[2024-01-24 13:52:12,512] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,515] [INFO] DQC Reference Directory: /var/lib/cwl/stga3d47b76-684e-40b0-9638-52c022f08238/dqc_reference
[2024-01-24 13:52:13,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:13,735] [INFO] Task started: Prodigal
[2024-01-24 13:52:13,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e3a1722-da4d-4ca0-9606-68bd7680ae5c/GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/cds.fna -a GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:23,566] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:23,567] [INFO] Task started: HMMsearch
[2024-01-24 13:52:23,567] [INFO] Running command: hmmsearch --tblout GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3d47b76-684e-40b0-9638-52c022f08238/dqc_reference/reference_markers.hmm GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:23,814] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:23,816] [INFO] Found 6/6 markers.
[2024-01-24 13:52:23,850] [INFO] Query marker FASTA was written to GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:52:23,851] [INFO] Task started: Blastn
[2024-01-24 13:52:23,851] [INFO] Running command: blastn -query GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d47b76-684e-40b0-9638-52c022f08238/dqc_reference/reference_markers.fasta -out GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:24,778] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:24,782] [INFO] Selected 21 target genomes.
[2024-01-24 13:52:24,783] [INFO] Target genome list was writen to GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:52:24,798] [INFO] Task started: fastANI
[2024-01-24 13:52:24,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e3a1722-da4d-4ca0-9606-68bd7680ae5c/GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna.gz --refList GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:40,667] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:40,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3d47b76-684e-40b0-9638-52c022f08238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:40,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3d47b76-684e-40b0-9638-52c022f08238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:40,688] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:52:40,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:40,688] [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
Sphingomonas guangdongensis	strain=CGMCC 1.12672	GCA_900199185.1	1141890	1141890	type	True	100.0	1177	1178	95	conclusive
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	80.0872	590	1178	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.9437	583	1178	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.9011	549	1178	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.8648	512	1178	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.8232	587	1178	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	79.7979	456	1178	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.7855	595	1178	95	below_threshold
Sphingomonas palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	79.7359	503	1178	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.5378	573	1178	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	79.4016	520	1178	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	79.3745	504	1178	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	79.1972	477	1178	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.1831	472	1178	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	79.16	480	1178	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	79.0935	474	1178	95	below_threshold
Sphingomonas pokkalii	strain=L3B27	GCA_003096275.1	2175090	2175090	type	True	78.9634	430	1178	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	78.5902	466	1178	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	78.5461	458	1178	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.1481	363	1178	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.0461	383	1178	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:40,690] [INFO] DFAST Taxonomy check result was written to GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:52:40,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:40,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:40,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3d47b76-684e-40b0-9638-52c022f08238/dqc_reference/checkm_data
[2024-01-24 13:52:40,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:40,732] [INFO] Task started: CheckM
[2024-01-24 13:52:40,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/checkm_input GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:53:12,251] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:12,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:12,327] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:12,328] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:12,328] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:53:12,328] [INFO] Task started: Blastn
[2024-01-24 13:53:12,329] [INFO] Running command: blastn -query GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga3d47b76-684e-40b0-9638-52c022f08238/dqc_reference/reference_markers_gtdb.fasta -out GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:14,074] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:14,078] [INFO] Selected 23 target genomes.
[2024-01-24 13:53:14,078] [INFO] Target genome list was writen to GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:14,107] [INFO] Task started: fastANI
[2024-01-24 13:53:14,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e3a1722-da4d-4ca0-9606-68bd7680ae5c/GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna.gz --refList GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:31,697] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:31,719] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:31,720] [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_900199185.1	s__Sphingomonas guangdongensis	100.0	1177	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001421785.1	s__Sphingomonas sp001421785	80.4858	593	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937575.1	s__Sphingomonas aeriglobus	80.3181	614	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641735.1	s__Sphingomonas metalli	80.0775	591	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	79.9521	609	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_900115745.1	s__Sphingomonas rubra	79.9481	545	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012035195.1	s__Sphingomonas sp012035195	79.8593	593	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556185.1	s__Sphingomonas sp001556185	79.7682	412	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.51	96.51	0.87	0.87	2	-
GCF_003951315.1	s__Sphingomonas sp003951315	79.634	528	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	79.5532	580	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	79.5037	578	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503355.1	s__Sphingomonas sp005503355	79.502	500	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017744835.1	s__Sphingomonas sp017744835	79.3737	516	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903644135.1	s__Sphingomonas sp903644135	79.319	314	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304635.1	s__Sphingomonas sp017304635	79.2759	492	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344685.1	s__Sphingomonas sp013344685	79.1946	482	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	79.1773	495	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_002797435.1	s__Sphingomonas koreensis	79.1561	480	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_009789535.1	s__Sphingomonas carotinifaciens	79.0774	477	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.06	97.19	0.97	0.90	4	-
GCF_000712135.1	s__Sphingomonas sp000712135	78.9709	466	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	78.8514	489	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	78.1278	365	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822915.1	s__Sphingomonas sp013822915	76.6635	143	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:31,721] [INFO] GTDB search result was written to GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:31,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:31,727] [INFO] DFAST_QC result json was written to GCF_900199185.1_IMG-taxon_2718218511_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:53:31,727] [INFO] DFAST_QC completed!
[2024-01-24 13:53:31,727] [INFO] Total running time: 0h1m19s