[2024-01-24 12:21:55,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:55,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:55,391] [INFO] DQC Reference Directory: /var/lib/cwl/stgeef6b147-502f-4c69-95ef-e06ed4084814/dqc_reference
[2024-01-24 12:21:56,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:56,602] [INFO] Task started: Prodigal
[2024-01-24 12:21:56,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ec42dcb-ea88-414e-a833-8f5470b90d5b/GCF_000016645.1_ASM1664v1_genomic.fna.gz | prodigal -d GCF_000016645.1_ASM1664v1_genomic.fna/cds.fna -a GCF_000016645.1_ASM1664v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:16,076] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:16,076] [INFO] Task started: HMMsearch
[2024-01-24 12:22:16,077] [INFO] Running command: hmmsearch --tblout GCF_000016645.1_ASM1664v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeef6b147-502f-4c69-95ef-e06ed4084814/dqc_reference/reference_markers.hmm GCF_000016645.1_ASM1664v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:16,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:16,401] [INFO] Found 6/6 markers.
[2024-01-24 12:22:16,456] [INFO] Query marker FASTA was written to GCF_000016645.1_ASM1664v1_genomic.fna/markers.fasta
[2024-01-24 12:22:16,456] [INFO] Task started: Blastn
[2024-01-24 12:22:16,456] [INFO] Running command: blastn -query GCF_000016645.1_ASM1664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeef6b147-502f-4c69-95ef-e06ed4084814/dqc_reference/reference_markers.fasta -out GCF_000016645.1_ASM1664v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:17,141] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:17,148] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:17,148] [INFO] Target genome list was writen to GCF_000016645.1_ASM1664v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:17,154] [INFO] Task started: fastANI
[2024-01-24 12:22:17,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ec42dcb-ea88-414e-a833-8f5470b90d5b/GCF_000016645.1_ASM1664v1_genomic.fna.gz --refList GCF_000016645.1_ASM1664v1_genomic.fna/target_genomes.txt --output GCF_000016645.1_ASM1664v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:38,119] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:38,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeef6b147-502f-4c69-95ef-e06ed4084814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:38,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeef6b147-502f-4c69-95ef-e06ed4084814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:38,134] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:22:38,134] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:38,134] [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
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	100.0	2032	2032	95	conclusive
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	99.997	2009	2032	95	conclusive
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	99.9776	1979	2032	95	conclusive
Flavobacterium defluvii	strain=DSM 17963	GCA_900129555.1	370979	370979	type	True	86.1129	1267	2032	95	below_threshold
Flavobacterium panici		GCA_903819335.1	2654843	2654843	type	True	86.1101	1326	2032	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	85.9779	1227	2032	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	84.5504	1337	2032	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	84.4551	1176	2032	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	84.3906	1197	2032	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	84.2763	1226	2032	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	83.8939	1247	2032	95	below_threshold
Flavobacterium anhuiense	strain=CGMCC 1.6859	GCA_900101855.1	459526	459526	suspected-type	True	83.8584	1220	2032	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	83.631	1206	2032	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	83.6037	1074	2032	95	below_threshold
Flavobacterium zhairuonense	strain=A5.7	GCA_004352915.1	2493631	2493631	type	True	83.519	1139	2032	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.2903	187	2032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:38,136] [INFO] DFAST Taxonomy check result was written to GCF_000016645.1_ASM1664v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:38,136] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:38,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:38,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeef6b147-502f-4c69-95ef-e06ed4084814/dqc_reference/checkm_data
[2024-01-24 12:22:38,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:38,195] [INFO] Task started: CheckM
[2024-01-24 12:22:38,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000016645.1_ASM1664v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000016645.1_ASM1664v1_genomic.fna/checkm_input GCF_000016645.1_ASM1664v1_genomic.fna/checkm_result
[2024-01-24 12:23:35,220] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:35,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:35,250] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:35,251] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:35,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000016645.1_ASM1664v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:35,251] [INFO] Task started: Blastn
[2024-01-24 12:23:35,251] [INFO] Running command: blastn -query GCF_000016645.1_ASM1664v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeef6b147-502f-4c69-95ef-e06ed4084814/dqc_reference/reference_markers_gtdb.fasta -out GCF_000016645.1_ASM1664v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:36,248] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:36,262] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:36,262] [INFO] Target genome list was writen to GCF_000016645.1_ASM1664v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:36,280] [INFO] Task started: fastANI
[2024-01-24 12:23:36,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ec42dcb-ea88-414e-a833-8f5470b90d5b/GCF_000016645.1_ASM1664v1_genomic.fna.gz --refList GCF_000016645.1_ASM1664v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000016645.1_ASM1664v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:03,248] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:03,265] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:03,265] [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_000016645.1	s__Flavobacterium johnsoniae	100.0	2031	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	conclusive
GCF_900129555.1	s__Flavobacterium defluvii	86.1474	1263	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210235.1	s__Flavobacterium sp002210235	86.124	1342	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.80	96.54	0.96	0.91	4	-
GCF_900129795.1	s__Flavobacterium sp900129795	85.9223	1308	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_001428525.1	s__Flavobacterium sp001428525	85.9219	1310	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482975.1	s__Flavobacterium sp002482975	85.9187	1299	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429765.1	s__Flavobacterium sp001429765	85.0501	1258	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.97	0.97	2	-
GCF_013388355.1	s__Flavobacterium sp013388355	84.8412	877	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002303885.1	s__Flavobacterium sp002303885	84.4788	1233	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	84.468	1175	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	84.4465	1202	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735615.1	s__Flavobacterium sp016735615	84.2591	1171	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312915.1	s__Flavobacterium sp003312915	84.1008	1143	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101855.1	s__Flavobacterium anhuiense	83.8818	1217	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.61	97.43	0.90	0.88	4	-
GCF_900112575.1	s__Flavobacterium phragmitis	83.877	1249	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	83.8123	1209	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009711135.1	s__Flavobacterium sp009711135	83.8062	1139	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425445.1	s__Flavobacterium denitrificans	83.6014	1074	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352915.1	s__Flavobacterium zhairuonense	83.5128	1139	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362055.1	s__Flavobacterium sp004362055	83.4339	1110	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833855.1	s__Flavobacterium sp017833855	83.0197	1130	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182285.1	s__Flavobacterium sp015182285	83.0186	1225	2032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:03,267] [INFO] GTDB search result was written to GCF_000016645.1_ASM1664v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:03,267] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:03,271] [INFO] DFAST_QC result json was written to GCF_000016645.1_ASM1664v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:03,272] [INFO] DFAST_QC completed!
[2024-01-24 12:24:03,272] [INFO] Total running time: 0h2m8s