[2024-01-24 13:40:55,312] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,317] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,318] [INFO] DQC Reference Directory: /var/lib/cwl/stgce435fd0-1f61-4780-a923-361190e456e0/dqc_reference
[2024-01-24 13:40:56,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,678] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg91c2f4b3-a234-4348-beac-3be183dc275f/GCF_003970355.1_ASM397035v1_genomic.fna.gz | prodigal -d GCF_003970355.1_ASM397035v1_genomic.fna/cds.fna -a GCF_003970355.1_ASM397035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:12,051] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:12,051] [INFO] Task started: HMMsearch
[2024-01-24 13:41:12,052] [INFO] Running command: hmmsearch --tblout GCF_003970355.1_ASM397035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce435fd0-1f61-4780-a923-361190e456e0/dqc_reference/reference_markers.hmm GCF_003970355.1_ASM397035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:12,327] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:12,328] [INFO] Found 6/6 markers.
[2024-01-24 13:41:12,364] [INFO] Query marker FASTA was written to GCF_003970355.1_ASM397035v1_genomic.fna/markers.fasta
[2024-01-24 13:41:12,365] [INFO] Task started: Blastn
[2024-01-24 13:41:12,365] [INFO] Running command: blastn -query GCF_003970355.1_ASM397035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce435fd0-1f61-4780-a923-361190e456e0/dqc_reference/reference_markers.fasta -out GCF_003970355.1_ASM397035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:13,090] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:13,094] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:13,095] [INFO] Target genome list was writen to GCF_003970355.1_ASM397035v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:13,099] [INFO] Task started: fastANI
[2024-01-24 13:41:13,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg91c2f4b3-a234-4348-beac-3be183dc275f/GCF_003970355.1_ASM397035v1_genomic.fna.gz --refList GCF_003970355.1_ASM397035v1_genomic.fna/target_genomes.txt --output GCF_003970355.1_ASM397035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:27,205] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:27,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce435fd0-1f61-4780-a923-361190e456e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:27,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce435fd0-1f61-4780-a923-361190e456e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:27,219] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:27,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:27,220] [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 bomense	strain=RB1N8	GCA_003970355.1	2497483	2497483	type	True	100.0	1136	1136	95	conclusive
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	85.1665	745	1136	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	84.9296	744	1136	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	84.8452	785	1136	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	84.6701	733	1136	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	84.6501	757	1136	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	84.3693	782	1136	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	84.294	753	1136	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	83.582	699	1136	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	83.5089	700	1136	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	82.2237	682	1136	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	81.635	663	1136	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.7087	436	1136	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.0824	365	1136	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.0202	353	1136	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.9281	318	1136	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.5415	179	1136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:27,221] [INFO] DFAST Taxonomy check result was written to GCF_003970355.1_ASM397035v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:27,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:27,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:27,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce435fd0-1f61-4780-a923-361190e456e0/dqc_reference/checkm_data
[2024-01-24 13:41:27,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:27,265] [INFO] Task started: CheckM
[2024-01-24 13:41:27,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970355.1_ASM397035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970355.1_ASM397035v1_genomic.fna/checkm_input GCF_003970355.1_ASM397035v1_genomic.fna/checkm_result
[2024-01-24 13:42:13,430] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:13,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,455] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:13,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:13,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970355.1_ASM397035v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:13,456] [INFO] Task started: Blastn
[2024-01-24 13:42:13,456] [INFO] Running command: blastn -query GCF_003970355.1_ASM397035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce435fd0-1f61-4780-a923-361190e456e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970355.1_ASM397035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:14,390] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:14,394] [INFO] Selected 15 target genomes.
[2024-01-24 13:42:14,394] [INFO] Target genome list was writen to GCF_003970355.1_ASM397035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:14,422] [INFO] Task started: fastANI
[2024-01-24 13:42:14,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg91c2f4b3-a234-4348-beac-3be183dc275f/GCF_003970355.1_ASM397035v1_genomic.fna.gz --refList GCF_003970355.1_ASM397035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970355.1_ASM397035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:26,085] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:26,100] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:26,101] [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_003968755.1	s__Flavobacterium sp003968755	96.4413	920	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.86	96.58	0.85	0.82	9	conclusive
GCF_900112975.1	s__Flavobacterium xueshanense	85.1751	744	1136	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	84.9692	741	1136	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	84.8767	784	1136	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	84.7581	775	1136	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	84.7056	730	1136	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	84.5617	775	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_004349315.1	s__Flavobacterium sp004349315	84.3735	781	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.90	0.90	2	-
GCF_004349195.1	s__Flavobacterium sp004349195	84.2983	752	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350545.1	s__Flavobacterium glaciei	83.5185	699	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017995345.1	s__Flavobacterium sp017995345	82.6702	554	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.61	99.55	0.85	0.83	4	-
GCF_007097265.1	s__Flavobacterium gawalongense	82.204	684	1136	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	82.0765	678	1136	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	82.0052	646	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142885.1	s__Flavobacterium xinjiangense	81.6137	665	1136	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 13:42:26,103] [INFO] GTDB search result was written to GCF_003970355.1_ASM397035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:26,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:26,107] [INFO] DFAST_QC result json was written to GCF_003970355.1_ASM397035v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:26,108] [INFO] DFAST_QC completed!
[2024-01-24 13:42:26,108] [INFO] Total running time: 0h1m31s