[2024-01-25 18:14:20,595] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:20,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:20,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cd3c34d-1fac-49bd-a706-576f1332515f/dqc_reference
[2024-01-25 18:14:21,726] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:21,727] [INFO] Task started: Prodigal
[2024-01-25 18:14:21,727] [INFO] Running command: gunzip -c /var/lib/cwl/stgdba3cc52-0be2-4a6f-9ec0-1cd37e0d5620/GCF_013328205.1_ASM1332820v1_genomic.fna.gz | prodigal -d GCF_013328205.1_ASM1332820v1_genomic.fna/cds.fna -a GCF_013328205.1_ASM1332820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:30,926] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:30,927] [INFO] Task started: HMMsearch
[2024-01-25 18:14:30,927] [INFO] Running command: hmmsearch --tblout GCF_013328205.1_ASM1332820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cd3c34d-1fac-49bd-a706-576f1332515f/dqc_reference/reference_markers.hmm GCF_013328205.1_ASM1332820v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:31,132] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:31,134] [INFO] Found 6/6 markers.
[2024-01-25 18:14:31,163] [INFO] Query marker FASTA was written to GCF_013328205.1_ASM1332820v1_genomic.fna/markers.fasta
[2024-01-25 18:14:31,163] [INFO] Task started: Blastn
[2024-01-25 18:14:31,163] [INFO] Running command: blastn -query GCF_013328205.1_ASM1332820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cd3c34d-1fac-49bd-a706-576f1332515f/dqc_reference/reference_markers.fasta -out GCF_013328205.1_ASM1332820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:32,012] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:32,015] [INFO] Selected 12 target genomes.
[2024-01-25 18:14:32,015] [INFO] Target genome list was writen to GCF_013328205.1_ASM1332820v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:32,023] [INFO] Task started: fastANI
[2024-01-25 18:14:32,023] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba3cc52-0be2-4a6f-9ec0-1cd37e0d5620/GCF_013328205.1_ASM1332820v1_genomic.fna.gz --refList GCF_013328205.1_ASM1332820v1_genomic.fna/target_genomes.txt --output GCF_013328205.1_ASM1332820v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:42,846] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:42,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cd3c34d-1fac-49bd-a706-576f1332515f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:42,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cd3c34d-1fac-49bd-a706-576f1332515f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:42,855] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:14:42,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:42,856] [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 hominis	strain=HHU CXW	GCA_013328205.1	2741495	2741495	type	True	100.0	1166	1168	95	conclusive
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	87.5432	841	1168	95	below_threshold
Sphingomonas palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	86.594	844	1168	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	81.8587	593	1168	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	81.649	719	1168	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	81.6031	700	1168	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	81.4745	650	1168	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	81.4407	721	1168	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	81.3794	677	1168	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	81.3122	626	1168	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	79.7969	561	1168	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	79.3456	507	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:42,857] [INFO] DFAST Taxonomy check result was written to GCF_013328205.1_ASM1332820v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:42,857] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:42,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:42,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cd3c34d-1fac-49bd-a706-576f1332515f/dqc_reference/checkm_data
[2024-01-25 18:14:42,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:42,896] [INFO] Task started: CheckM
[2024-01-25 18:14:42,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013328205.1_ASM1332820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013328205.1_ASM1332820v1_genomic.fna/checkm_input GCF_013328205.1_ASM1332820v1_genomic.fna/checkm_result
[2024-01-25 18:15:11,635] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:11,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:11,654] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:11,654] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:11,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013328205.1_ASM1332820v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:11,655] [INFO] Task started: Blastn
[2024-01-25 18:15:11,655] [INFO] Running command: blastn -query GCF_013328205.1_ASM1332820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cd3c34d-1fac-49bd-a706-576f1332515f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013328205.1_ASM1332820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:13,161] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:13,164] [INFO] Selected 17 target genomes.
[2024-01-25 18:15:13,164] [INFO] Target genome list was writen to GCF_013328205.1_ASM1332820v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:13,176] [INFO] Task started: fastANI
[2024-01-25 18:15:13,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgdba3cc52-0be2-4a6f-9ec0-1cd37e0d5620/GCF_013328205.1_ASM1332820v1_genomic.fna.gz --refList GCF_013328205.1_ASM1332820v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013328205.1_ASM1332820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:27,627] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:27,638] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:27,638] [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_013328205.1	s__Sphingomonas hominis	100.0	1166	1168	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_900109565.1	s__Sphingomonas palmae	86.594	844	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382485.1	s__Sphingomonas sp000382485	86.1648	773	1168	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	81.6515	696	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199415.1	s__Sphingomonas endophytica	81.4989	647	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.00	98.00	0.92	0.92	2	-
GCF_002374855.1	s__Sphingomonas adhaesiva	81.4772	699	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.76	99.56	0.89	0.87	3	-
GCF_014193845.1	s__Sphingomonas sp014193845	81.2862	687	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_000427645.1	s__Sphingomonas phyllosphaerae	81.2836	628	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506455.1	s__Sphingomonas sp902506455	81.0548	642	1168	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	80.4792	646	1168	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	80.4638	599	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820445.1	s__Sphingomonas sp016820445	80.0829	560	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.21	97.21	0.90	0.90	2	-
GCF_003050705.1	s__Sphingomonas aurantiaca	79.8288	597	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.29	95.02	0.87	0.86	4	-
GCF_900115295.1	s__Sphingomonas sp900115295	79.4194	548	1168	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	79.37	505	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016743815.1	s__Sphingomonas sp016743815	79.0742	487	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956315.1	s__Sphingomonas_G montana	78.1311	366	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:27,640] [INFO] GTDB search result was written to GCF_013328205.1_ASM1332820v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:27,641] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:27,644] [INFO] DFAST_QC result json was written to GCF_013328205.1_ASM1332820v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:27,644] [INFO] DFAST_QC completed!
[2024-01-25 18:15:27,644] [INFO] Total running time: 0h1m7s