[2024-01-24 13:55:40,598] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:40,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:40,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg59fd539f-16f1-498e-bc11-ddae0414bc9b/dqc_reference
[2024-01-24 13:55:41,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:41,791] [INFO] Task started: Prodigal
[2024-01-24 13:55:41,792] [INFO] Running command: gunzip -c /var/lib/cwl/stg345ee3df-e7aa-452b-9ab3-ddc13ef62a5b/GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna.gz | prodigal -d GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/cds.fna -a GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:02,523] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:02,524] [INFO] Task started: HMMsearch
[2024-01-24 13:56:02,524] [INFO] Running command: hmmsearch --tblout GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59fd539f-16f1-498e-bc11-ddae0414bc9b/dqc_reference/reference_markers.hmm GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:02,988] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:02,990] [INFO] Found 6/6 markers.
[2024-01-24 13:56:03,046] [INFO] Query marker FASTA was written to GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/markers.fasta
[2024-01-24 13:56:03,046] [INFO] Task started: Blastn
[2024-01-24 13:56:03,046] [INFO] Running command: blastn -query GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/markers.fasta -db /var/lib/cwl/stg59fd539f-16f1-498e-bc11-ddae0414bc9b/dqc_reference/reference_markers.fasta -out GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:04,084] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:04,089] [INFO] Selected 14 target genomes.
[2024-01-24 13:56:04,089] [INFO] Target genome list was writen to GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/target_genomes.txt
[2024-01-24 13:56:04,126] [INFO] Task started: fastANI
[2024-01-24 13:56:04,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg345ee3df-e7aa-452b-9ab3-ddc13ef62a5b/GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna.gz --refList GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/target_genomes.txt --output GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:25,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:25,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59fd539f-16f1-498e-bc11-ddae0414bc9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:25,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59fd539f-16f1-498e-bc11-ddae0414bc9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:25,891] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:25,891] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:25,891] [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 glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	100.0	2159	2163	95	conclusive
Burkholderia glumae	strain=ATCC 33617	GCA_000960995.1	337	337	type	True	99.9968	2158	2163	95	conclusive
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	92.6084	1650	2163	95	below_threshold
Burkholderia plantarii	strain=ATCC 43733	GCA_001411805.1	41899	41899	type	True	92.5426	1721	2163	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	92.4697	1705	2163	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	83.5795	1212	2163	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	83.5199	1265	2163	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	83.1565	1219	2163	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	81.0118	1011	2163	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	76.0566	350	2163	95	below_threshold
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	75.7613	117	2163	95	below_threshold
Geomonas silvestris	strain=Red330	GCA_014193515.1	2740184	2740184	type	True	75.0904	95	2163	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	75.0067	98	2163	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	74.8414	187	2163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:25,893] [INFO] DFAST Taxonomy check result was written to GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/tc_result.tsv
[2024-01-24 13:56:25,893] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:25,894] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:25,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59fd539f-16f1-498e-bc11-ddae0414bc9b/dqc_reference/checkm_data
[2024-01-24 13:56:25,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:25,960] [INFO] Task started: CheckM
[2024-01-24 13:56:25,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/checkm_input GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/checkm_result
[2024-01-24 13:57:31,743] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:31,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:31,773] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:31,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:31,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/markers.fasta)
[2024-01-24 13:57:31,774] [INFO] Task started: Blastn
[2024-01-24 13:57:31,775] [INFO] Running command: blastn -query GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/markers.fasta -db /var/lib/cwl/stg59fd539f-16f1-498e-bc11-ddae0414bc9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:33,780] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:33,783] [INFO] Selected 15 target genomes.
[2024-01-24 13:57:33,783] [INFO] Target genome list was writen to GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:33,793] [INFO] Task started: fastANI
[2024-01-24 13:57:33,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg345ee3df-e7aa-452b-9ab3-ddc13ef62a5b/GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna.gz --refList GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/target_genomes_gtdb.txt --output GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:57,914] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:57,928] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:57,929] [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_000960995.1	s__Burkholderia glumae	99.9968	2158	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.66	99.30	0.96	0.92	18	conclusive
GCF_001411805.1	s__Burkholderia plantarii	92.5104	1722	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.45	95.52	0.94	0.88	5	-
GCA_009914575.1	s__Burkholderia gladioli_B	87.1787	407	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000959725.1	s__Burkholderia gladioli	87.0976	1563	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.34	97.08	0.90	0.82	265	-
GCF_017104645.1	s__Burkholderia sp017104645	86.4523	1229	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499075.1	s__Burkholderia pseudomultivorans	83.7774	1207	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.22	95.54	0.83	0.81	13	-
GCF_013403875.1	s__Burkholderia guangdongensis	83.5562	1018	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687455.2	s__Burkholderia sp000687455	83.5108	997	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012365.1	s__Burkholderia thailandensis	83.2889	1203	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.58	98.83	0.96	0.93	53	-
GCF_000011705.1	s__Burkholderia mallei	83.1826	1145	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.31	98.71	0.94	0.78	1780	-
GCF_902499125.1	s__Burkholderia arboris	83.1003	1225	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.82	96.20	0.94	0.91	3	-
GCF_001425045.1	s__Pseudoduganella sp001425045	76.9317	558	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425265.1	s__Pseudoduganella sp001425265	76.893	543	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299335.2	s__Alcanivorax_A pacificus	75.7613	117	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846755.1	s__Alcanivorax_A sp009846755	75.3723	103	2163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:57,930] [INFO] GTDB search result was written to GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:57,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:57,935] [INFO] DFAST_QC result json was written to GCF_902832765.1_Burkholderia_glumae_LMG_2196_genomic.fna/dqc_result.json
[2024-01-24 13:57:57,935] [INFO] DFAST_QC completed!
[2024-01-24 13:57:57,935] [INFO] Total running time: 0h2m17s