[2024-01-24 11:20:04,213] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dd314e1-3b70-4372-8e3d-23614ec61f76/dqc_reference
[2024-01-24 11:20:05,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,358] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,358] [INFO] Running command: gunzip -c /var/lib/cwl/stgfab44540-b29b-48e2-93fa-c8b5a6fd6825/GCF_014641735.1_ASM1464173v1_genomic.fna.gz | prodigal -d GCF_014641735.1_ASM1464173v1_genomic.fna/cds.fna -a GCF_014641735.1_ASM1464173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:15,594] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:15,594] [INFO] Task started: HMMsearch
[2024-01-24 11:20:15,594] [INFO] Running command: hmmsearch --tblout GCF_014641735.1_ASM1464173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dd314e1-3b70-4372-8e3d-23614ec61f76/dqc_reference/reference_markers.hmm GCF_014641735.1_ASM1464173v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:15,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:15,799] [INFO] Found 6/6 markers.
[2024-01-24 11:20:15,829] [INFO] Query marker FASTA was written to GCF_014641735.1_ASM1464173v1_genomic.fna/markers.fasta
[2024-01-24 11:20:15,830] [INFO] Task started: Blastn
[2024-01-24 11:20:15,830] [INFO] Running command: blastn -query GCF_014641735.1_ASM1464173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dd314e1-3b70-4372-8e3d-23614ec61f76/dqc_reference/reference_markers.fasta -out GCF_014641735.1_ASM1464173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:16,826] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:16,830] [INFO] Selected 25 target genomes.
[2024-01-24 11:20:16,830] [INFO] Target genome list was writen to GCF_014641735.1_ASM1464173v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:16,845] [INFO] Task started: fastANI
[2024-01-24 11:20:16,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab44540-b29b-48e2-93fa-c8b5a6fd6825/GCF_014641735.1_ASM1464173v1_genomic.fna.gz --refList GCF_014641735.1_ASM1464173v1_genomic.fna/target_genomes.txt --output GCF_014641735.1_ASM1464173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:37,354] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:37,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dd314e1-3b70-4372-8e3d-23614ec61f76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:37,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dd314e1-3b70-4372-8e3d-23614ec61f76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:37,373] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:37,373] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:37,373] [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 metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	100.0	1273	1275	95	conclusive
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	82.5768	752	1275	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	81.8641	664	1275	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	81.5766	666	1275	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	81.5481	715	1275	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	81.3735	647	1275	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	81.3058	669	1275	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	81.2664	657	1275	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	81.2656	538	1275	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	81.1441	613	1275	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	81.1321	653	1275	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	81.0823	675	1275	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	81.0509	631	1275	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	81.034	688	1275	95	below_threshold
Sphingomonas zeae	strain=DSM 100049	GCA_014197135.1	1646122	1646122	type	True	80.9995	650	1275	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_014199595.1	172044	172044	type	True	80.96	662	1275	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.909	671	1275	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	80.8983	667	1275	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	80.8037	651	1275	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	80.6017	673	1275	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	80.4194	577	1275	95	below_threshold
Sphingomonas lenta	strain=1PNM-20	GCA_002288825.1	1141887	1141887	type	True	80.1867	568	1275	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	80.1032	554	1275	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	80.0531	517	1275	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	79.3678	489	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:37,375] [INFO] DFAST Taxonomy check result was written to GCF_014641735.1_ASM1464173v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:37,375] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:37,375] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:37,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dd314e1-3b70-4372-8e3d-23614ec61f76/dqc_reference/checkm_data
[2024-01-24 11:20:37,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:37,412] [INFO] Task started: CheckM
[2024-01-24 11:20:37,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641735.1_ASM1464173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641735.1_ASM1464173v1_genomic.fna/checkm_input GCF_014641735.1_ASM1464173v1_genomic.fna/checkm_result
[2024-01-24 11:21:10,378] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:10,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:10,396] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:10,396] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:10,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641735.1_ASM1464173v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:10,396] [INFO] Task started: Blastn
[2024-01-24 11:21:10,396] [INFO] Running command: blastn -query GCF_014641735.1_ASM1464173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dd314e1-3b70-4372-8e3d-23614ec61f76/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641735.1_ASM1464173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:12,278] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:12,281] [INFO] Selected 21 target genomes.
[2024-01-24 11:21:12,281] [INFO] Target genome list was writen to GCF_014641735.1_ASM1464173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:12,306] [INFO] Task started: fastANI
[2024-01-24 11:21:12,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab44540-b29b-48e2-93fa-c8b5a6fd6825/GCF_014641735.1_ASM1464173v1_genomic.fna.gz --refList GCF_014641735.1_ASM1464173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641735.1_ASM1464173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:30,779] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:30,795] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:30,796] [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_014641735.1	s__Sphingomonas metalli	100.0	1273	1275	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_014199625.1	s__Sphingomonas abaci	82.5879	749	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003951315.1	s__Sphingomonas sp003951315	82.4729	725	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115745.1	s__Sphingomonas rubra	81.8442	668	1275	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	81.7468	714	1275	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	81.5885	695	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841615.1	s__Sphingomonas sp014841615	81.5644	681	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	81.5476	718	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_003355005.1	s__Sphingomonas sp003355005	81.4534	630	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197105.1	s__Sphingomonas jinjuensis	81.3582	648	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789535.1	s__Sphingomonas carotinifaciens	81.2882	666	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.06	97.19	0.97	0.90	4	-
GCF_002374835.1	s__Sphingomonas ginsenosidimutans	81.2025	607	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.62	98.43	0.85	0.81	6	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	81.0817	675	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014197135.1	s__Sphingomonas zeae	81.0143	647	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000739895.2	s__Sphingomonas paucimobilis	81.0136	634	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	-
GCF_016820445.1	s__Sphingomonas sp016820445	81.009	624	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.21	97.21	0.90	0.90	2	-
GCF_016427505.1	s__Sphingomonas sp016427505	80.9847	670	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139225.1	s__Sphingomonas sp018139225	80.8894	686	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_903644135.1	s__Sphingomonas sp903644135	80.7124	356	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476895.1	s__Sphingomonas endophytica_A	80.656	581	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110035.1	s__Sphingomonas gellani	80.0887	557	1275	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 11:21:30,797] [INFO] GTDB search result was written to GCF_014641735.1_ASM1464173v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:30,798] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:30,802] [INFO] DFAST_QC result json was written to GCF_014641735.1_ASM1464173v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:30,802] [INFO] DFAST_QC completed!
[2024-01-24 11:21:30,802] [INFO] Total running time: 0h1m27s