[2024-01-24 15:27:12,733] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg09e61c1c-d4b4-4dc8-aa06-ac9f338f6de2/dqc_reference
[2024-01-24 15:27:14,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:14,160] [INFO] Task started: Prodigal
[2024-01-24 15:27:14,160] [INFO] Running command: gunzip -c /var/lib/cwl/stg98081969-22c6-4280-ba2b-e567ebc4d4e7/GCF_902859845.1_LMG_29660_genomic.fna.gz | prodigal -d GCF_902859845.1_LMG_29660_genomic.fna/cds.fna -a GCF_902859845.1_LMG_29660_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:39,543] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:39,544] [INFO] Task started: HMMsearch
[2024-01-24 15:27:39,544] [INFO] Running command: hmmsearch --tblout GCF_902859845.1_LMG_29660_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09e61c1c-d4b4-4dc8-aa06-ac9f338f6de2/dqc_reference/reference_markers.hmm GCF_902859845.1_LMG_29660_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:39,984] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:39,986] [INFO] Found 6/6 markers.
[2024-01-24 15:27:40,047] [INFO] Query marker FASTA was written to GCF_902859845.1_LMG_29660_genomic.fna/markers.fasta
[2024-01-24 15:27:40,047] [INFO] Task started: Blastn
[2024-01-24 15:27:40,048] [INFO] Running command: blastn -query GCF_902859845.1_LMG_29660_genomic.fna/markers.fasta -db /var/lib/cwl/stg09e61c1c-d4b4-4dc8-aa06-ac9f338f6de2/dqc_reference/reference_markers.fasta -out GCF_902859845.1_LMG_29660_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:41,126] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:41,130] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:41,131] [INFO] Target genome list was writen to GCF_902859845.1_LMG_29660_genomic.fna/target_genomes.txt
[2024-01-24 15:27:41,138] [INFO] Task started: fastANI
[2024-01-24 15:27:41,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg98081969-22c6-4280-ba2b-e567ebc4d4e7/GCF_902859845.1_LMG_29660_genomic.fna.gz --refList GCF_902859845.1_LMG_29660_genomic.fna/target_genomes.txt --output GCF_902859845.1_LMG_29660_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:19,513] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:19,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09e61c1c-d4b4-4dc8-aa06-ac9f338f6de2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:19,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09e61c1c-d4b4-4dc8-aa06-ac9f338f6de2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:19,530] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:28:19,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:19,530] [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
Burkholderia puraquae	strain=LMG 29660	GCA_902859845.1	1904757	1904757	type	True	100.0	2658	2663	95	conclusive
Burkholderia puraquae	strain=CAMPA 1040	GCA_002099195.1	1904757	1904757	type	True	99.9895	2648	2663	95	conclusive
Burkholderia lata	strain=383	GCA_000012945.1	482957	482957	suspected-type	True	94.2035	2176	2663	95	below_threshold
Burkholderia aenigmatica	strain=LMG 13014	GCA_902499175.1	2015348	2015348	suspected-type	True	94.1189	2045	2663	95	below_threshold
Burkholderia contaminans	strain=LMG 23361	GCA_000987075.1	488447	488447	type	True	93.929	2213	2663	95	below_threshold
Burkholderia contaminans	strain=LMG 23361	GCA_001758385.2	488447	488447	type	True	93.9107	2215	2663	95	below_threshold
Burkholderia cepacia	strain=NBRC 14074	GCA_001528845.1	292	292	type	True	93.7099	2191	2663	95	below_threshold
Burkholderia cepacia	strain=ATCC 25416	GCA_000473485.1	292	292	type	True	93.6742	2233	2663	95	below_threshold
Burkholderia cepacia	strain=UCB 717	GCA_001411495.1	292	292	type	True	93.6734	2225	2663	95	below_threshold
Burkholderia catarinensis	strain=89	GCA_001883705.2	1108140	1108140	type	True	92.9571	2090	2663	95	below_threshold
Burkholderia cenocepacia	strain=NCTC13227	GCA_900446215.1	95486	95486	type	True	92.0456	2058	2663	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	90.5642	1890	2663	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	88.4489	1826	2663	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	88.3959	1776	2663	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.1843	1371	2663	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	81.0147	1219	2663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:19,532] [INFO] DFAST Taxonomy check result was written to GCF_902859845.1_LMG_29660_genomic.fna/tc_result.tsv
[2024-01-24 15:28:19,532] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:19,532] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:19,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09e61c1c-d4b4-4dc8-aa06-ac9f338f6de2/dqc_reference/checkm_data
[2024-01-24 15:28:19,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:19,629] [INFO] Task started: CheckM
[2024-01-24 15:28:19,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859845.1_LMG_29660_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859845.1_LMG_29660_genomic.fna/checkm_input GCF_902859845.1_LMG_29660_genomic.fna/checkm_result
[2024-01-24 15:29:38,100] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:38,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:38,130] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:38,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:38,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859845.1_LMG_29660_genomic.fna/markers.fasta)
[2024-01-24 15:29:38,132] [INFO] Task started: Blastn
[2024-01-24 15:29:38,132] [INFO] Running command: blastn -query GCF_902859845.1_LMG_29660_genomic.fna/markers.fasta -db /var/lib/cwl/stg09e61c1c-d4b4-4dc8-aa06-ac9f338f6de2/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859845.1_LMG_29660_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:40,269] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:40,273] [INFO] Selected 14 target genomes.
[2024-01-24 15:29:40,273] [INFO] Target genome list was writen to GCF_902859845.1_LMG_29660_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:40,284] [INFO] Task started: fastANI
[2024-01-24 15:29:40,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg98081969-22c6-4280-ba2b-e567ebc4d4e7/GCF_902859845.1_LMG_29660_genomic.fna.gz --refList GCF_902859845.1_LMG_29660_genomic.fna/target_genomes_gtdb.txt --output GCF_902859845.1_LMG_29660_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:11,812] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:11,828] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:11,828] [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_002099195.1	s__Burkholderia puraquae	99.9895	2648	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.50	95.00	0.89	0.80	3	conclusive
GCF_902499335.1	s__Burkholderia lata_B	94.6832	2231	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.27	95.15	0.87	0.83	7	-
GCF_000012945.1	s__Burkholderia lata	94.201	2177	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.57	95.30	0.88	0.82	11	-
GCF_902499175.1	s__Burkholderia aenigmatica	94.1369	2043	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.89	95.59	0.85	0.80	12	-
GCF_902833045.1	s__Burkholderia sp902833045	93.9781	2041	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.81	96.81	0.81	0.81	2	-
GCF_000987075.1	s__Burkholderia contaminans	93.9235	2214	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.97	95.20	0.90	0.82	86	-
GCF_001411495.1	s__Burkholderia cepacia	93.683	2224	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.84	96.33	0.89	0.79	182	-
GCF_902832845.1	s__Burkholderia metallica	93.194	2080	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.19	98.00	0.94	0.86	6	-
GCA_001883705.1	s__Burkholderia catarinensis	92.5961	1798	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001718835.1	s__Burkholderia cepacia_F	92.5811	1819	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902833225.1	s__Burkholderia sp902833225	92.5504	2123	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003853705.1	s__Burkholderia sp003853705	92.5143	2083	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732615.1	s__Burkholderia paludis	92.0	1959	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.34	99.33	0.95	0.95	4	-
GCF_000292915.1	s__Burkholderia cepacia_D	91.1662	1759	2663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:11,836] [INFO] GTDB search result was written to GCF_902859845.1_LMG_29660_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:11,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:11,841] [INFO] DFAST_QC result json was written to GCF_902859845.1_LMG_29660_genomic.fna/dqc_result.json
[2024-01-24 15:30:11,841] [INFO] DFAST_QC completed!
[2024-01-24 15:30:11,841] [INFO] Total running time: 0h2m59s