[2024-01-24 15:26:55,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgf069e5e5-be0f-49cf-aebd-97cbfcf28845/dqc_reference
[2024-01-24 15:26:56,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,667] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,667] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfba25cd-96f1-4a86-9e1d-65b5022a9582/GCF_015645385.1_ASM1564538v1_genomic.fna.gz | prodigal -d GCF_015645385.1_ASM1564538v1_genomic.fna/cds.fna -a GCF_015645385.1_ASM1564538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:08,992] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:08,993] [INFO] Task started: HMMsearch
[2024-01-24 15:27:08,993] [INFO] Running command: hmmsearch --tblout GCF_015645385.1_ASM1564538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf069e5e5-be0f-49cf-aebd-97cbfcf28845/dqc_reference/reference_markers.hmm GCF_015645385.1_ASM1564538v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:09,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:09,315] [INFO] Found 6/6 markers.
[2024-01-24 15:27:09,346] [INFO] Query marker FASTA was written to GCF_015645385.1_ASM1564538v1_genomic.fna/markers.fasta
[2024-01-24 15:27:09,347] [INFO] Task started: Blastn
[2024-01-24 15:27:09,347] [INFO] Running command: blastn -query GCF_015645385.1_ASM1564538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf069e5e5-be0f-49cf-aebd-97cbfcf28845/dqc_reference/reference_markers.fasta -out GCF_015645385.1_ASM1564538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:10,012] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:10,016] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:10,016] [INFO] Target genome list was writen to GCF_015645385.1_ASM1564538v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:10,021] [INFO] Task started: fastANI
[2024-01-24 15:27:10,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfba25cd-96f1-4a86-9e1d-65b5022a9582/GCF_015645385.1_ASM1564538v1_genomic.fna.gz --refList GCF_015645385.1_ASM1564538v1_genomic.fna/target_genomes.txt --output GCF_015645385.1_ASM1564538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:23,039] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:23,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf069e5e5-be0f-49cf-aebd-97cbfcf28845/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:23,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf069e5e5-be0f-49cf-aebd-97cbfcf28845/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:23,053] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:23,057] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:23,057] [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
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	100.0	1302	1303	95	conclusive
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	83.3437	965	1303	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	83.0787	939	1303	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	82.421	890	1303	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	82.2433	883	1303	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	81.7757	808	1303	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	81.1598	805	1303	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	80.7254	748	1303	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	80.4112	671	1303	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	80.0135	625	1303	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.732	275	1303	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.6598	266	1303	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2544	228	1303	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.1355	186	1303	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.7384	174	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:23,060] [INFO] DFAST Taxonomy check result was written to GCF_015645385.1_ASM1564538v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:23,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:23,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:23,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf069e5e5-be0f-49cf-aebd-97cbfcf28845/dqc_reference/checkm_data
[2024-01-24 15:27:23,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:23,101] [INFO] Task started: CheckM
[2024-01-24 15:27:23,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015645385.1_ASM1564538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015645385.1_ASM1564538v1_genomic.fna/checkm_input GCF_015645385.1_ASM1564538v1_genomic.fna/checkm_result
[2024-01-24 15:28:01,635] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:01,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:01,656] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:01,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:01,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015645385.1_ASM1564538v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:01,657] [INFO] Task started: Blastn
[2024-01-24 15:28:01,657] [INFO] Running command: blastn -query GCF_015645385.1_ASM1564538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf069e5e5-be0f-49cf-aebd-97cbfcf28845/dqc_reference/reference_markers_gtdb.fasta -out GCF_015645385.1_ASM1564538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:02,641] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:02,644] [INFO] Selected 11 target genomes.
[2024-01-24 15:28:02,645] [INFO] Target genome list was writen to GCF_015645385.1_ASM1564538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:02,654] [INFO] Task started: fastANI
[2024-01-24 15:28:02,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfba25cd-96f1-4a86-9e1d-65b5022a9582/GCF_015645385.1_ASM1564538v1_genomic.fna.gz --refList GCF_015645385.1_ASM1564538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015645385.1_ASM1564538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:13,160] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:13,170] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:13,170] [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_015645385.1	s__Winogradskyella sp015645385	100.0	1302	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013404085.1	s__Winogradskyella helgolandensis	83.3631	964	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_900099995.1	s__Winogradskyella thalassocola	83.0815	939	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	82.8182	903	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	82.5953	882	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_000427335.1	s__Winogradskyella psychrotolerans	82.4339	889	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403865.1	s__Winogradskyella costae	82.2345	884	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	81.9898	812	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403955.1	s__Winogradskyella vidalii	81.7675	810	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	81.1324	757	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	80.006	625	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:13,172] [INFO] GTDB search result was written to GCF_015645385.1_ASM1564538v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:13,173] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:13,176] [INFO] DFAST_QC result json was written to GCF_015645385.1_ASM1564538v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:13,176] [INFO] DFAST_QC completed!
[2024-01-24 15:28:13,176] [INFO] Total running time: 0h1m18s