[2024-01-24 12:06:25,106] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:25,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:25,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg529f46fb-db3a-4dbc-94e3-ef6b0692e1e7/dqc_reference
[2024-01-24 12:06:26,448] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:26,449] [INFO] Task started: Prodigal
[2024-01-24 12:06:26,449] [INFO] Running command: gunzip -c /var/lib/cwl/stg74b0427e-5769-4049-83a9-f0c76d1b6ac4/GCF_900239495.1_TNO010_V1_genomic.fna.gz | prodigal -d GCF_900239495.1_TNO010_V1_genomic.fna/cds.fna -a GCF_900239495.1_TNO010_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:34,124] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:34,124] [INFO] Task started: HMMsearch
[2024-01-24 12:06:34,124] [INFO] Running command: hmmsearch --tblout GCF_900239495.1_TNO010_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg529f46fb-db3a-4dbc-94e3-ef6b0692e1e7/dqc_reference/reference_markers.hmm GCF_900239495.1_TNO010_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:34,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:34,341] [INFO] Found 6/6 markers.
[2024-01-24 12:06:34,364] [INFO] Query marker FASTA was written to GCF_900239495.1_TNO010_V1_genomic.fna/markers.fasta
[2024-01-24 12:06:34,364] [INFO] Task started: Blastn
[2024-01-24 12:06:34,365] [INFO] Running command: blastn -query GCF_900239495.1_TNO010_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg529f46fb-db3a-4dbc-94e3-ef6b0692e1e7/dqc_reference/reference_markers.fasta -out GCF_900239495.1_TNO010_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:35,090] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:35,096] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:35,097] [INFO] Target genome list was writen to GCF_900239495.1_TNO010_V1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:35,102] [INFO] Task started: fastANI
[2024-01-24 12:06:35,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b0427e-5769-4049-83a9-f0c76d1b6ac4/GCF_900239495.1_TNO010_V1_genomic.fna.gz --refList GCF_900239495.1_TNO010_V1_genomic.fna/target_genomes.txt --output GCF_900239495.1_TNO010_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:45,561] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:45,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg529f46fb-db3a-4dbc-94e3-ef6b0692e1e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:45,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg529f46fb-db3a-4dbc-94e3-ef6b0692e1e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:45,573] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:45,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:45,573] [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 finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	100.0	910	910	95	conclusive
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	96.8963	801	910	95	conclusive
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	81.6428	552	910	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	81.0831	596	910	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	79.9439	459	910	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	79.2906	458	910	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	78.7822	405	910	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.5966	362	910	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.5401	354	910	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.5117	361	910	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.1514	342	910	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.7617	309	910	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.5332	278	910	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.3769	284	910	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:45,575] [INFO] DFAST Taxonomy check result was written to GCF_900239495.1_TNO010_V1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:45,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:45,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:45,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg529f46fb-db3a-4dbc-94e3-ef6b0692e1e7/dqc_reference/checkm_data
[2024-01-24 12:06:45,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:45,605] [INFO] Task started: CheckM
[2024-01-24 12:06:45,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900239495.1_TNO010_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900239495.1_TNO010_V1_genomic.fna/checkm_input GCF_900239495.1_TNO010_V1_genomic.fna/checkm_result
[2024-01-24 12:07:12,282] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:12,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:12,298] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:12,298] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:12,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900239495.1_TNO010_V1_genomic.fna/markers.fasta)
[2024-01-24 12:07:12,299] [INFO] Task started: Blastn
[2024-01-24 12:07:12,299] [INFO] Running command: blastn -query GCF_900239495.1_TNO010_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg529f46fb-db3a-4dbc-94e3-ef6b0692e1e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900239495.1_TNO010_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:13,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:13,189] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:13,190] [INFO] Target genome list was writen to GCF_900239495.1_TNO010_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:13,209] [INFO] Task started: fastANI
[2024-01-24 12:07:13,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b0427e-5769-4049-83a9-f0c76d1b6ac4/GCF_900239495.1_TNO010_V1_genomic.fna.gz --refList GCF_900239495.1_TNO010_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_900239495.1_TNO010_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:19,558] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:19,565] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:19,565] [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_900239495.1	s__Tenacibaculum finnmarkense	100.0	910	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	96.8963	98.86	98.40	0.93	0.91	7	conclusive
GCF_900239185.1	s__Tenacibaculum finnmarkense_A	96.8963	801	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	96.8963	99.00	98.36	0.95	0.91	6	conclusive
GCF_900239345.1	s__Tenacibaculum dicentrarchi	93.7576	800	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_900239505.1	s__Tenacibaculum piscium	88.0434	658	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.64	99.33	0.97	0.95	5	-
GCF_001693415.1	s__Tenacibaculum soleae	81.2842	551	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	81.1053	594	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_002836595.1	s__Tenacibaculum sp002836595	81.0852	595	910	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 12:07:19,567] [INFO] GTDB search result was written to GCF_900239495.1_TNO010_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:19,567] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:19,572] [INFO] DFAST_QC result json was written to GCF_900239495.1_TNO010_V1_genomic.fna/dqc_result.json
[2024-01-24 12:07:19,572] [INFO] DFAST_QC completed!
[2024-01-24 12:07:19,572] [INFO] Total running time: 0h0m54s