[2024-01-24 11:30:49,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,410] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3d967c5-462f-4fef-9071-f8c596481cb6/dqc_reference
[2024-01-24 11:30:50,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,636] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,636] [INFO] Running command: gunzip -c /var/lib/cwl/stg6721698e-6212-42f1-82bd-601a3419d147/GCF_007830385.1_ASM783038v1_genomic.fna.gz | prodigal -d GCF_007830385.1_ASM783038v1_genomic.fna/cds.fna -a GCF_007830385.1_ASM783038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:04,118] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:04,118] [INFO] Task started: HMMsearch
[2024-01-24 11:31:04,119] [INFO] Running command: hmmsearch --tblout GCF_007830385.1_ASM783038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3d967c5-462f-4fef-9071-f8c596481cb6/dqc_reference/reference_markers.hmm GCF_007830385.1_ASM783038v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:04,377] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:04,379] [INFO] Found 6/6 markers.
[2024-01-24 11:31:04,408] [INFO] Query marker FASTA was written to GCF_007830385.1_ASM783038v1_genomic.fna/markers.fasta
[2024-01-24 11:31:04,408] [INFO] Task started: Blastn
[2024-01-24 11:31:04,409] [INFO] Running command: blastn -query GCF_007830385.1_ASM783038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3d967c5-462f-4fef-9071-f8c596481cb6/dqc_reference/reference_markers.fasta -out GCF_007830385.1_ASM783038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:05,089] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:05,093] [INFO] Selected 10 target genomes.
[2024-01-24 11:31:05,093] [INFO] Target genome list was writen to GCF_007830385.1_ASM783038v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:05,100] [INFO] Task started: fastANI
[2024-01-24 11:31:05,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg6721698e-6212-42f1-82bd-601a3419d147/GCF_007830385.1_ASM783038v1_genomic.fna.gz --refList GCF_007830385.1_ASM783038v1_genomic.fna/target_genomes.txt --output GCF_007830385.1_ASM783038v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:11,381] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:11,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3d967c5-462f-4fef-9071-f8c596481cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:11,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3d967c5-462f-4fef-9071-f8c596481cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:11,391] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:31:11,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:11,392] [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 cauense	strain=CGMCC 1.7270	GCA_007830385.1	510946	510946	type	True	100.0	1002	1006	95	conclusive
Flavobacterium cauense	strain=R2A-7	GCA_000498475.1	510946	510946	type	True	99.991	1002	1006	95	conclusive
Flavobacterium cauense	strain=R2A-7	GCA_000769815.1	510946	510946	type	True	99.9876	993	1006	95	conclusive
Flavobacterium saliperosum	strain=CGMCC 1.3801	GCA_900100625.1	329186	329186	type	True	85.5191	754	1006	95	below_threshold
Flavobacterium saliperosum	strain=S13	GCA_000498515.1	329186	329186	type	True	85.4335	748	1006	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	78.1712	261	1006	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.1483	239	1006	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.954	269	1006	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.8917	261	1006	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.4733	186	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:31:11,394] [INFO] DFAST Taxonomy check result was written to GCF_007830385.1_ASM783038v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:11,394] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:11,394] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:11,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3d967c5-462f-4fef-9071-f8c596481cb6/dqc_reference/checkm_data
[2024-01-24 11:31:11,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:11,430] [INFO] Task started: CheckM
[2024-01-24 11:31:11,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830385.1_ASM783038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830385.1_ASM783038v1_genomic.fna/checkm_input GCF_007830385.1_ASM783038v1_genomic.fna/checkm_result
[2024-01-24 11:31:53,014] [INFO] Task succeeded: CheckM
[2024-01-24 11:31:53,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:31:53,036] [INFO] ===== Completeness check finished =====
[2024-01-24 11:31:53,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:31:53,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830385.1_ASM783038v1_genomic.fna/markers.fasta)
[2024-01-24 11:31:53,037] [INFO] Task started: Blastn
[2024-01-24 11:31:53,038] [INFO] Running command: blastn -query GCF_007830385.1_ASM783038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3d967c5-462f-4fef-9071-f8c596481cb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830385.1_ASM783038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:53,963] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:53,967] [INFO] Selected 8 target genomes.
[2024-01-24 11:31:53,967] [INFO] Target genome list was writen to GCF_007830385.1_ASM783038v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:31:53,974] [INFO] Task started: fastANI
[2024-01-24 11:31:53,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg6721698e-6212-42f1-82bd-601a3419d147/GCF_007830385.1_ASM783038v1_genomic.fna.gz --refList GCF_007830385.1_ASM783038v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830385.1_ASM783038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:31:59,231] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:59,242] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:31:59,242] [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_000498475.1	s__Flavobacterium cauense	99.991	1002	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCF_900100625.1	s__Flavobacterium saliperosum	85.5192	754	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000498535.1	s__Flavobacterium limnosediminis	82.6409	673	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498495.1	s__Flavobacterium enshiense	80.8819	609	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000430025.1	s__Flavobacterium suncheonense	80.2535	563	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014639535.1	s__Flavobacterium palustre	77.5611	206	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889745.1	s__Flavobacterium sp903889745	77.2193	162	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428305.1	s__Flavobacterium sp002428305	77.1077	165	1006	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 11:31:59,244] [INFO] GTDB search result was written to GCF_007830385.1_ASM783038v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:31:59,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:31:59,247] [INFO] DFAST_QC result json was written to GCF_007830385.1_ASM783038v1_genomic.fna/dqc_result.json
[2024-01-24 11:31:59,247] [INFO] DFAST_QC completed!
[2024-01-24 11:31:59,247] [INFO] Total running time: 0h1m10s