[2024-01-24 13:40:34,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,352] [INFO] DQC Reference Directory: /var/lib/cwl/stga87ff90c-e108-47f1-885f-4f4895b27147/dqc_reference
[2024-01-24 13:40:35,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,784] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg41502518-426c-4df7-9736-dbaa576a6cee/GCF_004792695.1_ASM479269v1_genomic.fna.gz | prodigal -d GCF_004792695.1_ASM479269v1_genomic.fna/cds.fna -a GCF_004792695.1_ASM479269v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,568] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,568] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,568] [INFO] Running command: hmmsearch --tblout GCF_004792695.1_ASM479269v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga87ff90c-e108-47f1-885f-4f4895b27147/dqc_reference/reference_markers.hmm GCF_004792695.1_ASM479269v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:48,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:48,858] [INFO] Found 6/6 markers.
[2024-01-24 13:40:48,909] [INFO] Query marker FASTA was written to GCF_004792695.1_ASM479269v1_genomic.fna/markers.fasta
[2024-01-24 13:40:48,909] [INFO] Task started: Blastn
[2024-01-24 13:40:48,909] [INFO] Running command: blastn -query GCF_004792695.1_ASM479269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga87ff90c-e108-47f1-885f-4f4895b27147/dqc_reference/reference_markers.fasta -out GCF_004792695.1_ASM479269v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,055] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,059] [INFO] Selected 22 target genomes.
[2024-01-24 13:40:50,059] [INFO] Target genome list was writen to GCF_004792695.1_ASM479269v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,079] [INFO] Task started: fastANI
[2024-01-24 13:40:50,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg41502518-426c-4df7-9736-dbaa576a6cee/GCF_004792695.1_ASM479269v1_genomic.fna.gz --refList GCF_004792695.1_ASM479269v1_genomic.fna/target_genomes.txt --output GCF_004792695.1_ASM479269v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:14,248] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:14,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga87ff90c-e108-47f1-885f-4f4895b27147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:14,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga87ff90c-e108-47f1-885f-4f4895b27147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:14,273] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:14,273] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:14,274] [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 naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	100.0	1436	1436	95	conclusive
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	99.9993	1434	1436	95	conclusive
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	85.8077	1051	1436	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	85.5314	1021	1436	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	82.9972	926	1436	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	82.9407	873	1436	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	82.1971	843	1436	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	81.8256	778	1436	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	81.8243	761	1436	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	80.8387	683	1436	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	80.8156	688	1436	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	80.7332	703	1436	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	80.0618	640	1436	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.9716	652	1436	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	79.8778	631	1436	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.6637	660	1436	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.9003	549	1436	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	77.6978	375	1436	95	below_threshold
Blastochloris viridis	strain=DSM 133	GCA_001548155.2	1079	1079	type	True	76.0935	202	1436	95	below_threshold
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	76.0447	202	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,276] [INFO] DFAST Taxonomy check result was written to GCF_004792695.1_ASM479269v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:14,277] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:14,277] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:14,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga87ff90c-e108-47f1-885f-4f4895b27147/dqc_reference/checkm_data
[2024-01-24 13:41:14,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:14,322] [INFO] Task started: CheckM
[2024-01-24 13:41:14,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004792695.1_ASM479269v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004792695.1_ASM479269v1_genomic.fna/checkm_input GCF_004792695.1_ASM479269v1_genomic.fna/checkm_result
[2024-01-24 13:41:55,575] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:55,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:55,599] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:55,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:55,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004792695.1_ASM479269v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:55,601] [INFO] Task started: Blastn
[2024-01-24 13:41:55,601] [INFO] Running command: blastn -query GCF_004792695.1_ASM479269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga87ff90c-e108-47f1-885f-4f4895b27147/dqc_reference/reference_markers_gtdb.fasta -out GCF_004792695.1_ASM479269v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:57,698] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:57,703] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:57,704] [INFO] Target genome list was writen to GCF_004792695.1_ASM479269v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:57,734] [INFO] Task started: fastANI
[2024-01-24 13:41:57,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg41502518-426c-4df7-9736-dbaa576a6cee/GCF_004792695.1_ASM479269v1_genomic.fna.gz --refList GCF_004792695.1_ASM479269v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004792695.1_ASM479269v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:18,992] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:19,011] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:19,012] [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_004792695.1	s__Sphingomonas naasensis	100.0	1436	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001428865.1	s__Sphingomonas sp001428865	86.4681	1058	1436	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	86.2534	1032	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	85.8343	1038	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796605.1	s__Sphingomonas sp002796605	85.7806	1055	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792685.1	s__Sphingomonas gei	85.5314	1021	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	84.1077	892	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449795.1	s__Sphingomonas sp018449795	83.448	808	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096895.1	s__Sphingomonas sp003096895	83.1637	898	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416555.1	s__Sphingomonas sp013416555	83.1133	914	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418975.1	s__Sphingomonas sp017418975	83.0434	889	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	83.001	899	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	82.9529	857	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	82.1592	847	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091475.1	s__Sphingomonas azotifigens	81.7438	789	1436	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	80.7334	703	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCF_001557215.1	s__Sphingomonas sp001557215	80.0548	563	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.6369	462	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307295.1	s__Sphingopyxis macrogoltabida_B	78.0518	460	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152865.1	s__Sphingobium cupriresistens	77.6894	376	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	-
GCF_001402875.1	s__Blastochloris viridis	76.0327	204	1436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:19,013] [INFO] GTDB search result was written to GCF_004792695.1_ASM479269v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:19,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:19,019] [INFO] DFAST_QC result json was written to GCF_004792695.1_ASM479269v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:19,019] [INFO] DFAST_QC completed!
[2024-01-24 13:42:19,019] [INFO] Total running time: 0h1m45s