[2024-01-24 12:30:05,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg50e38098-3449-4b30-9ff6-a34f78aafb7b/dqc_reference
[2024-01-24 12:30:07,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,246] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,246] [INFO] Running command: gunzip -c /var/lib/cwl/stga2a7510f-d811-41e9-9ed4-d3dda9cdd61f/GCF_010211745.1_ASM1021174v1_genomic.fna.gz | prodigal -d GCF_010211745.1_ASM1021174v1_genomic.fna/cds.fna -a GCF_010211745.1_ASM1021174v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:15,998] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:15,998] [INFO] Task started: HMMsearch
[2024-01-24 12:30:15,998] [INFO] Running command: hmmsearch --tblout GCF_010211745.1_ASM1021174v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50e38098-3449-4b30-9ff6-a34f78aafb7b/dqc_reference/reference_markers.hmm GCF_010211745.1_ASM1021174v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:16,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:16,263] [INFO] Found 6/6 markers.
[2024-01-24 12:30:16,288] [INFO] Query marker FASTA was written to GCF_010211745.1_ASM1021174v1_genomic.fna/markers.fasta
[2024-01-24 12:30:16,288] [INFO] Task started: Blastn
[2024-01-24 12:30:16,288] [INFO] Running command: blastn -query GCF_010211745.1_ASM1021174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50e38098-3449-4b30-9ff6-a34f78aafb7b/dqc_reference/reference_markers.fasta -out GCF_010211745.1_ASM1021174v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:17,227] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:17,230] [INFO] Selected 28 target genomes.
[2024-01-24 12:30:17,230] [INFO] Target genome list was writen to GCF_010211745.1_ASM1021174v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:17,259] [INFO] Task started: fastANI
[2024-01-24 12:30:17,260] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a7510f-d811-41e9-9ed4-d3dda9cdd61f/GCF_010211745.1_ASM1021174v1_genomic.fna.gz --refList GCF_010211745.1_ASM1021174v1_genomic.fna/target_genomes.txt --output GCF_010211745.1_ASM1021174v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:37,498] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:37,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50e38098-3449-4b30-9ff6-a34f78aafb7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:37,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50e38098-3449-4b30-9ff6-a34f78aafb7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:37,514] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:37,514] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:37,515] [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
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	100.0	972	972	95	conclusive
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	83.6355	646	972	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	82.8924	612	972	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	82.3823	579	972	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	82.2185	571	972	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	82.1037	631	972	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	82.0593	645	972	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	82.0189	640	972	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	81.9353	588	972	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	81.9051	622	972	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	81.8672	605	972	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	81.8462	558	972	95	below_threshold
Pseudoxanthomonas sacheonensis	strain=DSM 19373	GCA_010093305.1	443615	443615	type	True	81.8369	621	972	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	81.819	558	972	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	81.3891	523	972	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.018	565	972	95	below_threshold
Pseudoxanthomonas indica	strain=P15	GCA_900167565.1	428993	428993	type	True	80.9614	580	972	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.9304	451	972	95	below_threshold
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	80.9265	572	972	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	80.7808	500	972	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	80.7045	543	972	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	80.6777	493	972	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	80.6546	491	972	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	80.5001	484	972	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	80.4794	582	972	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	80.0393	444	972	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	79.906	431	972	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	79.6484	434	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:37,516] [INFO] DFAST Taxonomy check result was written to GCF_010211745.1_ASM1021174v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:37,517] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:37,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:37,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50e38098-3449-4b30-9ff6-a34f78aafb7b/dqc_reference/checkm_data
[2024-01-24 12:30:37,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:37,550] [INFO] Task started: CheckM
[2024-01-24 12:30:37,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010211745.1_ASM1021174v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010211745.1_ASM1021174v1_genomic.fna/checkm_input GCF_010211745.1_ASM1021174v1_genomic.fna/checkm_result
[2024-01-24 12:31:09,806] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:09,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:09,831] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:09,832] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:09,832] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010211745.1_ASM1021174v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:09,832] [INFO] Task started: Blastn
[2024-01-24 12:31:09,832] [INFO] Running command: blastn -query GCF_010211745.1_ASM1021174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50e38098-3449-4b30-9ff6-a34f78aafb7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_010211745.1_ASM1021174v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:11,686] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:11,689] [INFO] Selected 27 target genomes.
[2024-01-24 12:31:11,689] [INFO] Target genome list was writen to GCF_010211745.1_ASM1021174v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:11,702] [INFO] Task started: fastANI
[2024-01-24 12:31:11,702] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a7510f-d811-41e9-9ed4-d3dda9cdd61f/GCF_010211745.1_ASM1021174v1_genomic.fna.gz --refList GCF_010211745.1_ASM1021174v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010211745.1_ASM1021174v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:32,052] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:32,067] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:32,068] [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_010211745.1	s__Pseudoxanthomonas_A kalamensis	100.0	972	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	83.6275	647	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972865.1	s__Pseudoxanthomonas suwonensis_B	82.4363	629	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093225.1	s__Pseudoxanthomonas koreensis	82.3597	580	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431505.1	s__Stenotrophomonas daejeonensis	82.1744	574	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218945.1	s__Pseudoxanthomonas_A sp019218945	82.1723	644	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.15	98.62	0.97	0.96	4	-
GCF_010211765.1	s__Pseudoxanthomonas kaohsiungensis	82.068	609	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	82.0256	636	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215535.1	s__Pseudoxanthomonas_A wuyuanensis	82.0203	648	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	81.9942	589	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	81.929	589	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900018785.1	s__Xanthomonas_B massiliensis	81.857	558	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004284655.1	s__Pseudoxanthomonas_A spadix_A	81.8539	588	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.46	98.41	0.91	0.91	3	-
GCF_010093305.1	s__Pseudoxanthomonas_A sacheonensis	81.837	621	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851815.1	s__Pseudoxanthomonas_A sp014851815	81.7526	592	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004284195.1	s__Pseudoxanthomonas_A sp004284195	81.6327	609	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	97.94	97.04	0.92	0.87	11	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	81.5242	581	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	81.5033	550	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900104085.1	s__Pseudoxanthomonas_A sp900104085	81.1192	595	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859305.1	s__Luteimonas wenzhouensis	81.1019	547	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_000472505.1	s__Luteimonas sp000472505	81.0637	573	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_016774335.1	s__Luteimonas sp016774335	81.0037	567	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	80.7809	500	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357985.1	s__Luteimonas aestuarii	80.716	542	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352845.1	s__Luteimonas terricola	80.6957	491	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006265115.1	s__Arenimonas terrae	80.0395	444	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747155.1	s__Arenimonas metalli	79.9444	428	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:32,070] [INFO] GTDB search result was written to GCF_010211745.1_ASM1021174v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:32,071] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:32,076] [INFO] DFAST_QC result json was written to GCF_010211745.1_ASM1021174v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:32,076] [INFO] DFAST_QC completed!
[2024-01-24 12:31:32,076] [INFO] Total running time: 0h1m27s