[2024-01-24 11:26:54,312] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,316] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf3b5532-cbfe-4322-ba23-7fde6b220c77/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd5ef103-2885-4cd5-aaf9-af6cc53f58f6/GCF_001697185.1_ASM169718v1_genomic.fna.gz | prodigal -d GCF_001697185.1_ASM169718v1_genomic.fna/cds.fna -a GCF_001697185.1_ASM169718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:08,880] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:08,881] [INFO] Task started: HMMsearch
[2024-01-24 11:27:08,881] [INFO] Running command: hmmsearch --tblout GCF_001697185.1_ASM169718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf3b5532-cbfe-4322-ba23-7fde6b220c77/dqc_reference/reference_markers.hmm GCF_001697185.1_ASM169718v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:09,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:09,188] [INFO] Found 6/6 markers.
[2024-01-24 11:27:09,219] [INFO] Query marker FASTA was written to GCF_001697185.1_ASM169718v1_genomic.fna/markers.fasta
[2024-01-24 11:27:09,220] [INFO] Task started: Blastn
[2024-01-24 11:27:09,220] [INFO] Running command: blastn -query GCF_001697185.1_ASM169718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf3b5532-cbfe-4322-ba23-7fde6b220c77/dqc_reference/reference_markers.fasta -out GCF_001697185.1_ASM169718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:09,951] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:09,954] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:09,954] [INFO] Target genome list was writen to GCF_001697185.1_ASM169718v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:09,971] [INFO] Task started: fastANI
[2024-01-24 11:27:09,971] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd5ef103-2885-4cd5-aaf9-af6cc53f58f6/GCF_001697185.1_ASM169718v1_genomic.fna.gz --refList GCF_001697185.1_ASM169718v1_genomic.fna/target_genomes.txt --output GCF_001697185.1_ASM169718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:16,579] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:16,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf3b5532-cbfe-4322-ba23-7fde6b220c77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:16,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf3b5532-cbfe-4322-ba23-7fde6b220c77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:16,596] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:16,597] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:16,597] [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
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	100.0	1140	1142	95	conclusive
Wenyingzhuangia marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	85.3405	687	1142	95	below_threshold
Wenyingzhuangia marina	strain=DSM 100572	GCA_900130035.1	1195760	1195760	type	True	85.3144	690	1142	95	below_threshold
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	82.3219	628	1142	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	81.7078	591	1142	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.6472	181	1142	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.5813	175	1142	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.3843	182	1142	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.2968	199	1142	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.9619	183	1142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:16,599] [INFO] DFAST Taxonomy check result was written to GCF_001697185.1_ASM169718v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:16,600] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:16,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:16,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf3b5532-cbfe-4322-ba23-7fde6b220c77/dqc_reference/checkm_data
[2024-01-24 11:27:16,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:16,642] [INFO] Task started: CheckM
[2024-01-24 11:27:16,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001697185.1_ASM169718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001697185.1_ASM169718v1_genomic.fna/checkm_input GCF_001697185.1_ASM169718v1_genomic.fna/checkm_result
[2024-01-24 11:27:51,498] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:51,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:51,518] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:51,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:51,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001697185.1_ASM169718v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:51,519] [INFO] Task started: Blastn
[2024-01-24 11:27:51,519] [INFO] Running command: blastn -query GCF_001697185.1_ASM169718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf3b5532-cbfe-4322-ba23-7fde6b220c77/dqc_reference/reference_markers_gtdb.fasta -out GCF_001697185.1_ASM169718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:52,451] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:52,455] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:52,455] [INFO] Target genome list was writen to GCF_001697185.1_ASM169718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:52,480] [INFO] Task started: fastANI
[2024-01-24 11:27:52,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd5ef103-2885-4cd5-aaf9-af6cc53f58f6/GCF_001697185.1_ASM169718v1_genomic.fna.gz --refList GCF_001697185.1_ASM169718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001697185.1_ASM169718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:58,248] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:58,259] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:58,259] [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_001697185.1	s__Wenyingzhuangia fucanilytica	100.0	1140	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900130035.1	s__Wenyingzhuangia marina	85.2927	692	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011927765.1	s__Wenyingzhuangia aestuarii	82.2895	630	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762155.1	s__Wenyingzhuangia heitensis	81.7287	589	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220525.1	s__Ochrovirga pacifica	79.3709	407	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ochrovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	77.6221	246	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002120225.1	s__Tenacibaculum holothuriorum	77.0406	172	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813905.1	s__Aureibaculum marinum	76.3592	129	1142	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:58,261] [INFO] GTDB search result was written to GCF_001697185.1_ASM169718v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:58,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:58,264] [INFO] DFAST_QC result json was written to GCF_001697185.1_ASM169718v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:58,264] [INFO] DFAST_QC completed!
[2024-01-24 11:27:58,265] [INFO] Total running time: 0h1m4s