b0-8d6d-42c5-91b1-739ff3708fce/dqc_reference/reference_markers.hmm GCA_024644655.1_ASM2464465v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:48:06,299] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:48:06,300] [INFO] Found 6/6 markers.
[2023-06-29 23:48:06,339] [INFO] Query marker FASTA was written to GCA_024644655.1_ASM2464465v1_genomic.fna/markers.fasta
[2023-06-29 23:48:06,340] [INFO] Task started: Blastn
[2023-06-29 23:48:06,340] [INFO] Running command: blastn -query GCA_024644655.1_ASM2464465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg251af6b0-8d6d-42c5-91b1-739ff3708fce/dqc_reference/reference_markers.fasta -out GCA_024644655.1_ASM2464465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:48:07,044] [INFO] Task succeeded: Blastn
[2023-06-29 23:48:07,048] [INFO] Selected 24 target genomes.
[2023-06-29 23:48:07,049] [INFO] Target genome list was writen to GCA_024644655.1_ASM2464465v1_genomic.fna/target_genomes.txt
[2023-06-29 23:48:07,054] [INFO] Task started: fastANI
[2023-06-29 23:48:07,054] [INFO] Running command: fastANI --query /var/lib/cwl/stgb02a7e50-cc3e-4656-bfe5-8613697cb50e/GCA_024644655.1_ASM2464465v1_genomic.fna.gz --refList GCA_024644655.1_ASM2464465v1_genomic.fna/target_genomes.txt --output GCA_024644655.1_ASM2464465v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:48:21,174] [INFO] Task succeeded: fastANI
[2023-06-29 23:48:21,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg251af6b0-8d6d-42c5-91b1-739ff3708fce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:48:21,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg251af6b0-8d6d-42c5-91b1-739ff3708fce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:48:21,193] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:48:21,193] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:48:21,193] [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 phycosphaerae	strain=MK012	GCA_010119235.1	2697515	2697515	type	True	78.8752	332	929	95	below_threshold
Flavobacterium silvisoli	strain=RD-2-33	GCA_004329815.1	2529433	2529433	type	True	78.6678	268	929	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	78.6545	274	929	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	78.4029	244	929	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	78.3158	250	929	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	78.1658	190	929	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	78.1204	196	929	95	below_threshold
Flavobacterium aciduliphilum	strain=DSM 25663	GCA_003268855.1	1101402	1101402	type	True	77.6493	199	929	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	77.58	162	929	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.5114	118	929	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	77.4939	147	929	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.3572	159	929	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.3471	152	929	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	77.339	141	929	95	below_threshold
Flavobacterium cucumis	strain=DSM 18830	GCA_900148835.1	416016	416016	type	True	77.293	146	929	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	77.2106	157	929	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.2089	143	929	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	77.1864	135	929	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	77.1417	153	929	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	77.0064	136	929	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.9699	137	929	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	76.855	147	929	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	76.855	147	929	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:48:21,196] [INFO] DFAST Taxonomy check result was written to GCA_024644655.1_ASM2464465v1_genomic.fna/tc_result.tsv
[2023-06-29 23:48:21,196] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:48:21,196] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:48:21,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg251af6b0-8d6d-42c5-91b1-739ff3708fce/dqc_reference/checkm_data
[2023-06-29 23:48:21,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:48:21,230] [INFO] Task started: CheckM
[2023-06-29 23:48:21,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024644655.1_ASM2464465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024644655.1_ASM2464465v1_genomic.fna/checkm_input GCA_024644655.1_ASM2464465v1_genomic.fna/checkm_result
[2023-06-29 23:48:59,635] [INFO] Task succeeded: CheckM
[2023-06-29 23:48:59,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.61%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 23:48:59,658] [INFO] ===== Completeness check finished =====
[2023-06-29 23:48:59,659] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:48:59,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024644655.1_ASM2464465v1_genomic.fna/markers.fasta)
[2023-06-29 23:48:59,659] [INFO] Task started: Blastn
[2023-06-29 23:48:59,660] [INFO] Running command: blastn -query GCA_024644655.1_ASM2464465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg251af6b0-8d6d-42c5-91b1-739ff3708fce/dqc_reference/reference_markers_gtdb.fasta -out GCA_024644655.1_ASM2464465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:49:00,643] [INFO] Task succeeded: Blastn
[2023-06-29 23:49:00,648] [INFO] Selected 24 target genomes.
[2023-06-29 23:49:00,649] [INFO] Target genome list was writen to GCA_024644655.1_ASM2464465v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:49:00,674] [INFO] Task started: fastANI
[2023-06-29 23:49:00,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgb02a7e50-cc3e-4656-bfe5-8613697cb50e/GCA_024644655.1_ASM2464465v1_genomic.fna.gz --refList GCA_024644655.1_ASM2464465v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024644655.1_ASM2464465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:49:14,537] [INFO] Task succeeded: fastANI
[2023-06-29 23:49:14,556] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 23:49:14,556] [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_010119235.1	s__Flavobacterium phycosphaerae	78.8899	331	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014486695.1	s__Flavobacterium buctense	78.8114	269	929	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	78.7823	289	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004329815.1	s__Flavobacterium silvisoli	78.6678	268	929	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	78.6545	274	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013072765.1	s__Flavobacterium sp013072765	78.6524	287	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634615.1	s__Flavobacterium sp002482945	78.4713	312	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.37	98.37	0.85	0.85	2	-
GCF_012911605.1	s__Flavobacterium sp012911605	78.4192	243	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362665.1	s__Flavobacterium dankookense	78.3086	249	929	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	78.2172	231	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913315.1	s__Flavobacterium sp903913315	77.9314	243	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.66	99.66	0.86	0.86	2	-
GCA_017303755.1	s__Flavobacterium sp017303755	77.824	219	929	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	77.6324	146	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169355.1	s__Flavobacterium sp000169355	77.6114	164	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCA_003497625.1	s__Flavobacterium sp003497625	77.4731	156	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_014379405.1	s__Flavobacterium sp014379405	77.4657	100	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642275.1	s__Flavobacterium lutivivi	77.4487	221	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016525.1	s__Flavobacterium sufflavum	77.3417	140	929	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	77.2446	159	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
GCF_900112975.1	s__Flavobacterium xueshanense	77.1864	135	929	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	77.1034	123	929	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	77.0227	138	929	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	76.9361	132	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	76.855	147	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-29 23:49:14,558] [INFO] GTDB search result was written to GCA_024644655.1_ASM2464465v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:49:14,559] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:49:14,564] [INFO] DFAST_QC result json was written to GCA_024644655.1_ASM2464465v1_genomic.fna/dqc_result.json
[2023-06-29 23:49:14,564] [INFO] DFAST_QC completed!
[2023-06-29 23:49:14,564] [INFO] Total running time: 0h1m21s