[2024-01-24 12:42:08,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:08,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:08,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ddaff91-c1a0-4f98-8a61-dfc1ccd93ccd/dqc_reference
[2024-01-24 12:42:10,178] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,179] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a803346-354e-4d49-9aad-2882207fc55a/GCF_024925465.1_ASM2492546v1_genomic.fna.gz | prodigal -d GCF_024925465.1_ASM2492546v1_genomic.fna/cds.fna -a GCF_024925465.1_ASM2492546v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:31,073] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:31,073] [INFO] Task started: HMMsearch
[2024-01-24 12:42:31,074] [INFO] Running command: hmmsearch --tblout GCF_024925465.1_ASM2492546v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ddaff91-c1a0-4f98-8a61-dfc1ccd93ccd/dqc_reference/reference_markers.hmm GCF_024925465.1_ASM2492546v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:31,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:31,388] [INFO] Found 6/6 markers.
[2024-01-24 12:42:31,433] [INFO] Query marker FASTA was written to GCF_024925465.1_ASM2492546v1_genomic.fna/markers.fasta
[2024-01-24 12:42:31,434] [INFO] Task started: Blastn
[2024-01-24 12:42:31,434] [INFO] Running command: blastn -query GCF_024925465.1_ASM2492546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ddaff91-c1a0-4f98-8a61-dfc1ccd93ccd/dqc_reference/reference_markers.fasta -out GCF_024925465.1_ASM2492546v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:32,523] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:32,527] [INFO] Selected 10 target genomes.
[2024-01-24 12:42:32,527] [INFO] Target genome list was writen to GCF_024925465.1_ASM2492546v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:32,532] [INFO] Task started: fastANI
[2024-01-24 12:42:32,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a803346-354e-4d49-9aad-2882207fc55a/GCF_024925465.1_ASM2492546v1_genomic.fna.gz --refList GCF_024925465.1_ASM2492546v1_genomic.fna/target_genomes.txt --output GCF_024925465.1_ASM2492546v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:48,202] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:48,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ddaff91-c1a0-4f98-8a61-dfc1ccd93ccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:48,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ddaff91-c1a0-4f98-8a61-dfc1ccd93ccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:48,214] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:42:48,214] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:48,214] [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
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	100.0	1894	1895	95	conclusive
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	99.8906	1707	1895	95	conclusive
Ralstonia solanacearum	strain=NCPPB 325	GCA_015910705.1	305	305	type	True	91.3455	1434	1895	95	below_threshold
Ralstonia solanacearum	strain=K60	GCA_002251695.1	305	305	type	True	91.319	1431	1895	95	below_threshold
Ralstonia mannitolilytica	strain=LMG 6866	GCA_905397375.1	105219	105219	type	True	85.5208	1061	1895	95	below_threshold
Ralstonia insidiosa	strain=CCUG 46789	GCA_008801405.1	190721	190721	type	True	85.1525	1069	1895	95	below_threshold
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	84.6697	1062	1895	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	80.8567	774	1895	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.948	700	1895	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.1204	537	1895	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:48,216] [INFO] DFAST Taxonomy check result was written to GCF_024925465.1_ASM2492546v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:48,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:48,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:48,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ddaff91-c1a0-4f98-8a61-dfc1ccd93ccd/dqc_reference/checkm_data
[2024-01-24 12:42:48,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:48,271] [INFO] Task started: CheckM
[2024-01-24 12:42:48,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024925465.1_ASM2492546v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024925465.1_ASM2492546v1_genomic.fna/checkm_input GCF_024925465.1_ASM2492546v1_genomic.fna/checkm_result
[2024-01-24 12:44:06,774] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:06,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:06,799] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:06,799] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:06,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024925465.1_ASM2492546v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:06,800] [INFO] Task started: Blastn
[2024-01-24 12:44:06,800] [INFO] Running command: blastn -query GCF_024925465.1_ASM2492546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ddaff91-c1a0-4f98-8a61-dfc1ccd93ccd/dqc_reference/reference_markers_gtdb.fasta -out GCF_024925465.1_ASM2492546v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:09,009] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:09,015] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:09,015] [INFO] Target genome list was writen to GCF_024925465.1_ASM2492546v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:09,065] [INFO] Task started: fastANI
[2024-01-24 12:44:09,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a803346-354e-4d49-9aad-2882207fc55a/GCF_024925465.1_ASM2492546v1_genomic.fna.gz --refList GCF_024925465.1_ASM2492546v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024925465.1_ASM2492546v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:44:24,083] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:24,100] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:44:24,100] [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_003999715.1	s__Ralstonia pseudosolanacearum	95.8192	1573	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.86	95.79	0.91	0.82	165	conclusive
GCF_016743075.1	s__Ralstonia syzygii	92.363	1328	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.48	97.12	0.87	0.80	19	-
GCF_002251695.1	s__Ralstonia solanacearum	91.3255	1432	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.27	95.49	0.87	0.78	131	-
GCA_002298975.1	s__Ralstonia sp002298975	85.761	1105	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905397375.1	s__Ralstonia mannitolilytica	85.5191	1060	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.68	96.05	0.93	0.87	14	-
GCF_001078575.1	s__Ralstonia sp001078575	85.2206	1094	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.81	99.41	0.97	0.93	9	-
GCF_000801955.1	s__Ralstonia sp000801955	85.2028	1103	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620465.1	s__Ralstonia sp000620465	85.0737	1079	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.59	96.59	0.94	0.94	2	-
GCF_007997035.1	s__Ralstonia sp007997035	85.0276	1026	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016429285.1	s__Ralstonia sp016429285	84.8906	990	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016466415.1	s__Ralstonia pickettii	84.7212	1055	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.89	95.45	0.93	0.86	44	-
GCF_000607165.1	s__Ralstonia pickettii_A	84.489	1068	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.13	99.13	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:44:24,102] [INFO] GTDB search result was written to GCF_024925465.1_ASM2492546v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:44:24,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:44:24,192] [INFO] DFAST_QC result json was written to GCF_024925465.1_ASM2492546v1_genomic.fna/dqc_result.json
[2024-01-24 12:44:24,192] [INFO] DFAST_QC completed!
[2024-01-24 12:44:24,192] [INFO] Total running time: 0h2m15s