[2024-01-24 12:31:50,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:50,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:50,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg2971a43a-bff7-47a3-a8c3-1e048983b9ba/dqc_reference
[2024-01-24 12:31:51,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:51,839] [INFO] Task started: Prodigal
[2024-01-24 12:31:51,839] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e41c220-4b6d-4307-b668-4d4a5b11a353/GCF_000498535.1_Flim1.0_genomic.fna.gz | prodigal -d GCF_000498535.1_Flim1.0_genomic.fna/cds.fna -a GCF_000498535.1_Flim1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:06,461] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:06,462] [INFO] Task started: HMMsearch
[2024-01-24 12:32:06,462] [INFO] Running command: hmmsearch --tblout GCF_000498535.1_Flim1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2971a43a-bff7-47a3-a8c3-1e048983b9ba/dqc_reference/reference_markers.hmm GCF_000498535.1_Flim1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:06,717] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:06,718] [INFO] Found 6/6 markers.
[2024-01-24 12:32:06,753] [INFO] Query marker FASTA was written to GCF_000498535.1_Flim1.0_genomic.fna/markers.fasta
[2024-01-24 12:32:06,754] [INFO] Task started: Blastn
[2024-01-24 12:32:06,754] [INFO] Running command: blastn -query GCF_000498535.1_Flim1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2971a43a-bff7-47a3-a8c3-1e048983b9ba/dqc_reference/reference_markers.fasta -out GCF_000498535.1_Flim1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:07,455] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:07,459] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:07,459] [INFO] Target genome list was writen to GCF_000498535.1_Flim1.0_genomic.fna/target_genomes.txt
[2024-01-24 12:32:07,465] [INFO] Task started: fastANI
[2024-01-24 12:32:07,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e41c220-4b6d-4307-b668-4d4a5b11a353/GCF_000498535.1_Flim1.0_genomic.fna.gz --refList GCF_000498535.1_Flim1.0_genomic.fna/target_genomes.txt --output GCF_000498535.1_Flim1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:15,232] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:15,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2971a43a-bff7-47a3-a8c3-1e048983b9ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:15,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2971a43a-bff7-47a3-a8c3-1e048983b9ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:15,246] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:15,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:15,246] [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 limnosediminis	strain=JC2902	GCA_000498535.1	1401027	1401027	type	True	100.0	1127	1128	95	conclusive
Flavobacterium saliperosum	strain=S13	GCA_000498515.1	329186	329186	type	True	83.182	654	1128	95	below_threshold
Flavobacterium saliperosum	strain=CGMCC 1.3801	GCA_900100625.1	329186	329186	type	True	83.0559	676	1128	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000769815.1	510946	510946	type	True	82.6546	672	1128	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000498475.1	510946	510946	type	True	82.6445	682	1128	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000498495.1	1341165	1341165	type	True	82.5999	754	1128	95	below_threshold
Flavobacterium cauense	strain=CGMCC 1.7270	GCA_007830385.1	510946	510946	type	True	82.5995	677	1128	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000769895.1	1341165	1341165	type	True	82.583	761	1128	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.95	251	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:15,248] [INFO] DFAST Taxonomy check result was written to GCF_000498535.1_Flim1.0_genomic.fna/tc_result.tsv
[2024-01-24 12:32:15,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:15,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:15,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2971a43a-bff7-47a3-a8c3-1e048983b9ba/dqc_reference/checkm_data
[2024-01-24 12:32:15,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:15,286] [INFO] Task started: CheckM
[2024-01-24 12:32:15,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000498535.1_Flim1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000498535.1_Flim1.0_genomic.fna/checkm_input GCF_000498535.1_Flim1.0_genomic.fna/checkm_result
[2024-01-24 12:33:00,445] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:00,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:00,469] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:00,469] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:00,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000498535.1_Flim1.0_genomic.fna/markers.fasta)
[2024-01-24 12:33:00,470] [INFO] Task started: Blastn
[2024-01-24 12:33:00,470] [INFO] Running command: blastn -query GCF_000498535.1_Flim1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg2971a43a-bff7-47a3-a8c3-1e048983b9ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_000498535.1_Flim1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:01,390] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:01,395] [INFO] Selected 7 target genomes.
[2024-01-24 12:33:01,395] [INFO] Target genome list was writen to GCF_000498535.1_Flim1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:01,406] [INFO] Task started: fastANI
[2024-01-24 12:33:01,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e41c220-4b6d-4307-b668-4d4a5b11a353/GCF_000498535.1_Flim1.0_genomic.fna.gz --refList GCF_000498535.1_Flim1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000498535.1_Flim1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:06,525] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:06,539] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:06,540] [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_000498535.1	s__Flavobacterium limnosediminis	100.0	1127	1128	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_900100625.1	s__Flavobacterium saliperosum	83.0685	675	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000498475.1	s__Flavobacterium cauense	82.6446	682	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000498495.1	s__Flavobacterium enshiense	82.6073	753	1128	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	79.7192	473	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013389455.1	s__Flavobacterium sp001898245	78.7154	320	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.49	98.42	0.93	0.92	4	-
GCF_004122165.1	s__Flavobacterium sp004122165	78.0428	213	1128	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
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[2024-01-24 12:33:06,542] [INFO] GTDB search result was written to GCF_000498535.1_Flim1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:06,543] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:06,547] [INFO] DFAST_QC result json was written to GCF_000498535.1_Flim1.0_genomic.fna/dqc_result.json
[2024-01-24 12:33:06,548] [INFO] DFAST_QC completed!
[2024-01-24 12:33:06,548] [INFO] Total running time: 0h1m16s