[2024-01-24 11:30:49,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,201] [INFO] DQC Reference Directory: /var/lib/cwl/stgf45f553f-f1e8-433a-9c4e-60444a5fce93/dqc_reference
[2024-01-24 11:30:50,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,432] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,432] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c6ac455-6585-4bc4-aec8-c7e87262cbc6/GCF_023656565.1_ASM2365656v1_genomic.fna.gz | prodigal -d GCF_023656565.1_ASM2365656v1_genomic.fna/cds.fna -a GCF_023656565.1_ASM2365656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:08,307] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:08,307] [INFO] Task started: HMMsearch
[2024-01-24 11:31:08,308] [INFO] Running command: hmmsearch --tblout GCF_023656565.1_ASM2365656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf45f553f-f1e8-433a-9c4e-60444a5fce93/dqc_reference/reference_markers.hmm GCF_023656565.1_ASM2365656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:08,598] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:08,600] [INFO] Found 6/6 markers.
[2024-01-24 11:31:08,644] [INFO] Query marker FASTA was written to GCF_023656565.1_ASM2365656v1_genomic.fna/markers.fasta
[2024-01-24 11:31:08,645] [INFO] Task started: Blastn
[2024-01-24 11:31:08,645] [INFO] Running command: blastn -query GCF_023656565.1_ASM2365656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf45f553f-f1e8-433a-9c4e-60444a5fce93/dqc_reference/reference_markers.fasta -out GCF_023656565.1_ASM2365656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:09,331] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:09,335] [INFO] Selected 16 target genomes.
[2024-01-24 11:31:09,336] [INFO] Target genome list was writen to GCF_023656565.1_ASM2365656v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:09,343] [INFO] Task started: fastANI
[2024-01-24 11:31:09,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c6ac455-6585-4bc4-aec8-c7e87262cbc6/GCF_023656565.1_ASM2365656v1_genomic.fna.gz --refList GCF_023656565.1_ASM2365656v1_genomic.fna/target_genomes.txt --output GCF_023656565.1_ASM2365656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:29,304] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:29,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf45f553f-f1e8-433a-9c4e-60444a5fce93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:29,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf45f553f-f1e8-433a-9c4e-60444a5fce93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:29,318] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:31:29,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:29,318] [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 tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	100.0	1759	1760	95	conclusive
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	88.5725	1367	1760	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	88.4085	1354	1760	95	below_threshold
Flavobacterium ginsenosidimutans	strain=THG 01	GCA_003254625.1	687844	687844	type	True	88.4005	1403	1760	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	88.3474	1348	1760	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	88.0846	1345	1760	95	below_threshold
Flavobacterium anhuiense	strain=CGMCC 1.6859	GCA_900101855.1	459526	459526	suspected-type	True	87.6502	1349	1760	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	85.5491	1268	1760	95	below_threshold
Flavobacterium fluviale	strain=HYN0086	GCA_003312915.1	2249356	2249356	type	True	85.4224	1212	1760	95	below_threshold
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	85.2789	1261	1760	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	85.2492	1267	1760	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	83.7181	1039	1760	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.6734	1178	1760	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.5775	1058	1760	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	83.4317	1088	1760	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.2115	221	1760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:31:29,320] [INFO] DFAST Taxonomy check result was written to GCF_023656565.1_ASM2365656v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:29,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:29,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:29,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf45f553f-f1e8-433a-9c4e-60444a5fce93/dqc_reference/checkm_data
[2024-01-24 11:31:29,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:29,376] [INFO] Task started: CheckM
[2024-01-24 11:31:29,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023656565.1_ASM2365656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023656565.1_ASM2365656v1_genomic.fna/checkm_input GCF_023656565.1_ASM2365656v1_genomic.fna/checkm_result
[2024-01-24 11:32:21,510] [INFO] Task succeeded: CheckM
[2024-01-24 11:32:21,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:32:21,533] [INFO] ===== Completeness check finished =====
[2024-01-24 11:32:21,534] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:32:21,534] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023656565.1_ASM2365656v1_genomic.fna/markers.fasta)
[2024-01-24 11:32:21,535] [INFO] Task started: Blastn
[2024-01-24 11:32:21,535] [INFO] Running command: blastn -query GCF_023656565.1_ASM2365656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf45f553f-f1e8-433a-9c4e-60444a5fce93/dqc_reference/reference_markers_gtdb.fasta -out GCF_023656565.1_ASM2365656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:32:22,500] [INFO] Task succeeded: Blastn
[2024-01-24 11:32:22,504] [INFO] Selected 17 target genomes.
[2024-01-24 11:32:22,505] [INFO] Target genome list was writen to GCF_023656565.1_ASM2365656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:32:22,518] [INFO] Task started: fastANI
[2024-01-24 11:32:22,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c6ac455-6585-4bc4-aec8-c7e87262cbc6/GCF_023656565.1_ASM2365656v1_genomic.fna.gz --refList GCF_023656565.1_ASM2365656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023656565.1_ASM2365656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:44,345] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:44,372] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:32:44,372] [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_002303885.1	s__Flavobacterium sp002303885	94.987	1552	1760	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	88.9378	1444	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013388355.1	s__Flavobacterium sp013388355	88.7945	1042	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405855.1	s__Flavobacterium sp002399805	88.666	1412	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	88.5622	1368	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254625.1	s__Flavobacterium ginsenosidimutans	88.4005	1403	1760	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	88.3475	1348	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004151235.1	s__Flavobacterium anhuiense_A	87.9229	1367	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826975.1	s__Flavobacterium sp009826975	87.6435	1343	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744675.1	s__Flavobacterium sp017744675	87.5218	1354	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	85.5648	1303	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCF_003312915.1	s__Flavobacterium sp003312915	85.4224	1212	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429295.1	s__Flavobacterium sp001429295	85.3691	1263	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.90	97.90	0.95	0.95	2	-
GCF_013393195.1	s__Flavobacterium collinsii_A	85.3646	1266	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112575.1	s__Flavobacterium phragmitis	85.2492	1267	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016645.1	s__Flavobacterium johnsoniae	84.3688	1203	1760	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_000425445.1	s__Flavobacterium denitrificans	83.7142	1040	1760	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 11:32:44,375] [INFO] GTDB search result was written to GCF_023656565.1_ASM2365656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:44,375] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:44,379] [INFO] DFAST_QC result json was written to GCF_023656565.1_ASM2365656v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:44,379] [INFO] DFAST_QC completed!
[2024-01-24 11:32:44,379] [INFO] Total running time: 0h1m55s