[2023-06-28 22:31:17,406] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:31:17,411] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:31:17,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bd4ceee-aaaf-4f55-9453-28b4a0bedadf/dqc_reference
[2023-06-28 22:31:19,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:31:19,079] [INFO] Task started: Prodigal
[2023-06-28 22:31:19,080] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7010e98-ed16-492c-b5f1-71062e0a6c1b/GCA_017987335.1_ASM1798733v1_genomic.fna.gz | prodigal -d GCA_017987335.1_ASM1798733v1_genomic.fna/cds.fna -a GCA_017987335.1_ASM1798733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:31:28,800] [INFO] Task succeeded: Prodigal
[2023-06-28 22:31:28,801] [INFO] Task started: HMMsearch
[2023-06-28 22:31:28,801] [INFO] Running command: hmmsearch --tblout GCA_017987335.1_ASM1798733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bd4ceee-aaaf-4f55-9453-28b4a0bedadf/dqc_reference/reference_markers.hmm GCA_017987335.1_ASM1798733v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:31:29,025] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:31:29,026] [INFO] Found 6/6 markers.
[2023-06-28 22:31:29,057] [INFO] Query marker FASTA was written to GCA_017987335.1_ASM1798733v1_genomic.fna/markers.fasta
[2023-06-28 22:31:29,057] [INFO] Task started: Blastn
[2023-06-28 22:31:29,057] [INFO] Running command: blastn -query GCA_017987335.1_ASM1798733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bd4ceee-aaaf-4f55-9453-28b4a0bedadf/dqc_reference/reference_markers.fasta -out GCA_017987335.1_ASM1798733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:31:29,886] [INFO] Task succeeded: Blastn
[2023-06-28 22:31:29,892] [INFO] Selected 24 target genomes.
[2023-06-28 22:31:29,893] [INFO] Target genome list was writen to GCA_017987335.1_ASM1798733v1_genomic.fna/target_genomes.txt
[2023-06-28 22:31:29,897] [INFO] Task started: fastANI
[2023-06-28 22:31:29,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7010e98-ed16-492c-b5f1-71062e0a6c1b/GCA_017987335.1_ASM1798733v1_genomic.fna.gz --refList GCA_017987335.1_ASM1798733v1_genomic.fna/target_genomes.txt --output GCA_017987335.1_ASM1798733v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:31:46,756] [INFO] Task succeeded: fastANI
[2023-06-28 22:31:46,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bd4ceee-aaaf-4f55-9453-28b4a0bedadf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:31:46,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bd4ceee-aaaf-4f55-9453-28b4a0bedadf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:31:46,779] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:31:46,779] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:31:46,780] [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
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	79.2672	464	892	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	77.8651	212	892	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.7905	288	892	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	77.7708	195	892	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	77.7526	259	892	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	77.7377	211	892	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	77.7056	251	892	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	77.6671	166	892	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	77.6492	192	892	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	77.6261	193	892	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	77.5723	210	892	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	77.5451	152	892	95	below_threshold
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	77.5096	159	892	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.4852	164	892	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	77.4669	196	892	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	77.4526	169	892	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.4513	237	892	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	77.4471	196	892	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	77.4469	175	892	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	77.3074	179	892	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	77.1584	170	892	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001564415.1	1985254	1985254	pathovar	True	76.8965	161	892	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001402235.1	1985254	1985254	pathovar	True	76.8491	151	892	95	below_threshold
Xanthomonas phaseoli	strain=NCPPB 1833	GCA_017746675.1	1985254	1985254	pathovar	True	76.8227	163	892	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:31:46,782] [INFO] DFAST Taxonomy check result was written to GCA_017987335.1_ASM1798733v1_genomic.fna/tc_result.tsv
[2023-06-28 22:31:46,782] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:31:46,782] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:31:46,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bd4ceee-aaaf-4f55-9453-28b4a0bedadf/dqc_reference/checkm_data
[2023-06-28 22:31:46,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:31:46,815] [INFO] Task started: CheckM
[2023-06-28 22:31:46,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017987335.1_ASM1798733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017987335.1_ASM1798733v1_genomic.fna/checkm_input GCA_017987335.1_ASM1798733v1_genomic.fna/checkm_result
[2023-06-28 22:32:23,967] [INFO] Task succeeded: CheckM
[2023-06-28 22:32:23,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:32:23,990] [INFO] ===== Completeness check finished =====
[2023-06-28 22:32:23,990] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:32:23,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017987335.1_ASM1798733v1_genomic.fna/markers.fasta)
[2023-06-28 22:32:23,991] [INFO] Task started: Blastn
[2023-06-28 22:32:23,991] [INFO] Running command: blastn -query GCA_017987335.1_ASM1798733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bd4ceee-aaaf-4f55-9453-28b4a0bedadf/dqc_reference/reference_markers_gtdb.fasta -out GCA_017987335.1_ASM1798733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:32:25,448] [INFO] Task succeeded: Blastn
[2023-06-28 22:32:25,453] [INFO] Selected 12 target genomes.
[2023-06-28 22:32:25,454] [INFO] Target genome list was writen to GCA_017987335.1_ASM1798733v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:32:25,483] [INFO] Task started: fastANI
[2023-06-28 22:32:25,483] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7010e98-ed16-492c-b5f1-71062e0a6c1b/GCA_017987335.1_ASM1798733v1_genomic.fna.gz --refList GCA_017987335.1_ASM1798733v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017987335.1_ASM1798733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:32:34,712] [INFO] Task succeeded: fastANI
[2023-06-28 22:32:34,732] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:32:34,733] [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_016712865.1	s__Dokdonella sp016712865	99.4682	871	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	99.46	99.45	0.98	0.98	3	conclusive
GCA_004295005.1	s__Dokdonella sp004295005	89.4424	735	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899855.1	s__Dokdonella sp001899855	79.5553	456	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707485.1	s__Dokdonella sp016707485	79.4194	448	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	99.34	99.18	0.96	0.94	4	-
GCF_900115085.1	s__Dokdonella immobilis	79.2632	466	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721015.1	s__Dokdonella sp016721015	78.8388	397	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302215.1	s__Dokdonella sp017302215	78.3821	330	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	77.9644	230	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363655.1	s__Tahibacter aquaticus	77.6931	252	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242485.1	s__SZAS-103 sp018242485	77.2936	165	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015905245.1	s__Luteibacter sp015905245	77.2757	163	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	98.85	98.84	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-28 22:32:34,735] [INFO] GTDB search result was written to GCA_017987335.1_ASM1798733v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:32:34,735] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:32:34,740] [INFO] DFAST_QC result json was written to GCA_017987335.1_ASM1798733v1_genomic.fna/dqc_result.json
[2023-06-28 22:32:34,740] [INFO] DFAST_QC completed!
[2023-06-28 22:32:34,741] [INFO] Total running time: 0h1m17s