[2023-06-13 22:42:41,704] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:42:41,706] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:42:41,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a19403c-65c2-4d57-819c-d1983756f1e9/dqc_reference
[2023-06-13 22:42:42,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:42:42,946] [INFO] Task started: Prodigal
[2023-06-13 22:42:42,947] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9f12a03-71bb-4c85-8dba-e868420f9163/GCA_947488535.1_ZE-Oct18-57_genomic.fna.gz | prodigal -d GCA_947488535.1_ZE-Oct18-57_genomic.fna/cds.fna -a GCA_947488535.1_ZE-Oct18-57_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:42:47,328] [INFO] Task succeeded: Prodigal
[2023-06-13 22:42:47,329] [INFO] Task started: HMMsearch
[2023-06-13 22:42:47,329] [INFO] Running command: hmmsearch --tblout GCA_947488535.1_ZE-Oct18-57_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a19403c-65c2-4d57-819c-d1983756f1e9/dqc_reference/reference_markers.hmm GCA_947488535.1_ZE-Oct18-57_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:42:47,541] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:42:47,543] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf9f12a03-71bb-4c85-8dba-e868420f9163/GCA_947488535.1_ZE-Oct18-57_genomic.fna.gz]
[2023-06-13 22:42:47,565] [INFO] Query marker FASTA was written to GCA_947488535.1_ZE-Oct18-57_genomic.fna/markers.fasta
[2023-06-13 22:42:47,565] [INFO] Task started: Blastn
[2023-06-13 22:42:47,565] [INFO] Running command: blastn -query GCA_947488535.1_ZE-Oct18-57_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a19403c-65c2-4d57-819c-d1983756f1e9/dqc_reference/reference_markers.fasta -out GCA_947488535.1_ZE-Oct18-57_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:42:48,245] [INFO] Task succeeded: Blastn
[2023-06-13 22:42:48,249] [INFO] Selected 14 target genomes.
[2023-06-13 22:42:48,250] [INFO] Target genome list was writen to GCA_947488535.1_ZE-Oct18-57_genomic.fna/target_genomes.txt
[2023-06-13 22:42:48,251] [INFO] Task started: fastANI
[2023-06-13 22:42:48,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f12a03-71bb-4c85-8dba-e868420f9163/GCA_947488535.1_ZE-Oct18-57_genomic.fna.gz --refList GCA_947488535.1_ZE-Oct18-57_genomic.fna/target_genomes.txt --output GCA_947488535.1_ZE-Oct18-57_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:42:55,958] [INFO] Task succeeded: fastANI
[2023-06-13 22:42:55,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a19403c-65c2-4d57-819c-d1983756f1e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:42:55,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a19403c-65c2-4d57-819c-d1983756f1e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:42:55,976] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:42:55,977] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:42:55,977] [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 aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	79.4168	200	372	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	79.4046	204	372	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	79.3408	200	372	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	78.9422	149	372	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	78.7004	158	372	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	78.4015	134	372	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	78.3211	168	372	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	78.3117	168	372	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.9408	112	372	95	below_threshold
Flavobacterium lacus	strain=CGMCC 1.12504	GCA_003268815.1	1353778	1353778	type	True	77.7308	102	372	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.7296	107	372	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.6857	66	372	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.667	108	372	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.3693	81	372	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:42:55,980] [INFO] DFAST Taxonomy check result was written to GCA_947488535.1_ZE-Oct18-57_genomic.fna/tc_result.tsv
[2023-06-13 22:42:55,981] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:42:55,981] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:42:55,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a19403c-65c2-4d57-819c-d1983756f1e9/dqc_reference/checkm_data
[2023-06-13 22:42:55,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:42:56,004] [INFO] Task started: CheckM
[2023-06-13 22:42:56,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947488535.1_ZE-Oct18-57_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947488535.1_ZE-Oct18-57_genomic.fna/checkm_input GCA_947488535.1_ZE-Oct18-57_genomic.fna/checkm_result
[2023-06-13 22:43:16,078] [INFO] Task succeeded: CheckM
[2023-06-13 22:43:16,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 12.96%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-13 22:43:16,112] [INFO] ===== Completeness check finished =====
[2023-06-13 22:43:16,113] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:43:16,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947488535.1_ZE-Oct18-57_genomic.fna/markers.fasta)
[2023-06-13 22:43:16,113] [INFO] Task started: Blastn
[2023-06-13 22:43:16,114] [INFO] Running command: blastn -query GCA_947488535.1_ZE-Oct18-57_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a19403c-65c2-4d57-819c-d1983756f1e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_947488535.1_ZE-Oct18-57_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:43:17,021] [INFO] Task succeeded: Blastn
[2023-06-13 22:43:17,026] [INFO] Selected 10 target genomes.
[2023-06-13 22:43:17,027] [INFO] Target genome list was writen to GCA_947488535.1_ZE-Oct18-57_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:43:17,027] [INFO] Task started: fastANI
[2023-06-13 22:43:17,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f12a03-71bb-4c85-8dba-e868420f9163/GCA_947488535.1_ZE-Oct18-57_genomic.fna.gz --refList GCA_947488535.1_ZE-Oct18-57_genomic.fna/target_genomes_gtdb.txt --output GCA_947488535.1_ZE-Oct18-57_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:43:22,057] [INFO] Task succeeded: fastANI
[2023-06-13 22:43:22,071] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 22:43:22,071] [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
GCA_903838055.1	s__Flavobacterium sp903838055	81.0624	254	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.95	0.98	0.97	3	-
GCA_013298525.1	s__Flavobacterium sp013298525	79.6449	189	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	79.6058	212	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525665.1	s__Flavobacterium sp003525665	79.5733	195	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	79.4046	204	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCA_903913315.1	s__Flavobacterium sp903913315	79.3786	183	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.66	99.66	0.86	0.86	2	-
GCA_903879645.1	s__Flavobacterium sp903879645	79.199	171	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362665.1	s__Flavobacterium dankookense	78.9562	148	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888655.1	s__Flavobacterium sp903888655	78.8868	148	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303755.1	s__Flavobacterium sp017303755	78.7435	165	372	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 22:43:22,074] [INFO] GTDB search result was written to GCA_947488535.1_ZE-Oct18-57_genomic.fna/result_gtdb.tsv
[2023-06-13 22:43:22,074] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:43:22,078] [INFO] DFAST_QC result json was written to GCA_947488535.1_ZE-Oct18-57_genomic.fna/dqc_result.json
[2023-06-13 22:43:22,078] [INFO] DFAST_QC completed!
[2023-06-13 22:43:22,078] [INFO] Total running time: 0h0m40s