[2024-01-24 12:45:09,803] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:09,809] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:09,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg56aac3f4-219f-49dc-9fbe-203f01f1ed97/dqc_reference
[2024-01-24 12:45:13,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,082] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg037e6e18-d2c4-48f0-bdc1-2b50a89220f8/GCF_002266855.1_ASM226685v1_genomic.fna.gz | prodigal -d GCF_002266855.1_ASM226685v1_genomic.fna/cds.fna -a GCF_002266855.1_ASM226685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:24,959] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:24,959] [INFO] Task started: HMMsearch
[2024-01-24 12:45:24,960] [INFO] Running command: hmmsearch --tblout GCF_002266855.1_ASM226685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56aac3f4-219f-49dc-9fbe-203f01f1ed97/dqc_reference/reference_markers.hmm GCF_002266855.1_ASM226685v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:25,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:25,257] [INFO] Found 6/6 markers.
[2024-01-24 12:45:25,292] [INFO] Query marker FASTA was written to GCF_002266855.1_ASM226685v1_genomic.fna/markers.fasta
[2024-01-24 12:45:25,292] [INFO] Task started: Blastn
[2024-01-24 12:45:25,292] [INFO] Running command: blastn -query GCF_002266855.1_ASM226685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56aac3f4-219f-49dc-9fbe-203f01f1ed97/dqc_reference/reference_markers.fasta -out GCF_002266855.1_ASM226685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:25,965] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:25,969] [INFO] Selected 22 target genomes.
[2024-01-24 12:45:25,969] [INFO] Target genome list was writen to GCF_002266855.1_ASM226685v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:25,979] [INFO] Task started: fastANI
[2024-01-24 12:45:25,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg037e6e18-d2c4-48f0-bdc1-2b50a89220f8/GCF_002266855.1_ASM226685v1_genomic.fna.gz --refList GCF_002266855.1_ASM226685v1_genomic.fna/target_genomes.txt --output GCF_002266855.1_ASM226685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:39,429] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:39,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56aac3f4-219f-49dc-9fbe-203f01f1ed97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:39,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56aac3f4-219f-49dc-9fbe-203f01f1ed97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:39,446] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:39,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:39,447] [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 aurantia	strain=WNB302	GCA_002266855.1	1915063	1915063	type	True	99.9999	1057	1057	95	conclusive
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.1431	225	1057	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.6663	278	1057	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.6663	278	1057	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	77.5739	215	1057	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.5403	235	1057	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.5169	195	1057	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	77.507	271	1057	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	77.4791	200	1057	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.437	132	1057	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.4367	237	1057	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.3994	208	1057	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.3779	97	1057	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	77.3591	199	1057	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.3525	211	1057	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.278	111	1057	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.2129	186	1057	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.143	118	1057	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.1406	230	1057	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	77.1199	112	1057	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.907	144	1057	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.8805	122	1057	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:39,449] [INFO] DFAST Taxonomy check result was written to GCF_002266855.1_ASM226685v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:39,449] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:39,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:39,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56aac3f4-219f-49dc-9fbe-203f01f1ed97/dqc_reference/checkm_data
[2024-01-24 12:45:39,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:39,486] [INFO] Task started: CheckM
[2024-01-24 12:45:39,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002266855.1_ASM226685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002266855.1_ASM226685v1_genomic.fna/checkm_input GCF_002266855.1_ASM226685v1_genomic.fna/checkm_result
[2024-01-24 12:46:17,182] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:17,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:17,202] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:17,202] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:17,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002266855.1_ASM226685v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:17,203] [INFO] Task started: Blastn
[2024-01-24 12:46:17,203] [INFO] Running command: blastn -query GCF_002266855.1_ASM226685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56aac3f4-219f-49dc-9fbe-203f01f1ed97/dqc_reference/reference_markers_gtdb.fasta -out GCF_002266855.1_ASM226685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:18,073] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:18,078] [INFO] Selected 21 target genomes.
[2024-01-24 12:46:18,078] [INFO] Target genome list was writen to GCF_002266855.1_ASM226685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:18,107] [INFO] Task started: fastANI
[2024-01-24 12:46:18,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg037e6e18-d2c4-48f0-bdc1-2b50a89220f8/GCF_002266855.1_ASM226685v1_genomic.fna.gz --refList GCF_002266855.1_ASM226685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002266855.1_ASM226685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:30,530] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:30,551] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:30,551] [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_002266855.1	s__Winogradskyella aurantia	99.9999	1057	1057	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_014243395.1	s__Winogradskyella flava	78.1431	225	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017581965.1	s__Winogradskyella sp017581965	77.9292	331	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869935.1	s__Winogradskyella algicola	77.7606	256	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	77.6689	277	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003260205.1	s__Winogradskyella tangerina	77.571	216	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	77.5431	234	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	77.5374	246	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335675.1	s__Winogradskyella sp003335675	77.5361	233	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709615.1	s__Winogradskyella ouciana	77.5051	272	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCF_014635865.1	s__Winogradskyella haliclonae	77.5009	196	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971725.1	s__Winogradskyella sp001971725	77.395	254	1057	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	77.381	208	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	77.3736	235	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	77.367	208	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645385.1	s__Winogradskyella sp015645385	77.3395	232	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346845.1	s__Winogradskyella wandonensis	77.2282	185	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712105.1	s__Winogradskyella sp003712105	77.2048	182	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	77.1602	247	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042245.1	s__Winogradskyella sp013042245	77.1229	167	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCA_004211785.1	s__Winogradskyella sp004211785	76.8066	156	1057	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 12:46:30,553] [INFO] GTDB search result was written to GCF_002266855.1_ASM226685v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:30,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:30,558] [INFO] DFAST_QC result json was written to GCF_002266855.1_ASM226685v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:30,558] [INFO] DFAST_QC completed!
[2024-01-24 12:46:30,558] [INFO] Total running time: 0h1m21s