[2024-01-24 12:30:18,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:18,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:18,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f6dd29e-0230-4289-8361-f18248cb2309/dqc_reference
[2024-01-24 12:30:19,754] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:19,755] [INFO] Task started: Prodigal
[2024-01-24 12:30:19,755] [INFO] Running command: gunzip -c /var/lib/cwl/stgc577abb1-0e4a-4b10-9687-346bf31651cf/GCF_014138495.1_ASM1413849v1_genomic.fna.gz | prodigal -d GCF_014138495.1_ASM1413849v1_genomic.fna/cds.fna -a GCF_014138495.1_ASM1413849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:36,888] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:36,888] [INFO] Task started: HMMsearch
[2024-01-24 12:30:36,889] [INFO] Running command: hmmsearch --tblout GCF_014138495.1_ASM1413849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f6dd29e-0230-4289-8361-f18248cb2309/dqc_reference/reference_markers.hmm GCF_014138495.1_ASM1413849v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:37,222] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:37,223] [INFO] Found 6/6 markers.
[2024-01-24 12:30:37,256] [INFO] Query marker FASTA was written to GCF_014138495.1_ASM1413849v1_genomic.fna/markers.fasta
[2024-01-24 12:30:37,257] [INFO] Task started: Blastn
[2024-01-24 12:30:37,257] [INFO] Running command: blastn -query GCF_014138495.1_ASM1413849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f6dd29e-0230-4289-8361-f18248cb2309/dqc_reference/reference_markers.fasta -out GCF_014138495.1_ASM1413849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:37,949] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:37,952] [INFO] Selected 12 target genomes.
[2024-01-24 12:30:37,953] [INFO] Target genome list was writen to GCF_014138495.1_ASM1413849v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:37,957] [INFO] Task started: fastANI
[2024-01-24 12:30:37,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgc577abb1-0e4a-4b10-9687-346bf31651cf/GCF_014138495.1_ASM1413849v1_genomic.fna.gz --refList GCF_014138495.1_ASM1413849v1_genomic.fna/target_genomes.txt --output GCF_014138495.1_ASM1413849v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:47,721] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:47,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f6dd29e-0230-4289-8361-f18248cb2309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:47,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f6dd29e-0230-4289-8361-f18248cb2309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:47,731] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:47,732] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:30:47,732] [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 gossypii	strain=DSM 100397	GCA_014138495.1	1646119	1646119	type	True	100.0	1264	1264	95	inconclusive
Flavobacterium endophyticum	strain=DSM 29537	GCA_003634455.1	1540163	1540163	type	True	97.1937	1172	1264	95	inconclusive
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	81.8067	834	1264	95	below_threshold
Flavobacterium lindanitolerans	strain=IP-10	GCA_002846575.1	428988	428988	type	True	81.5596	820	1264	95	below_threshold
Flavobacterium lindanitolerans	strain=DSM 21886	GCA_003663835.1	428988	428988	type	True	81.5554	833	1264	95	below_threshold
Flavobacterium macacae	strain=YIM 102600	GCA_003865365.1	2488993	2488993	type	True	79.8977	484	1264	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	78.0023	156	1264	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.8786	202	1264	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.6208	136	1264	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	77.6119	188	1264	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	77.3539	95	1264	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:47,733] [INFO] DFAST Taxonomy check result was written to GCF_014138495.1_ASM1413849v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:47,734] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:47,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:47,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f6dd29e-0230-4289-8361-f18248cb2309/dqc_reference/checkm_data
[2024-01-24 12:30:47,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:47,782] [INFO] Task started: CheckM
[2024-01-24 12:30:47,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138495.1_ASM1413849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138495.1_ASM1413849v1_genomic.fna/checkm_input GCF_014138495.1_ASM1413849v1_genomic.fna/checkm_result
[2024-01-24 12:31:37,098] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:37,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:37,122] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:37,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:37,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138495.1_ASM1413849v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:37,123] [INFO] Task started: Blastn
[2024-01-24 12:31:37,123] [INFO] Running command: blastn -query GCF_014138495.1_ASM1413849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f6dd29e-0230-4289-8361-f18248cb2309/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138495.1_ASM1413849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:38,146] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:38,149] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:38,150] [INFO] Target genome list was writen to GCF_014138495.1_ASM1413849v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:38,158] [INFO] Task started: fastANI
[2024-01-24 12:31:38,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgc577abb1-0e4a-4b10-9687-346bf31651cf/GCF_014138495.1_ASM1413849v1_genomic.fna.gz --refList GCF_014138495.1_ASM1413849v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138495.1_ASM1413849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:46,069] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:46,086] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:46,086] [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_003634455.1	s__Flavobacterium endophyticum	97.1937	1172	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.19	97.19	0.95	0.95	2	conclusive
GCF_006385255.1	s__Flavobacterium microcysteis	81.8005	835	1264	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	81.5678	819	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.86	97.14	0.91	0.85	11	-
GCF_003865365.1	s__Flavobacterium macacae	79.8863	485	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422705.1	s__Flavobacterium soli	78.8933	274	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007109225.1	s__Flavobacterium sp007109225	78.4902	172	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009915155.1	s__Flavobacterium sp009915155	78.4027	258	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	78.1769	165	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007341385.1	s__Flavobacterium daemonense	78.0883	206	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097635.1	s__Flavobacterium psychrotolerans	78.0317	155	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280815.1	s__Flavobacterium sp002280815	77.8818	144	1264	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	77.592	169	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:46,088] [INFO] GTDB search result was written to GCF_014138495.1_ASM1413849v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:46,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:46,093] [INFO] DFAST_QC result json was written to GCF_014138495.1_ASM1413849v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:46,093] [INFO] DFAST_QC completed!
[2024-01-24 12:31:46,094] [INFO] Total running time: 0h1m28s