[2024-01-24 12:23:35,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:35,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:35,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg44611b70-92ff-4ee1-b6dd-c9e613bfbc3f/dqc_reference
[2024-01-24 12:23:37,249] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:37,250] [INFO] Task started: Prodigal
[2024-01-24 12:23:37,250] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a380cca-861f-4b78-8d3a-7a38d0a44920/GCF_007097245.1_ASM709724v1_genomic.fna.gz | prodigal -d GCF_007097245.1_ASM709724v1_genomic.fna/cds.fna -a GCF_007097245.1_ASM709724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:53,238] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:53,239] [INFO] Task started: HMMsearch
[2024-01-24 12:23:53,239] [INFO] Running command: hmmsearch --tblout GCF_007097245.1_ASM709724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44611b70-92ff-4ee1-b6dd-c9e613bfbc3f/dqc_reference/reference_markers.hmm GCF_007097245.1_ASM709724v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:53,513] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:53,516] [INFO] Found 6/6 markers.
[2024-01-24 12:23:53,551] [INFO] Query marker FASTA was written to GCF_007097245.1_ASM709724v1_genomic.fna/markers.fasta
[2024-01-24 12:23:53,551] [INFO] Task started: Blastn
[2024-01-24 12:23:53,551] [INFO] Running command: blastn -query GCF_007097245.1_ASM709724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44611b70-92ff-4ee1-b6dd-c9e613bfbc3f/dqc_reference/reference_markers.fasta -out GCF_007097245.1_ASM709724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:54,247] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:54,253] [INFO] Selected 23 target genomes.
[2024-01-24 12:23:54,254] [INFO] Target genome list was writen to GCF_007097245.1_ASM709724v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:54,262] [INFO] Task started: fastANI
[2024-01-24 12:23:54,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a380cca-861f-4b78-8d3a-7a38d0a44920/GCF_007097245.1_ASM709724v1_genomic.fna.gz --refList GCF_007097245.1_ASM709724v1_genomic.fna/target_genomes.txt --output GCF_007097245.1_ASM709724v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:10,405] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:10,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44611b70-92ff-4ee1-b6dd-c9e613bfbc3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:10,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44611b70-92ff-4ee1-b6dd-c9e613bfbc3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:10,424] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:10,424] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:10,424] [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 restrictum	strain=LB1R34	GCA_007097245.1	2594428	2594428	type	True	100.0	1215	1217	95	conclusive
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.6755	477	1217	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	79.5559	432	1217	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	79.3426	405	1217	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	79.2887	437	1217	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	79.2846	435	1217	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	79.2707	470	1217	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	79.1781	427	1217	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	79.1324	484	1217	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.1209	436	1217	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	79.0787	446	1217	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	79.0576	455	1217	95	below_threshold
Flavobacterium omnivorum	strain=CGMCC 1.2747	GCA_900099915.1	178355	178355	type	True	79.0516	413	1217	95	below_threshold
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	78.9615	436	1217	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	78.9388	367	1217	95	below_threshold
Flavobacterium aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	78.6308	410	1217	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	78.6202	395	1217	95	below_threshold
Flavobacterium micromati	strain=DSM 17659	GCA_900129585.1	229205	229205	type	True	78.5659	333	1217	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.0477	313	1217	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.6257	207	1217	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.544	68	1217	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	77.34	103	1217	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	77.1608	179	1217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:10,427] [INFO] DFAST Taxonomy check result was written to GCF_007097245.1_ASM709724v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:10,427] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:10,428] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:10,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44611b70-92ff-4ee1-b6dd-c9e613bfbc3f/dqc_reference/checkm_data
[2024-01-24 12:24:10,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:10,471] [INFO] Task started: CheckM
[2024-01-24 12:24:10,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007097245.1_ASM709724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007097245.1_ASM709724v1_genomic.fna/checkm_input GCF_007097245.1_ASM709724v1_genomic.fna/checkm_result
[2024-01-24 12:24:57,639] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:57,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:57,667] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:57,667] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:57,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007097245.1_ASM709724v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:57,668] [INFO] Task started: Blastn
[2024-01-24 12:24:57,668] [INFO] Running command: blastn -query GCF_007097245.1_ASM709724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44611b70-92ff-4ee1-b6dd-c9e613bfbc3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007097245.1_ASM709724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:58,579] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:58,585] [INFO] Selected 19 target genomes.
[2024-01-24 12:24:58,585] [INFO] Target genome list was writen to GCF_007097245.1_ASM709724v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:58,597] [INFO] Task started: fastANI
[2024-01-24 12:24:58,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a380cca-861f-4b78-8d3a-7a38d0a44920/GCF_007097245.1_ASM709724v1_genomic.fna.gz --refList GCF_007097245.1_ASM709724v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007097245.1_ASM709724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:12,201] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:12,223] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:12,223] [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_007097245.1	s__Flavobacterium sp007097245	100.0	1215	1217	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_007097265.1	s__Flavobacterium gawalongense	79.6522	480	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_000812945.1	s__Flavobacterium sp000812945	79.6223	514	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097655.1	s__Flavobacterium laiguense	79.5559	432	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097385.1	s__Flavobacterium sp007097385	79.4837	451	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752255.1	s__Flavobacterium sp015752255	79.2737	437	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097365.1	s__Flavobacterium franklandianum	79.2716	470	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCF_013284035.1	s__Flavobacterium sp003096795	79.2378	460	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCF_003312425.1	s__Flavobacterium psychrolimnae	79.0896	444	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920895.1	s__Flavobacterium alvei	79.07	455	1217	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	79.0082	445	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277675.1	s__Flavobacterium soyangense	78.979	416	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254745.1	s__Flavobacterium aquariorum	78.9551	437	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413745.1	s__Flavobacterium sp002413745	78.9082	419	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
GCA_013823965.1	s__Flavobacterium sp013823965	78.633	381	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129585.1	s__Flavobacterium micromati	78.5792	332	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	78.5019	285	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861155.1	s__Flavobacterium sp903861155	78.4218	350	1217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.81	99.81	0.91	0.91	2	-
GCF_000425465.1	s__Flavobacterium filum	77.1602	180	1217	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 12:25:12,225] [INFO] GTDB search result was written to GCF_007097245.1_ASM709724v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:12,226] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:12,231] [INFO] DFAST_QC result json was written to GCF_007097245.1_ASM709724v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:12,231] [INFO] DFAST_QC completed!
[2024-01-24 12:25:12,231] [INFO] Total running time: 0h1m36s