[2024-01-24 12:14:09,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,816] [INFO] DQC Reference Directory: /var/lib/cwl/stga0afb7a4-2838-4317-afa5-74171c251dfa/dqc_reference
[2024-01-24 12:14:11,218] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,219] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,220] [INFO] Running command: gunzip -c /var/lib/cwl/stg89651f8b-3a0a-4423-926b-7b7cfc65c16f/GCF_007097265.1_ASM709726v1_genomic.fna.gz | prodigal -d GCF_007097265.1_ASM709726v1_genomic.fna/cds.fna -a GCF_007097265.1_ASM709726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:26,559] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:26,559] [INFO] Task started: HMMsearch
[2024-01-24 12:14:26,559] [INFO] Running command: hmmsearch --tblout GCF_007097265.1_ASM709726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0afb7a4-2838-4317-afa5-74171c251dfa/dqc_reference/reference_markers.hmm GCF_007097265.1_ASM709726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:26,886] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:26,887] [INFO] Found 6/6 markers.
[2024-01-24 12:14:26,939] [INFO] Query marker FASTA was written to GCF_007097265.1_ASM709726v1_genomic.fna/markers.fasta
[2024-01-24 12:14:26,939] [INFO] Task started: Blastn
[2024-01-24 12:14:26,939] [INFO] Running command: blastn -query GCF_007097265.1_ASM709726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0afb7a4-2838-4317-afa5-74171c251dfa/dqc_reference/reference_markers.fasta -out GCF_007097265.1_ASM709726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:27,687] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:27,690] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:27,691] [INFO] Target genome list was writen to GCF_007097265.1_ASM709726v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:27,698] [INFO] Task started: fastANI
[2024-01-24 12:14:27,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg89651f8b-3a0a-4423-926b-7b7cfc65c16f/GCF_007097265.1_ASM709726v1_genomic.fna.gz --refList GCF_007097265.1_ASM709726v1_genomic.fna/target_genomes.txt --output GCF_007097265.1_ASM709726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:40,002] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:40,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0afb7a4-2838-4317-afa5-74171c251dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:40,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0afb7a4-2838-4317-afa5-74171c251dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:40,028] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:40,028] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:40,028] [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 gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	100.0	1289	1295	95	conclusive
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	84.8306	789	1295	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	84.5292	800	1295	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	83.3628	787	1295	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	83.274	680	1295	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	83.1659	764	1295	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	83.0656	709	1295	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	82.7171	720	1295	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	82.0221	684	1295	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	79.0892	541	1295	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.4747	399	1295	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.4718	422	1295	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.2604	408	1295	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.0157	207	1295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:40,039] [INFO] DFAST Taxonomy check result was written to GCF_007097265.1_ASM709726v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:40,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:40,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:40,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0afb7a4-2838-4317-afa5-74171c251dfa/dqc_reference/checkm_data
[2024-01-24 12:14:40,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:40,100] [INFO] Task started: CheckM
[2024-01-24 12:14:40,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007097265.1_ASM709726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007097265.1_ASM709726v1_genomic.fna/checkm_input GCF_007097265.1_ASM709726v1_genomic.fna/checkm_result
[2024-01-24 12:15:26,713] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:26,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:26,741] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:26,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:26,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007097265.1_ASM709726v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:26,742] [INFO] Task started: Blastn
[2024-01-24 12:15:26,743] [INFO] Running command: blastn -query GCF_007097265.1_ASM709726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0afb7a4-2838-4317-afa5-74171c251dfa/dqc_reference/reference_markers_gtdb.fasta -out GCF_007097265.1_ASM709726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:27,752] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:27,760] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:27,760] [INFO] Target genome list was writen to GCF_007097265.1_ASM709726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:27,770] [INFO] Task started: fastANI
[2024-01-24 12:15:27,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg89651f8b-3a0a-4423-926b-7b7cfc65c16f/GCF_007097265.1_ASM709726v1_genomic.fna.gz --refList GCF_007097265.1_ASM709726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007097265.1_ASM709726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:35,233] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:35,249] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:35,249] [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_007097265.1	s__Flavobacterium gawalongense	100.0	1287	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	conclusive
GCF_000812945.1	s__Flavobacterium sp000812945	87.7202	913	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744835.1	s__Flavobacterium sp000744835	85.8829	840	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349195.1	s__Flavobacterium sp004349195	84.7878	792	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349315.1	s__Flavobacterium sp004349315	84.5496	798	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.90	0.90	2	-
GCF_002754315.1	s__Flavobacterium sp002754315	84.413	805	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_900108015.1	s__Flavobacterium urumqiense	83.1501	765	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312425.1	s__Flavobacterium psychrolimnae	83.0717	709	1295	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 12:15:35,252] [INFO] GTDB search result was written to GCF_007097265.1_ASM709726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:35,253] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:35,260] [INFO] DFAST_QC result json was written to GCF_007097265.1_ASM709726v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:35,260] [INFO] DFAST_QC completed!
[2024-01-24 12:15:35,260] [INFO] Total running time: 0h1m25s