[2024-01-24 11:34:41,432] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8fcf1da-eb55-48d0-a4d3-b7747aa8fcda/dqc_reference
[2024-01-24 11:34:42,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,640] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgad382140-324e-4cc8-9d48-5e457b4f9797/GCF_900608545.1_3723STDY6437371_genomic.fna.gz | prodigal -d GCF_900608545.1_3723STDY6437371_genomic.fna/cds.fna -a GCF_900608545.1_3723STDY6437371_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:03,964] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:03,964] [INFO] Task started: HMMsearch
[2024-01-24 11:35:03,964] [INFO] Running command: hmmsearch --tblout GCF_900608545.1_3723STDY6437371_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8fcf1da-eb55-48d0-a4d3-b7747aa8fcda/dqc_reference/reference_markers.hmm GCF_900608545.1_3723STDY6437371_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:04,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:04,412] [INFO] Found 6/6 markers.
[2024-01-24 11:35:04,464] [INFO] Query marker FASTA was written to GCF_900608545.1_3723STDY6437371_genomic.fna/markers.fasta
[2024-01-24 11:35:04,464] [INFO] Task started: Blastn
[2024-01-24 11:35:04,465] [INFO] Running command: blastn -query GCF_900608545.1_3723STDY6437371_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8fcf1da-eb55-48d0-a4d3-b7747aa8fcda/dqc_reference/reference_markers.fasta -out GCF_900608545.1_3723STDY6437371_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:05,417] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:05,420] [INFO] Selected 10 target genomes.
[2024-01-24 11:35:05,421] [INFO] Target genome list was writen to GCF_900608545.1_3723STDY6437371_genomic.fna/target_genomes.txt
[2024-01-24 11:35:05,432] [INFO] Task started: fastANI
[2024-01-24 11:35:05,432] [INFO] Running command: fastANI --query /var/lib/cwl/stgad382140-324e-4cc8-9d48-5e457b4f9797/GCF_900608545.1_3723STDY6437371_genomic.fna.gz --refList GCF_900608545.1_3723STDY6437371_genomic.fna/target_genomes.txt --output GCF_900608545.1_3723STDY6437371_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:31,089] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:31,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8fcf1da-eb55-48d0-a4d3-b7747aa8fcda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:31,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8fcf1da-eb55-48d0-a4d3-b7747aa8fcda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:31,098] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:35:31,099] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:31,099] [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 oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	100.0	2376	2378	95	conclusive
Burkholderia oklahomensis	strain=C6786	GCA_000959365.1	342113	342113	type	True	99.9995	2375	2378	95	conclusive
Burkholderia oklahomensis	strain=C6786	GCA_001522135.2	342113	342113	type	True	99.9995	2376	2378	95	conclusive
Burkholderia oklahomensis	strain=LMG 23618	GCA_902829515.1	342113	342113	type	True	99.9875	2334	2378	95	conclusive
Burkholderia oklahomensis	strain=C6786	GCA_000170375.1	342113	342113	type	True	99.8262	1986	2378	95	conclusive
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	86.019	1501	2378	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	85.9697	1449	2378	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	84.851	1422	2378	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.4091	1328	2378	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	81.0762	1087	2378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:31,100] [INFO] DFAST Taxonomy check result was written to GCF_900608545.1_3723STDY6437371_genomic.fna/tc_result.tsv
[2024-01-24 11:35:31,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:31,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:31,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8fcf1da-eb55-48d0-a4d3-b7747aa8fcda/dqc_reference/checkm_data
[2024-01-24 11:35:31,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:31,166] [INFO] Task started: CheckM
[2024-01-24 11:35:31,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900608545.1_3723STDY6437371_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900608545.1_3723STDY6437371_genomic.fna/checkm_input GCF_900608545.1_3723STDY6437371_genomic.fna/checkm_result
[2024-01-24 11:36:43,295] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:43,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:43,315] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:43,316] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:43,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900608545.1_3723STDY6437371_genomic.fna/markers.fasta)
[2024-01-24 11:36:43,316] [INFO] Task started: Blastn
[2024-01-24 11:36:43,316] [INFO] Running command: blastn -query GCF_900608545.1_3723STDY6437371_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8fcf1da-eb55-48d0-a4d3-b7747aa8fcda/dqc_reference/reference_markers_gtdb.fasta -out GCF_900608545.1_3723STDY6437371_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:45,173] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:45,176] [INFO] Selected 5 target genomes.
[2024-01-24 11:36:45,176] [INFO] Target genome list was writen to GCF_900608545.1_3723STDY6437371_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:45,180] [INFO] Task started: fastANI
[2024-01-24 11:36:45,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgad382140-324e-4cc8-9d48-5e457b4f9797/GCF_900608545.1_3723STDY6437371_genomic.fna.gz --refList GCF_900608545.1_3723STDY6437371_genomic.fna/target_genomes_gtdb.txt --output GCF_900608545.1_3723STDY6437371_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:57,850] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:57,856] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:57,856] [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_000959365.1	s__Burkholderia oklahomensis	99.9995	2375	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.42	95.09	0.95	0.85	15	conclusive
GCF_001524625.2	s__Burkholderia sp001524625	92.0351	1927	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.38	99.33	0.93	0.91	11	-
GCF_001462435.1	s__Burkholderia humptydooensis	91.9343	1796	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.52	99.18	0.95	0.92	12	-
GCF_000012365.1	s__Burkholderia thailandensis	91.2133	1842	2378	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	90.9859	1677	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.31	98.71	0.94	0.78	1780	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:57,857] [INFO] GTDB search result was written to GCF_900608545.1_3723STDY6437371_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:57,858] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:57,861] [INFO] DFAST_QC result json was written to GCF_900608545.1_3723STDY6437371_genomic.fna/dqc_result.json
[2024-01-24 11:36:57,861] [INFO] DFAST_QC completed!
[2024-01-24 11:36:57,861] [INFO] Total running time: 0h2m16s