[2023-06-30 12:26:20,413] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:26:20,415] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:26:20,415] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb8b40c4-6df6-4196-9e0b-b1538094d023/dqc_reference
[2023-06-30 12:26:23,027] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:26:23,028] [INFO] Task started: Prodigal
[2023-06-30 12:26:23,028] [INFO] Running command: gunzip -c /var/lib/cwl/stge2dca365-13ff-437d-8116-cc9db7b3d3ab/GCA_016722385.1_ASM1672238v1_genomic.fna.gz | prodigal -d GCA_016722385.1_ASM1672238v1_genomic.fna/cds.fna -a GCA_016722385.1_ASM1672238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:26:34,671] [INFO] Task succeeded: Prodigal
[2023-06-30 12:26:34,672] [INFO] Task started: HMMsearch
[2023-06-30 12:26:34,672] [INFO] Running command: hmmsearch --tblout GCA_016722385.1_ASM1672238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb8b40c4-6df6-4196-9e0b-b1538094d023/dqc_reference/reference_markers.hmm GCA_016722385.1_ASM1672238v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:26:34,942] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:26:34,944] [INFO] Found 6/6 markers.
[2023-06-30 12:26:34,988] [INFO] Query marker FASTA was written to GCA_016722385.1_ASM1672238v1_genomic.fna/markers.fasta
[2023-06-30 12:26:34,988] [INFO] Task started: Blastn
[2023-06-30 12:26:34,988] [INFO] Running command: blastn -query GCA_016722385.1_ASM1672238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb8b40c4-6df6-4196-9e0b-b1538094d023/dqc_reference/reference_markers.fasta -out GCA_016722385.1_ASM1672238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:26:36,005] [INFO] Task succeeded: Blastn
[2023-06-30 12:26:36,009] [INFO] Selected 32 target genomes.
[2023-06-30 12:26:36,010] [INFO] Target genome list was writen to GCA_016722385.1_ASM1672238v1_genomic.fna/target_genomes.txt
[2023-06-30 12:26:36,031] [INFO] Task started: fastANI
[2023-06-30 12:26:36,031] [INFO] Running command: fastANI --query /var/lib/cwl/stge2dca365-13ff-437d-8116-cc9db7b3d3ab/GCA_016722385.1_ASM1672238v1_genomic.fna.gz --refList GCA_016722385.1_ASM1672238v1_genomic.fna/target_genomes.txt --output GCA_016722385.1_ASM1672238v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:26:57,289] [INFO] Task succeeded: fastANI
[2023-06-30 12:26:57,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb8b40c4-6df6-4196-9e0b-b1538094d023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:26:57,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb8b40c4-6df6-4196-9e0b-b1538094d023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:26:57,317] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:26:57,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:26:57,318] [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
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	78.3197	310	1186	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.1309	354	1186	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	78.0611	287	1186	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	78.0449	289	1186	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	78.0337	319	1186	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	78.0194	264	1186	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	77.997	254	1186	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	77.989	288	1186	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	77.9814	264	1186	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	77.9586	254	1186	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	77.91	248	1186	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.897	180	1186	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	77.8781	329	1186	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	77.8514	295	1186	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	77.8469	289	1186	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	77.8307	264	1186	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	77.8164	242	1186	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	77.7947	242	1186	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.7738	323	1186	95	below_threshold
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	77.7512	281	1186	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	77.7464	256	1186	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	77.711	204	1186	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	77.66	221	1186	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	77.6356	256	1186	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	77.6116	199	1186	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	77.5466	270	1186	95	below_threshold
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	77.5341	263	1186	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	77.5288	238	1186	95	below_threshold
Ahniella affigens	strain=D13	GCA_003015185.1	2021234	2021234	type	True	77.5017	215	1186	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	77.4136	187	1186	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	77.4	349	1186	95	below_threshold
[Pseudomonas] hibiscicola	strain=ATCC 19867	GCA_000382065.1	86189	86189	type	True	77.3485	241	1186	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:26:57,320] [INFO] DFAST Taxonomy check result was written to GCA_016722385.1_ASM1672238v1_genomic.fna/tc_result.tsv
[2023-06-30 12:26:57,320] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:26:57,321] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:26:57,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb8b40c4-6df6-4196-9e0b-b1538094d023/dqc_reference/checkm_data
[2023-06-30 12:26:57,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:26:57,364] [INFO] Task started: CheckM
[2023-06-30 12:26:57,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016722385.1_ASM1672238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016722385.1_ASM1672238v1_genomic.fna/checkm_input GCA_016722385.1_ASM1672238v1_genomic.fna/checkm_result
[2023-06-30 12:27:46,463] [INFO] Task succeeded: CheckM
[2023-06-30 12:27:46,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:27:46,488] [INFO] ===== Completeness check finished =====
[2023-06-30 12:27:46,489] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:27:46,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016722385.1_ASM1672238v1_genomic.fna/markers.fasta)
[2023-06-30 12:27:46,489] [INFO] Task started: Blastn
[2023-06-30 12:27:46,490] [INFO] Running command: blastn -query GCA_016722385.1_ASM1672238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb8b40c4-6df6-4196-9e0b-b1538094d023/dqc_reference/reference_markers_gtdb.fasta -out GCA_016722385.1_ASM1672238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:27:48,212] [INFO] Task succeeded: Blastn
[2023-06-30 12:27:48,216] [INFO] Selected 18 target genomes.
[2023-06-30 12:27:48,216] [INFO] Target genome list was writen to GCA_016722385.1_ASM1672238v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:27:48,250] [INFO] Task started: fastANI
[2023-06-30 12:27:48,251] [INFO] Running command: fastANI --query /var/lib/cwl/stge2dca365-13ff-437d-8116-cc9db7b3d3ab/GCA_016722385.1_ASM1672238v1_genomic.fna.gz --refList GCA_016722385.1_ASM1672238v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016722385.1_ASM1672238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:28:00,731] [INFO] Task succeeded: fastANI
[2023-06-30 12:28:00,750] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:28:00,750] [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
GCA_016721845.1	s__JADKHK01 sp016721845	98.8969	1116	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.21	98.90	0.96	0.94	3	conclusive
GCA_016182785.1	s__JADKHK01 sp016182785	82.8939	744	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703225.1	s__JADKHK01 sp016703225	82.5292	768	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.05	99.05	0.90	0.90	2	-
GCA_016708465.1	s__JADKHK01 sp016708465	82.311	755	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.43	99.22	0.94	0.94	3	-
GCF_000953855.2	s__Mizugakiibacter sediminis	78.1643	322	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712105.1	s__Ahniella sp016712105	78.1579	268	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__Ahniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	78.0609	271	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004118975.1	s__Luteimonas sp004118975	78.0386	248	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004143945.1	s__Dokdonella_A sp004143945	78.0235	289	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017997455.1	s__JAGOEZ01 sp017997455	78.0051	254	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JAGOEZ01	95.0	98.60	98.27	0.77	0.77	3	-
GCA_002483055.1	s__Dokdonella sp002483055	77.9667	282	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	77.9168	355	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843005.1	s__Rhodanobacter sp014843005	77.9061	214	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	77.8624	279	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCF_001632775.1	s__Dokdonella koreensis	77.797	320	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359965.1	s__Lysobacter segetis	77.5567	261	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829075.1	s__Luteibacter yeojuensis_B	77.4061	209	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000382065.1	s__Stenotrophomonas maltophilia_B	77.3474	241	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.83	97.17	0.91	0.87	24	-
--------------------------------------------------------------------------------
[2023-06-30 12:28:00,754] [INFO] GTDB search result was written to GCA_016722385.1_ASM1672238v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:28:00,755] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:28:00,764] [INFO] DFAST_QC result json was written to GCA_016722385.1_ASM1672238v1_genomic.fna/dqc_result.json
[2023-06-30 12:28:00,765] [INFO] DFAST_QC completed!
[2023-06-30 12:28:00,765] [INFO] Total running time: 0h1m40s