[2024-01-24 14:20:16,518] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:16,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:16,523] [INFO] DQC Reference Directory: /var/lib/cwl/stga7303dc0-a953-4d2f-b0ed-ba1d45c7a38b/dqc_reference
[2024-01-24 14:20:18,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:18,826] [INFO] Task started: Prodigal
[2024-01-24 14:20:18,827] [INFO] Running command: gunzip -c /var/lib/cwl/stgda9b9ef8-5bed-41ee-bec5-b2979beee988/GCF_026870155.1_ASM2687015v3_genomic.fna.gz | prodigal -d GCF_026870155.1_ASM2687015v3_genomic.fna/cds.fna -a GCF_026870155.1_ASM2687015v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:39,146] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:39,146] [INFO] Task started: HMMsearch
[2024-01-24 14:20:39,147] [INFO] Running command: hmmsearch --tblout GCF_026870155.1_ASM2687015v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7303dc0-a953-4d2f-b0ed-ba1d45c7a38b/dqc_reference/reference_markers.hmm GCF_026870155.1_ASM2687015v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:39,439] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:39,441] [INFO] Found 6/6 markers.
[2024-01-24 14:20:39,486] [INFO] Query marker FASTA was written to GCF_026870155.1_ASM2687015v3_genomic.fna/markers.fasta
[2024-01-24 14:20:39,487] [INFO] Task started: Blastn
[2024-01-24 14:20:39,487] [INFO] Running command: blastn -query GCF_026870155.1_ASM2687015v3_genomic.fna/markers.fasta -db /var/lib/cwl/stga7303dc0-a953-4d2f-b0ed-ba1d45c7a38b/dqc_reference/reference_markers.fasta -out GCF_026870155.1_ASM2687015v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:40,185] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:40,188] [INFO] Selected 19 target genomes.
[2024-01-24 14:20:40,189] [INFO] Target genome list was writen to GCF_026870155.1_ASM2687015v3_genomic.fna/target_genomes.txt
[2024-01-24 14:20:40,197] [INFO] Task started: fastANI
[2024-01-24 14:20:40,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgda9b9ef8-5bed-41ee-bec5-b2979beee988/GCF_026870155.1_ASM2687015v3_genomic.fna.gz --refList GCF_026870155.1_ASM2687015v3_genomic.fna/target_genomes.txt --output GCF_026870155.1_ASM2687015v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:56,993] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:56,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7303dc0-a953-4d2f-b0ed-ba1d45c7a38b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:56,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7303dc0-a953-4d2f-b0ed-ba1d45c7a38b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:57,015] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:57,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:57,015] [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 aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	85.7143	1087	1772	95	below_threshold
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	81.6155	830	1772	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	81.3417	828	1772	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_001761465.1	1492737	1492737	type	True	80.9499	748	1772	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_000735535.1	1492737	1492737	type	True	80.915	697	1772	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	80.2441	667	1772	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	78.9542	437	1772	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	78.8798	483	1772	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.8477	533	1772	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.7594	493	1772	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.7327	479	1772	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	78.7013	469	1772	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	78.6762	530	1772	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	78.625	426	1772	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_003148525.1	946678	946678	type	True	78.5572	481	1772	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	78.5119	461	1772	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.4888	524	1772	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	78.299	410	1772	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.4044	166	1772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:57,017] [INFO] DFAST Taxonomy check result was written to GCF_026870155.1_ASM2687015v3_genomic.fna/tc_result.tsv
[2024-01-24 14:20:57,017] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:57,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:57,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7303dc0-a953-4d2f-b0ed-ba1d45c7a38b/dqc_reference/checkm_data
[2024-01-24 14:20:57,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:57,069] [INFO] Task started: CheckM
[2024-01-24 14:20:57,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026870155.1_ASM2687015v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026870155.1_ASM2687015v3_genomic.fna/checkm_input GCF_026870155.1_ASM2687015v3_genomic.fna/checkm_result
[2024-01-24 14:21:53,979] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:53,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:54,001] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:54,002] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:54,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026870155.1_ASM2687015v3_genomic.fna/markers.fasta)
[2024-01-24 14:21:54,002] [INFO] Task started: Blastn
[2024-01-24 14:21:54,002] [INFO] Running command: blastn -query GCF_026870155.1_ASM2687015v3_genomic.fna/markers.fasta -db /var/lib/cwl/stga7303dc0-a953-4d2f-b0ed-ba1d45c7a38b/dqc_reference/reference_markers_gtdb.fasta -out GCF_026870155.1_ASM2687015v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:54,938] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:54,946] [INFO] Selected 9 target genomes.
[2024-01-24 14:21:54,946] [INFO] Target genome list was writen to GCF_026870155.1_ASM2687015v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:54,955] [INFO] Task started: fastANI
[2024-01-24 14:21:54,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgda9b9ef8-5bed-41ee-bec5-b2979beee988/GCF_026870155.1_ASM2687015v3_genomic.fna.gz --refList GCF_026870155.1_ASM2687015v3_genomic.fna/target_genomes_gtdb.txt --output GCF_026870155.1_ASM2687015v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:05,268] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:05,283] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:05,284] [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_015351475.1	s__Flavobacterium sp015351475	97.3707	1447	1772	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_003385115.1	s__Flavobacterium aquicola	85.6953	1089	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797935.1	s__Flavobacterium sp002797935	84.3951	1175	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813295.1	s__Flavobacterium sp002813295	82.3309	933	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284035.1	s__Flavobacterium sp003096795	81.7972	875	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCF_002001005.1	s__Flavobacterium sp002001005	81.7868	826	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761465.1	s__Flavobacterium gilvum	80.9606	742	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009909155.2	s__Flavobacterium undicola	78.9507	436	1772	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001507425.1	s__Flavobacterium sp001507425	78.7629	546	1772	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 14:22:05,286] [INFO] GTDB search result was written to GCF_026870155.1_ASM2687015v3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:05,287] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:05,290] [INFO] DFAST_QC result json was written to GCF_026870155.1_ASM2687015v3_genomic.fna/dqc_result.json
[2024-01-24 14:22:05,291] [INFO] DFAST_QC completed!
[2024-01-24 14:22:05,291] [INFO] Total running time: 0h1m49s