[2024-01-24 12:30:05,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,384] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfc3f25a-49ab-45a7-b0b2-160c375f7fdd/dqc_reference
[2024-01-24 12:30:07,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,249] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg788fb78c-f531-4843-b2db-21a9914549a2/GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/cds.fna -a GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:18,714] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:18,714] [INFO] Task started: HMMsearch
[2024-01-24 12:30:18,714] [INFO] Running command: hmmsearch --tblout GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfc3f25a-49ab-45a7-b0b2-160c375f7fdd/dqc_reference/reference_markers.hmm GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:19,002] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:19,003] [INFO] Found 6/6 markers.
[2024-01-24 12:30:19,030] [INFO] Query marker FASTA was written to GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:30:19,030] [INFO] Task started: Blastn
[2024-01-24 12:30:19,030] [INFO] Running command: blastn -query GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc3f25a-49ab-45a7-b0b2-160c375f7fdd/dqc_reference/reference_markers.fasta -out GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:19,700] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:19,708] [INFO] Selected 19 target genomes.
[2024-01-24 12:30:19,708] [INFO] Target genome list was writen to GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:30:19,730] [INFO] Task started: fastANI
[2024-01-24 12:30:19,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg788fb78c-f531-4843-b2db-21a9914549a2/GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna.gz --refList GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:35,615] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:35,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfc3f25a-49ab-45a7-b0b2-160c375f7fdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:35,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfc3f25a-49ab-45a7-b0b2-160c375f7fdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:35,627] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:35,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:35,627] [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 xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	100.0	1136	1139	95	conclusive
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	87.5324	831	1139	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	87.183	884	1139	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	86.6712	812	1139	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	86.6099	846	1139	95	below_threshold
Flavobacterium caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	86.0926	820	1139	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	85.5977	806	1139	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	85.5715	797	1139	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	85.2324	793	1139	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	85.1198	800	1139	95	below_threshold
Flavobacterium bomense	strain=RB1N8	GCA_003970355.1	2497483	2497483	type	True	85.0292	773	1139	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	84.4248	838	1139	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	84.164	735	1139	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	82.7635	730	1139	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.949	467	1139	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.2939	361	1139	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.2615	384	1139	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.0409	365	1139	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.0403	185	1139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:35,630] [INFO] DFAST Taxonomy check result was written to GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:30:35,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:35,631] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:35,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfc3f25a-49ab-45a7-b0b2-160c375f7fdd/dqc_reference/checkm_data
[2024-01-24 12:30:35,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:35,668] [INFO] Task started: CheckM
[2024-01-24 12:30:35,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/checkm_input GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:31:10,890] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:10,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:10,913] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:10,914] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:10,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:31:10,914] [INFO] Task started: Blastn
[2024-01-24 12:31:10,914] [INFO] Running command: blastn -query GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc3f25a-49ab-45a7-b0b2-160c375f7fdd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:11,896] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:11,899] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:11,899] [INFO] Target genome list was writen to GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:11,906] [INFO] Task started: fastANI
[2024-01-24 12:31:11,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg788fb78c-f531-4843-b2db-21a9914549a2/GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna.gz --refList GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:24,992] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:25,002] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:25,003] [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_900112975.1	s__Flavobacterium xueshanense	100.0	1136	1139	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_900110375.1	s__Flavobacterium sinopsychrotolerans	87.5613	828	1139	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	87.183	884	1139	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	86.8752	893	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634755.1	s__Flavobacterium limicola	86.6712	812	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003314435.2	s__Flavobacterium petrolei	86.5986	847	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_004349085.1	s__Flavobacterium caseinilyticum	86.1036	819	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754315.1	s__Flavobacterium sp002754315	85.8778	823	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_004349195.1	s__Flavobacterium sp004349195	85.574	808	1139	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	85.5715	797	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.90	0.90	2	-
GCF_003350545.1	s__Flavobacterium glaciei	85.2324	793	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003968755.1	s__Flavobacterium sp003968755	84.6688	757	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.86	96.58	0.85	0.82	9	-
GCF_900108015.1	s__Flavobacterium urumqiense	84.1616	736	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097265.1	s__Flavobacterium gawalongense	82.7586	730	1139	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	82.7009	714	1139	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	82.4402	700	1139	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 12:31:25,004] [INFO] GTDB search result was written to GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:25,004] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:25,007] [INFO] DFAST_QC result json was written to GCF_900112975.1_IMG-taxon_2617270785_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:31:25,007] [INFO] DFAST_QC completed!
[2024-01-24 12:31:25,007] [INFO] Total running time: 0h1m20s