[2023-06-28 19:21:33,190] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:21:33,193] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:21:33,193] [INFO] DQC Reference Directory: /var/lib/cwl/stg0cbc2827-dc5d-4238-bdfa-a56984286478/dqc_reference
[2023-06-28 19:21:35,431] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:21:35,432] [INFO] Task started: Prodigal
[2023-06-28 19:21:35,432] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c1fc4a3-0936-42ce-af6d-cea9a87f08ff/GCA_913774935.1_S2C23896_SP200_genomic.fna.gz | prodigal -d GCA_913774935.1_S2C23896_SP200_genomic.fna/cds.fna -a GCA_913774935.1_S2C23896_SP200_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:21:42,367] [INFO] Task succeeded: Prodigal
[2023-06-28 19:21:42,368] [INFO] Task started: HMMsearch
[2023-06-28 19:21:42,368] [INFO] Running command: hmmsearch --tblout GCA_913774935.1_S2C23896_SP200_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0cbc2827-dc5d-4238-bdfa-a56984286478/dqc_reference/reference_markers.hmm GCA_913774935.1_S2C23896_SP200_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:21:42,592] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:21:42,593] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6c1fc4a3-0936-42ce-af6d-cea9a87f08ff/GCA_913774935.1_S2C23896_SP200_genomic.fna.gz]
[2023-06-28 19:21:42,621] [INFO] Query marker FASTA was written to GCA_913774935.1_S2C23896_SP200_genomic.fna/markers.fasta
[2023-06-28 19:21:42,622] [INFO] Task started: Blastn
[2023-06-28 19:21:42,622] [INFO] Running command: blastn -query GCA_913774935.1_S2C23896_SP200_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cbc2827-dc5d-4238-bdfa-a56984286478/dqc_reference/reference_markers.fasta -out GCA_913774935.1_S2C23896_SP200_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:21:43,510] [INFO] Task succeeded: Blastn
[2023-06-28 19:21:43,514] [INFO] Selected 24 target genomes.
[2023-06-28 19:21:43,515] [INFO] Target genome list was writen to GCA_913774935.1_S2C23896_SP200_genomic.fna/target_genomes.txt
[2023-06-28 19:21:43,520] [INFO] Task started: fastANI
[2023-06-28 19:21:43,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c1fc4a3-0936-42ce-af6d-cea9a87f08ff/GCA_913774935.1_S2C23896_SP200_genomic.fna.gz --refList GCA_913774935.1_S2C23896_SP200_genomic.fna/target_genomes.txt --output GCA_913774935.1_S2C23896_SP200_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:22:00,729] [INFO] Task succeeded: fastANI
[2023-06-28 19:22:00,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0cbc2827-dc5d-4238-bdfa-a56984286478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:22:00,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0cbc2827-dc5d-4238-bdfa-a56984286478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:22:00,752] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:22:00,752] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:22:00,753] [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	79.9937	475	850	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	79.7332	465	850	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	79.6361	453	850	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	79.5823	424	850	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.3745	459	850	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.291	421	850	95	below_threshold
Sphingomonas aerolata	strain=NW12	GCA_003046295.1	185951	185951	type	True	79.2666	407	850	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	79.2641	417	850	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.2608	404	850	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	79.2361	419	850	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	79.227	416	850	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	79.1735	423	850	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	79.1562	377	850	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.1492	425	850	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.1344	446	850	95	below_threshold
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	79.1323	387	850	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	79.0821	381	850	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.0543	399	850	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.9686	398	850	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.9639	407	850	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	78.9561	411	850	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	78.8895	354	850	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.8118	422	850	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	78.709	396	850	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:22:00,755] [INFO] DFAST Taxonomy check result was written to GCA_913774935.1_S2C23896_SP200_genomic.fna/tc_result.tsv
[2023-06-28 19:22:00,755] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:22:00,756] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:22:00,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0cbc2827-dc5d-4238-bdfa-a56984286478/dqc_reference/checkm_data
[2023-06-28 19:22:00,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:22:00,784] [INFO] Task started: CheckM
[2023-06-28 19:22:00,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913774935.1_S2C23896_SP200_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913774935.1_S2C23896_SP200_genomic.fna/checkm_input GCA_913774935.1_S2C23896_SP200_genomic.fna/checkm_result
[2023-06-28 19:22:25,642] [INFO] Task succeeded: CheckM
[2023-06-28 19:22:25,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:22:25,666] [INFO] ===== Completeness check finished =====
[2023-06-28 19:22:25,666] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:22:25,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913774935.1_S2C23896_SP200_genomic.fna/markers.fasta)
[2023-06-28 19:22:25,667] [INFO] Task started: Blastn
[2023-06-28 19:22:25,667] [INFO] Running command: blastn -query GCA_913774935.1_S2C23896_SP200_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cbc2827-dc5d-4238-bdfa-a56984286478/dqc_reference/reference_markers_gtdb.fasta -out GCA_913774935.1_S2C23896_SP200_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:22:27,333] [INFO] Task succeeded: Blastn
[2023-06-28 19:22:27,339] [INFO] Selected 19 target genomes.
[2023-06-28 19:22:27,340] [INFO] Target genome list was writen to GCA_913774935.1_S2C23896_SP200_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:22:27,354] [INFO] Task started: fastANI
[2023-06-28 19:22:27,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c1fc4a3-0936-42ce-af6d-cea9a87f08ff/GCA_913774935.1_S2C23896_SP200_genomic.fna.gz --refList GCA_913774935.1_S2C23896_SP200_genomic.fna/target_genomes_gtdb.txt --output GCA_913774935.1_S2C23896_SP200_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:22:41,984] [INFO] Task succeeded: fastANI
[2023-06-28 19:22:42,014] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:22:42,015] [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_016937575.1	s__Sphingomonas aeriglobus	87.3124	726	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421785.1	s__Sphingomonas sp001421785	86.256	681	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199185.1	s__Sphingomonas guangdongensis	79.9765	477	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946805.1	s__Sphingomonas sp003946805	79.6396	446	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	79.5334	414	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	79.4973	437	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421765.1	s__Sphingomonas sp001421765	79.4969	454	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCA_017744835.1	s__Sphingomonas sp017744835	79.4484	420	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107325.1	s__Sphingomonas sp016107325	79.4435	431	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632225.1	s__Sphingomonas sp000632225	79.3536	434	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557215.1	s__Sphingomonas sp001557215	79.3159	364	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_014641735.1	s__Sphingomonas metalli	79.3059	421	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797435.1	s__Sphingomonas koreensis	79.2566	419	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_004792695.1	s__Sphingomonas naasensis	79.2078	435	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007859635.1	s__Sphingomonas panacisoli	79.1562	377	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927115.1	s__Sphingomonas sp012927115	79.1078	418	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	78.888	419	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884945.1	s__Sphingomonas sp903884945	78.3998	384	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173185.1	s__Sphingomonas sp004173185	78.065	340	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:22:42,017] [INFO] GTDB search result was written to GCA_913774935.1_S2C23896_SP200_genomic.fna/result_gtdb.tsv
[2023-06-28 19:22:42,018] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:22:42,023] [INFO] DFAST_QC result json was written to GCA_913774935.1_S2C23896_SP200_genomic.fna/dqc_result.json
[2023-06-28 19:22:42,023] [INFO] DFAST_QC completed!
[2023-06-28 19:22:42,023] [INFO] Total running time: 0h1m9s