[2024-01-24 11:20:49,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg827cf2ef-64cc-473e-92eb-0f7f0dce9204/dqc_reference
[2024-01-24 11:20:51,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,013] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg1296d0db-1159-4654-9783-9f1f45739fb4/GCF_003350545.1_ASM335054v1_genomic.fna.gz | prodigal -d GCF_003350545.1_ASM335054v1_genomic.fna/cds.fna -a GCF_003350545.1_ASM335054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:02,140] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:02,141] [INFO] Task started: HMMsearch
[2024-01-24 11:21:02,141] [INFO] Running command: hmmsearch --tblout GCF_003350545.1_ASM335054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg827cf2ef-64cc-473e-92eb-0f7f0dce9204/dqc_reference/reference_markers.hmm GCF_003350545.1_ASM335054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:02,375] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:02,376] [INFO] Found 6/6 markers.
[2024-01-24 11:21:02,405] [INFO] Query marker FASTA was written to GCF_003350545.1_ASM335054v1_genomic.fna/markers.fasta
[2024-01-24 11:21:02,406] [INFO] Task started: Blastn
[2024-01-24 11:21:02,406] [INFO] Running command: blastn -query GCF_003350545.1_ASM335054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg827cf2ef-64cc-473e-92eb-0f7f0dce9204/dqc_reference/reference_markers.fasta -out GCF_003350545.1_ASM335054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:03,093] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:03,098] [INFO] Selected 20 target genomes.
[2024-01-24 11:21:03,098] [INFO] Target genome list was writen to GCF_003350545.1_ASM335054v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:03,153] [INFO] Task started: fastANI
[2024-01-24 11:21:03,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg1296d0db-1159-4654-9783-9f1f45739fb4/GCF_003350545.1_ASM335054v1_genomic.fna.gz --refList GCF_003350545.1_ASM335054v1_genomic.fna/target_genomes.txt --output GCF_003350545.1_ASM335054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:18,491] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:18,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg827cf2ef-64cc-473e-92eb-0f7f0dce9204/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:18,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg827cf2ef-64cc-473e-92eb-0f7f0dce9204/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:18,512] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:21:18,512] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:18,513] [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 glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	100.0	1026	1029	95	conclusive
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	99.9865	1020	1029	95	conclusive
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	86.6718	788	1029	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	86.4102	808	1029	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	86.3458	768	1029	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	86.179	775	1029	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	85.4943	765	1029	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	85.4434	787	1029	95	below_threshold
Flavobacterium caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	85.3128	744	1029	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	85.2497	781	1029	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	83.7567	777	1029	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	82.6666	668	1029	95	below_threshold
Flavobacterium tiangeerense	strain=CGMCC 1.6847	GCA_007830355.1	459471	459471	type	True	81.6965	610	1029	95	below_threshold
Flavobacterium turcicum	strain=F-339	GCA_011365745.1	2764718	2764718	type	True	80.9483	546	1029	95	below_threshold
Flavobacterium erciyesense	strain=F-328	GCA_018069925.1	2825842	2825842	type	True	80.7868	557	1029	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	79.2594	431	1029	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.6634	380	1029	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.3583	390	1029	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	76.668	74	1029	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.2335	80	1029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:18,514] [INFO] DFAST Taxonomy check result was written to GCF_003350545.1_ASM335054v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:18,515] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:18,515] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:18,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg827cf2ef-64cc-473e-92eb-0f7f0dce9204/dqc_reference/checkm_data
[2024-01-24 11:21:18,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:18,550] [INFO] Task started: CheckM
[2024-01-24 11:21:18,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003350545.1_ASM335054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003350545.1_ASM335054v1_genomic.fna/checkm_input GCF_003350545.1_ASM335054v1_genomic.fna/checkm_result
[2024-01-24 11:21:54,587] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:54,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:54,609] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:54,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:54,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003350545.1_ASM335054v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:54,610] [INFO] Task started: Blastn
[2024-01-24 11:21:54,610] [INFO] Running command: blastn -query GCF_003350545.1_ASM335054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg827cf2ef-64cc-473e-92eb-0f7f0dce9204/dqc_reference/reference_markers_gtdb.fasta -out GCF_003350545.1_ASM335054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:55,610] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:55,615] [INFO] Selected 18 target genomes.
[2024-01-24 11:21:55,615] [INFO] Target genome list was writen to GCF_003350545.1_ASM335054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:55,629] [INFO] Task started: fastANI
[2024-01-24 11:21:55,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg1296d0db-1159-4654-9783-9f1f45739fb4/GCF_003350545.1_ASM335054v1_genomic.fna.gz --refList GCF_003350545.1_ASM335054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003350545.1_ASM335054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:10,951] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:10,978] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:10,978] [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_003350545.1	s__Flavobacterium glaciei	100.0	1026	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_003314435.2	s__Flavobacterium petrolei	86.68	788	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_002754315.1	s__Flavobacterium sp002754315	86.6171	822	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_003312425.1	s__Flavobacterium psychrolimnae	86.4101	809	1029	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	86.3708	802	1029	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	86.3303	769	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110375.1	s__Flavobacterium sinopsychrotolerans	86.1861	774	1029	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	85.4943	765	1029	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	85.4434	787	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.90	0.90	2	-
GCF_004349085.1	s__Flavobacterium caseinilyticum	85.3128	744	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112975.1	s__Flavobacterium xueshanense	85.2545	780	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812945.1	s__Flavobacterium sp000812945	82.6777	675	1029	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	82.6423	670	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_000744835.1	s__Flavobacterium sp000744835	82.6384	682	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150205.1	s__Flavobacterium sp002150205	81.9513	508	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830355.1	s__Flavobacterium tiangeerense	81.7084	609	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.91	95.91	0.85	0.85	2	-
GCF_009764685.1	s__Flavobacterium sp009764685	81.5115	581	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.83	99.83	0.96	0.96	2	-
GCF_018069925.1	s__Flavobacterium sp018069925	80.7868	557	1029	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 11:22:10,980] [INFO] GTDB search result was written to GCF_003350545.1_ASM335054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:10,981] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:10,988] [INFO] DFAST_QC result json was written to GCF_003350545.1_ASM335054v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:10,988] [INFO] DFAST_QC completed!
[2024-01-24 11:22:10,988] [INFO] Total running time: 0h1m21s