[2024-01-24 11:09:50,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,720] [INFO] DQC Reference Directory: /var/lib/cwl/stgb00f1dee-691b-467b-ac2a-179154349f83/dqc_reference
[2024-01-24 11:09:53,305] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,306] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,307] [INFO] Running command: gunzip -c /var/lib/cwl/stga2ba7566-2e38-4a63-982a-38ec6b718946/GCF_003097535.1_ASM309753v1_genomic.fna.gz | prodigal -d GCF_003097535.1_ASM309753v1_genomic.fna/cds.fna -a GCF_003097535.1_ASM309753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:11,526] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:11,526] [INFO] Task started: HMMsearch
[2024-01-24 11:10:11,526] [INFO] Running command: hmmsearch --tblout GCF_003097535.1_ASM309753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb00f1dee-691b-467b-ac2a-179154349f83/dqc_reference/reference_markers.hmm GCF_003097535.1_ASM309753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:11,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:11,794] [INFO] Found 6/6 markers.
[2024-01-24 11:10:11,825] [INFO] Query marker FASTA was written to GCF_003097535.1_ASM309753v1_genomic.fna/markers.fasta
[2024-01-24 11:10:11,826] [INFO] Task started: Blastn
[2024-01-24 11:10:11,826] [INFO] Running command: blastn -query GCF_003097535.1_ASM309753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00f1dee-691b-467b-ac2a-179154349f83/dqc_reference/reference_markers.fasta -out GCF_003097535.1_ASM309753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:12,475] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:12,479] [INFO] Selected 14 target genomes.
[2024-01-24 11:10:12,479] [INFO] Target genome list was writen to GCF_003097535.1_ASM309753v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:12,488] [INFO] Task started: fastANI
[2024-01-24 11:10:12,489] [INFO] Running command: fastANI --query /var/lib/cwl/stga2ba7566-2e38-4a63-982a-38ec6b718946/GCF_003097535.1_ASM309753v1_genomic.fna.gz --refList GCF_003097535.1_ASM309753v1_genomic.fna/target_genomes.txt --output GCF_003097535.1_ASM309753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:21,229] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:21,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb00f1dee-691b-467b-ac2a-179154349f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:21,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb00f1dee-691b-467b-ac2a-179154349f83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:21,243] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:10:21,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:21,244] [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 pallidum	strain=HYN0049	GCA_003097535.1	2172098	2172098	type	True	100.0	1184	1184	95	conclusive
Flavobacterium magnum	strain=HYN0048	GCA_003055625.1	2162713	2162713	type	True	81.099	717	1184	95	below_threshold
Flavobacterium psychrotolerans	strain=RB1R5	GCA_003097635.1	2169410	2169410	type	True	77.626	103	1184	95	below_threshold
Flavobacterium noncentrifugens	strain=CGMCC 1.10076	GCA_900100375.1	1128970	1128970	type	True	77.6016	258	1184	95	below_threshold
Flavobacterium noncentrifugens	strain=NBRC 108844	GCA_007992475.1	1128970	1128970	type	True	77.5719	259	1184	95	below_threshold
Flavobacterium lindanitolerans	strain=DSM 21886	GCA_003663835.1	428988	428988	type	True	77.5006	149	1184	95	below_threshold
Flavobacterium soli	strain=DSM 19725	GCA_000422705.1	344881	344881	type	True	77.4393	157	1184	95	below_threshold
Flavobacterium lindanitolerans	strain=IP-10	GCA_002846575.1	428988	428988	type	True	77.4062	150	1184	95	below_threshold
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	77.3983	131	1184	95	below_threshold
Flavobacterium supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	77.2574	103	1184	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	77.0767	108	1184	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	77.0297	99	1184	95	below_threshold
Flavobacterium caeni	strain=CGMCC 1.7031	GCA_900101895.1	490189	490189	type	True	76.8264	161	1184	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:21,246] [INFO] DFAST Taxonomy check result was written to GCF_003097535.1_ASM309753v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:21,246] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:21,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:21,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb00f1dee-691b-467b-ac2a-179154349f83/dqc_reference/checkm_data
[2024-01-24 11:10:21,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:21,284] [INFO] Task started: CheckM
[2024-01-24 11:10:21,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003097535.1_ASM309753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003097535.1_ASM309753v1_genomic.fna/checkm_input GCF_003097535.1_ASM309753v1_genomic.fna/checkm_result
[2024-01-24 11:11:15,034] [INFO] Task succeeded: CheckM
[2024-01-24 11:11:15,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:11:15,059] [INFO] ===== Completeness check finished =====
[2024-01-24 11:11:15,059] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:11:15,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003097535.1_ASM309753v1_genomic.fna/markers.fasta)
[2024-01-24 11:11:15,060] [INFO] Task started: Blastn
[2024-01-24 11:11:15,060] [INFO] Running command: blastn -query GCF_003097535.1_ASM309753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00f1dee-691b-467b-ac2a-179154349f83/dqc_reference/reference_markers_gtdb.fasta -out GCF_003097535.1_ASM309753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:11:15,933] [INFO] Task succeeded: Blastn
[2024-01-24 11:11:15,937] [INFO] Selected 15 target genomes.
[2024-01-24 11:11:15,937] [INFO] Target genome list was writen to GCF_003097535.1_ASM309753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:11:15,949] [INFO] Task started: fastANI
[2024-01-24 11:11:15,949] [INFO] Running command: fastANI --query /var/lib/cwl/stga2ba7566-2e38-4a63-982a-38ec6b718946/GCF_003097535.1_ASM309753v1_genomic.fna.gz --refList GCF_003097535.1_ASM309753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003097535.1_ASM309753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:11:26,712] [INFO] Task succeeded: fastANI
[2024-01-24 11:11:26,729] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:11:26,729] [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_003097535.1	s__Flavobacterium pallidum	100.0	1183	1184	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_003055625.1	s__Flavobacterium magnum	81.0856	716	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256285.1	s__Flavobacterium sp002256285	79.3034	474	1184	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	77.626	103	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100375.1	s__Flavobacterium noncentrifugens	77.5973	257	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002483285.1	s__Flavobacterium sp002483285	77.445	186	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385255.1	s__Flavobacterium microcysteis	77.4209	130	1184	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	77.4208	155	1184	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	77.4062	150	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.86	97.14	0.91	0.85	11	-
GCF_017875765.1	s__Flavobacterium sp017875765	77.3856	120	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_014748335.1	s__Flavobacterium sp014748335	77.1144	109	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003968755.1	s__Flavobacterium sp003968755	77.0927	91	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.86	96.58	0.85	0.82	9	-
GCF_900101895.1	s__Flavobacterium caeni	76.8397	160	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013401995.1	s__Flavobacterium agri	76.797	138	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903839195.1	s__Flavobacterium sp903839195	76.6163	85	1184	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:11:26,731] [INFO] GTDB search result was written to GCF_003097535.1_ASM309753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:11:26,731] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:11:26,735] [INFO] DFAST_QC result json was written to GCF_003097535.1_ASM309753v1_genomic.fna/dqc_result.json
[2024-01-24 11:11:26,735] [INFO] DFAST_QC completed!
[2024-01-24 11:11:26,735] [INFO] Total running time: 0h1m36s