[2024-01-24 14:28:17,878] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:17,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:17,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg1510f2b4-1f35-4613-baee-f305543cbde9/dqc_reference
[2024-01-24 14:28:20,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,482] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,482] [INFO] Running command: gunzip -c /var/lib/cwl/stg27a35762-5483-46ec-bdd5-79f34cf622bd/GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/cds.fna -a GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:35,087] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:35,088] [INFO] Task started: HMMsearch
[2024-01-24 14:28:35,088] [INFO] Running command: hmmsearch --tblout GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1510f2b4-1f35-4613-baee-f305543cbde9/dqc_reference/reference_markers.hmm GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:35,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:35,403] [INFO] Found 6/6 markers.
[2024-01-24 14:28:35,439] [INFO] Query marker FASTA was written to GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:28:35,440] [INFO] Task started: Blastn
[2024-01-24 14:28:35,440] [INFO] Running command: blastn -query GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1510f2b4-1f35-4613-baee-f305543cbde9/dqc_reference/reference_markers.fasta -out GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:36,196] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:36,200] [INFO] Selected 17 target genomes.
[2024-01-24 14:28:36,200] [INFO] Target genome list was writen to GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:28:36,207] [INFO] Task started: fastANI
[2024-01-24 14:28:36,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a35762-5483-46ec-bdd5-79f34cf622bd/GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna.gz --refList GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:50,242] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:50,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1510f2b4-1f35-4613-baee-f305543cbde9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:50,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1510f2b4-1f35-4613-baee-f305543cbde9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:50,262] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:50,262] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:50,263] [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 xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	99.9999	1281	1285	95	conclusive
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	87.8374	929	1285	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	83.3361	794	1285	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	83.0627	786	1285	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	82.9776	755	1285	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	82.6362	702	1285	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	82.6115	738	1285	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	82.4598	738	1285	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	82.4171	716	1285	95	below_threshold
Flavobacterium caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	82.1785	705	1285	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	82.0985	713	1285	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	81.5836	683	1285	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	79.3557	494	1285	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.7935	379	1285	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.3959	395	1285	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	76.6973	81	1285	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	76.2965	54	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:50,265] [INFO] DFAST Taxonomy check result was written to GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:28:50,265] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:50,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:50,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1510f2b4-1f35-4613-baee-f305543cbde9/dqc_reference/checkm_data
[2024-01-24 14:28:50,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:50,307] [INFO] Task started: CheckM
[2024-01-24 14:28:50,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/checkm_input GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:29:35,788] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:35,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:35,811] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:35,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:35,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:29:35,813] [INFO] Task started: Blastn
[2024-01-24 14:29:35,813] [INFO] Running command: blastn -query GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1510f2b4-1f35-4613-baee-f305543cbde9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:36,847] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:36,851] [INFO] Selected 14 target genomes.
[2024-01-24 14:29:36,851] [INFO] Target genome list was writen to GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:36,860] [INFO] Task started: fastANI
[2024-01-24 14:29:36,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a35762-5483-46ec-bdd5-79f34cf622bd/GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna.gz --refList GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:49,288] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:49,305] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:49,306] [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_900142885.1	s__Flavobacterium xinjiangense	99.9999	1281	1285	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_900108015.1	s__Flavobacterium urumqiense	87.8374	929	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875765.1	s__Flavobacterium sp017875765	84.3941	851	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_000812945.1	s__Flavobacterium sp000812945	84.2533	841	1285	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	83.7982	813	1285	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	83.3594	792	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_004349315.1	s__Flavobacterium sp004349315	83.06	787	1285	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	83.0343	770	1285	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	82.954	757	1285	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	82.4577	738	1285	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	82.4137	716	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_015752255.1	s__Flavobacterium sp015752255	82.3952	732	1285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349085.1	s__Flavobacterium caseinilyticum	82.1532	707	1285	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	82.088	714	1285	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 14:29:49,307] [INFO] GTDB search result was written to GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:49,308] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:49,312] [INFO] DFAST_QC result json was written to GCF_900142885.1_IMG-taxon_2663762760_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:29:49,312] [INFO] DFAST_QC completed!
[2024-01-24 14:29:49,312] [INFO] Total running time: 0h1m31s