[2024-01-24 11:26:38,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,846] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg1927ddc5-f7a1-4096-99ba-4e616b6e030f/dqc_reference
[2024-01-24 11:26:40,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,206] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,206] [INFO] Running command: gunzip -c /var/lib/cwl/stg81e00148-f657-47b2-b8a2-f164a3470612/GCF_003867015.1_ASM386701v1_genomic.fna.gz | prodigal -d GCF_003867015.1_ASM386701v1_genomic.fna/cds.fna -a GCF_003867015.1_ASM386701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:50,388] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:50,388] [INFO] Task started: HMMsearch
[2024-01-24 11:26:50,388] [INFO] Running command: hmmsearch --tblout GCF_003867015.1_ASM386701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1927ddc5-f7a1-4096-99ba-4e616b6e030f/dqc_reference/reference_markers.hmm GCF_003867015.1_ASM386701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:50,647] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:50,649] [INFO] Found 6/6 markers.
[2024-01-24 11:26:50,683] [INFO] Query marker FASTA was written to GCF_003867015.1_ASM386701v1_genomic.fna/markers.fasta
[2024-01-24 11:26:50,684] [INFO] Task started: Blastn
[2024-01-24 11:26:50,684] [INFO] Running command: blastn -query GCF_003867015.1_ASM386701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1927ddc5-f7a1-4096-99ba-4e616b6e030f/dqc_reference/reference_markers.fasta -out GCF_003867015.1_ASM386701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:51,336] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:51,340] [INFO] Selected 11 target genomes.
[2024-01-24 11:26:51,341] [INFO] Target genome list was writen to GCF_003867015.1_ASM386701v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:51,346] [INFO] Task started: fastANI
[2024-01-24 11:26:51,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg81e00148-f657-47b2-b8a2-f164a3470612/GCF_003867015.1_ASM386701v1_genomic.fna.gz --refList GCF_003867015.1_ASM386701v1_genomic.fna/target_genomes.txt --output GCF_003867015.1_ASM386701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:59,208] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:59,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1927ddc5-f7a1-4096-99ba-4e616b6e030f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:59,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1927ddc5-f7a1-4096-99ba-4e616b6e030f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:59,219] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:59,219] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:59,219] [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
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	100.0	1166	1170	95	conclusive
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	92.4961	877	1170	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	92.4126	879	1170	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	92.3634	879	1170	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	89.9073	926	1170	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	84.754	823	1170	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	79.6195	552	1170	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.3359	373	1170	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.2844	363	1170	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.848	311	1170	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.7646	288	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:59,221] [INFO] DFAST Taxonomy check result was written to GCF_003867015.1_ASM386701v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:59,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:59,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:59,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1927ddc5-f7a1-4096-99ba-4e616b6e030f/dqc_reference/checkm_data
[2024-01-24 11:26:59,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:59,262] [INFO] Task started: CheckM
[2024-01-24 11:26:59,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003867015.1_ASM386701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003867015.1_ASM386701v1_genomic.fna/checkm_input GCF_003867015.1_ASM386701v1_genomic.fna/checkm_result
[2024-01-24 11:27:33,246] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:33,247] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,265] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:33,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:33,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003867015.1_ASM386701v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:33,266] [INFO] Task started: Blastn
[2024-01-24 11:27:33,266] [INFO] Running command: blastn -query GCF_003867015.1_ASM386701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1927ddc5-f7a1-4096-99ba-4e616b6e030f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003867015.1_ASM386701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:34,205] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:34,209] [INFO] Selected 6 target genomes.
[2024-01-24 11:27:34,209] [INFO] Target genome list was writen to GCF_003867015.1_ASM386701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:34,215] [INFO] Task started: fastANI
[2024-01-24 11:27:34,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg81e00148-f657-47b2-b8a2-f164a3470612/GCF_003867015.1_ASM386701v1_genomic.fna.gz --refList GCF_003867015.1_ASM386701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003867015.1_ASM386701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:39,388] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:39,402] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:39,402] [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_003867015.1	s__Tenacibaculum singaporense	100.0	1166	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	conclusive
GCF_003867075.1	s__Tenacibaculum mesophilum	92.4697	876	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCF_003664185.1	s__Tenacibaculum discolor	89.9241	925	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_003387615.1	s__Tenacibaculum gallaicum	88.2829	927	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610735.1	s__Tenacibaculum lutimaris	86.0072	745	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	84.754	823	1170	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:39,404] [INFO] GTDB search result was written to GCF_003867015.1_ASM386701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:39,405] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:39,408] [INFO] DFAST_QC result json was written to GCF_003867015.1_ASM386701v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:39,408] [INFO] DFAST_QC completed!
[2024-01-24 11:27:39,409] [INFO] Total running time: 0h1m1s