[2024-01-25 17:43:05,428] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:05,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:05,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d8ac6cd-47fb-4846-b1eb-047f7808c326/dqc_reference
[2024-01-25 17:43:06,534] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:06,535] [INFO] Task started: Prodigal
[2024-01-25 17:43:06,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fc112b2-bd53-4295-8953-ce5c5639dc31/GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/cds.fna -a GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:19,203] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:19,204] [INFO] Task started: HMMsearch
[2024-01-25 17:43:19,204] [INFO] Running command: hmmsearch --tblout GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d8ac6cd-47fb-4846-b1eb-047f7808c326/dqc_reference/reference_markers.hmm GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:19,501] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:19,502] [INFO] Found 6/6 markers.
[2024-01-25 17:43:19,538] [INFO] Query marker FASTA was written to GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 17:43:19,539] [INFO] Task started: Blastn
[2024-01-25 17:43:19,539] [INFO] Running command: blastn -query GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d8ac6cd-47fb-4846-b1eb-047f7808c326/dqc_reference/reference_markers.fasta -out GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:20,209] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:20,212] [INFO] Selected 17 target genomes.
[2024-01-25 17:43:20,213] [INFO] Target genome list was writen to GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 17:43:20,241] [INFO] Task started: fastANI
[2024-01-25 17:43:20,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fc112b2-bd53-4295-8953-ce5c5639dc31/GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna.gz --refList GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:34,755] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:34,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d8ac6cd-47fb-4846-b1eb-047f7808c326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:34,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d8ac6cd-47fb-4846-b1eb-047f7808c326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:34,767] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:34,767] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:34,767] [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 gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	100.0	1441	1442	95	conclusive
Flavobacterium frigoris	strain=DSM 15719	GCA_900111075.1	229204	229204	type	True	89.2601	1003	1442	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	84.3067	837	1442	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	81.4071	725	1442	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	80.2192	629	1442	95	below_threshold
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	79.9268	495	1442	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	79.7941	537	1442	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	79.697	578	1442	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.6491	554	1442	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	79.591	487	1442	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.5653	562	1442	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	79.4722	528	1442	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.3267	440	1442	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.2176	364	1442	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.1066	355	1442	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.2244	188	1442	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	76.8572	119	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:34,769] [INFO] DFAST Taxonomy check result was written to GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 17:43:34,770] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:34,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:34,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d8ac6cd-47fb-4846-b1eb-047f7808c326/dqc_reference/checkm_data
[2024-01-25 17:43:34,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:34,815] [INFO] Task started: CheckM
[2024-01-25 17:43:34,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/checkm_input GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 17:44:12,753] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:12,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:12,773] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:12,773] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:12,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 17:44:12,774] [INFO] Task started: Blastn
[2024-01-25 17:44:12,774] [INFO] Running command: blastn -query GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d8ac6cd-47fb-4846-b1eb-047f7808c326/dqc_reference/reference_markers_gtdb.fasta -out GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:13,756] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:13,759] [INFO] Selected 7 target genomes.
[2024-01-25 17:44:13,759] [INFO] Target genome list was writen to GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:13,764] [INFO] Task started: fastANI
[2024-01-25 17:44:13,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fc112b2-bd53-4295-8953-ce5c5639dc31/GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna.gz --refList GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:20,286] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:20,292] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:20,292] [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_900107635.1	s__Flavobacterium gillisiae	100.0	1441	1442	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_900111075.1	s__Flavobacterium frigoris	89.2609	1004	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836475.1	s__Flavobacterium sp002836475	85.4962	881	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264055.1	s__Flavobacterium sp000264055	85.0428	885	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349145.1	s__Flavobacterium hiemivividum	84.2951	838	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	-
GCF_014305155.1	s__Flavobacterium sp014305155	80.2315	628	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013294025.1	s__Flavobacterium sp013294025	80.0062	506	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:20,294] [INFO] GTDB search result was written to GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:20,296] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:20,301] [INFO] DFAST_QC result json was written to GCF_900107635.1_IMG-taxon_2693429912_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 17:44:20,301] [INFO] DFAST_QC completed!
[2024-01-25 17:44:20,302] [INFO] Total running time: 0h1m15s