[2024-01-24 13:45:45,865] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,868] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg60c64b54-9671-4c8b-bfbb-32a8274e0040/dqc_reference
[2024-01-24 13:45:47,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,243] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,244] [INFO] Running command: gunzip -c /var/lib/cwl/stgefd5bf1c-8e16-428d-9ad4-895671058ea9/GCF_902499175.1_ASM90249917v1_genomic.fna.gz | prodigal -d GCF_902499175.1_ASM90249917v1_genomic.fna/cds.fna -a GCF_902499175.1_ASM90249917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:14,807] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:14,807] [INFO] Task started: HMMsearch
[2024-01-24 13:46:14,808] [INFO] Running command: hmmsearch --tblout GCF_902499175.1_ASM90249917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60c64b54-9671-4c8b-bfbb-32a8274e0040/dqc_reference/reference_markers.hmm GCF_902499175.1_ASM90249917v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:15,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:15,311] [INFO] Found 6/6 markers.
[2024-01-24 13:46:15,400] [INFO] Query marker FASTA was written to GCF_902499175.1_ASM90249917v1_genomic.fna/markers.fasta
[2024-01-24 13:46:15,401] [INFO] Task started: Blastn
[2024-01-24 13:46:15,401] [INFO] Running command: blastn -query GCF_902499175.1_ASM90249917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60c64b54-9671-4c8b-bfbb-32a8274e0040/dqc_reference/reference_markers.fasta -out GCF_902499175.1_ASM90249917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:16,523] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:16,526] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:16,527] [INFO] Target genome list was writen to GCF_902499175.1_ASM90249917v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:16,530] [INFO] Task started: fastANI
[2024-01-24 13:46:16,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgefd5bf1c-8e16-428d-9ad4-895671058ea9/GCF_902499175.1_ASM90249917v1_genomic.fna.gz --refList GCF_902499175.1_ASM90249917v1_genomic.fna/target_genomes.txt --output GCF_902499175.1_ASM90249917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:58,461] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:58,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60c64b54-9671-4c8b-bfbb-32a8274e0040/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:58,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60c64b54-9671-4c8b-bfbb-32a8274e0040/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:58,479] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:58,479] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:58,479] [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 aenigmatica	strain=LMG 13014	GCA_902499175.1	2015348	2015348	suspected-type	True	100.0	2878	2886	95	conclusive
Burkholderia lata	strain=383	GCA_000012945.1	482957	482957	suspected-type	True	94.2813	2214	2886	95	below_threshold
Burkholderia puraquae	strain=LMG 29660	GCA_902859845.1	1904757	1904757	type	True	94.1057	2052	2886	95	below_threshold
Burkholderia puraquae	strain=CAMPA 1040	GCA_002099195.1	1904757	1904757	type	True	94.0642	2066	2886	95	below_threshold
Burkholderia contaminans	strain=LMG 23361	GCA_000987075.1	488447	488447	type	True	93.6529	2110	2886	95	below_threshold
Burkholderia cepacia	strain=NBRC 14074	GCA_001528845.1	292	292	type	True	93.6316	2075	2886	95	below_threshold
Burkholderia cepacia	strain=ATCC 25416	GCA_003546465.1	292	292	type	True	93.577	2122	2886	95	below_threshold
Burkholderia cepacia	strain=ATCC 25416	GCA_000473485.1	292	292	type	True	93.5639	2116	2886	95	below_threshold
Burkholderia cepacia	strain=UCB 717	GCA_001411495.1	292	292	type	True	93.5618	2127	2886	95	below_threshold
Burkholderia contaminans	strain=LMG 23361	GCA_001758385.2	488447	488447	type	True	93.5237	2106	2886	95	below_threshold
Burkholderia metallica	strain=LMG 24068	GCA_902832845.1	488729	488729	type	True	92.9976	1970	2886	95	below_threshold
Burkholderia pyrrocinia	strain=DSM 10685	GCA_001028665.1	60550	60550	suspected-type	True	92.5825	1970	2886	95	below_threshold
Burkholderia cenocepacia	strain=NCTC13227	GCA_900446215.1	95486	95486	type	True	91.8733	2006	2886	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	90.5998	1916	2886	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	88.3623	1706	2886	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	88.3406	1744	2886	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.2169	1368	2886	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	81.0288	1258	2886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:58,482] [INFO] DFAST Taxonomy check result was written to GCF_902499175.1_ASM90249917v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:58,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:58,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:58,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60c64b54-9671-4c8b-bfbb-32a8274e0040/dqc_reference/checkm_data
[2024-01-24 13:46:58,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:58,577] [INFO] Task started: CheckM
[2024-01-24 13:46:58,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902499175.1_ASM90249917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902499175.1_ASM90249917v1_genomic.fna/checkm_input GCF_902499175.1_ASM90249917v1_genomic.fna/checkm_result
[2024-01-24 13:48:25,698] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:25,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:25,729] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:25,729] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:25,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902499175.1_ASM90249917v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:25,730] [INFO] Task started: Blastn
[2024-01-24 13:48:25,730] [INFO] Running command: blastn -query GCF_902499175.1_ASM90249917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60c64b54-9671-4c8b-bfbb-32a8274e0040/dqc_reference/reference_markers_gtdb.fasta -out GCF_902499175.1_ASM90249917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:27,794] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:27,798] [INFO] Selected 12 target genomes.
[2024-01-24 13:48:27,798] [INFO] Target genome list was writen to GCF_902499175.1_ASM90249917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:27,805] [INFO] Task started: fastANI
[2024-01-24 13:48:27,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgefd5bf1c-8e16-428d-9ad4-895671058ea9/GCF_902499175.1_ASM90249917v1_genomic.fna.gz --refList GCF_902499175.1_ASM90249917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902499175.1_ASM90249917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:55,287] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:55,304] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:55,304] [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_902499175.1	s__Burkholderia aenigmatica	100.0	2878	2886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.89	95.59	0.85	0.80	12	conclusive
GCF_000012945.1	s__Burkholderia lata	94.3201	2209	2886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.57	95.30	0.88	0.82	11	-
GCF_902499335.1	s__Burkholderia lata_B	94.2974	2188	2886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.27	95.15	0.87	0.83	7	-
GCF_002099195.1	s__Burkholderia puraquae	94.0612	2066	2886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.50	95.00	0.89	0.80	3	-
GCF_011605345.1	s__Burkholderia sp011605345	93.7057	2194	2886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987075.1	s__Burkholderia contaminans	93.6233	2114	2886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.97	95.20	0.90	0.82	86	-
GCF_902833045.1	s__Burkholderia sp902833045	93.6072	1966	2886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.81	96.81	0.81	0.81	2	-
GCF_001411495.1	s__Burkholderia cepacia	93.5369	2129	2886	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	93.0071	1969	2886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.19	98.00	0.94	0.86	6	-
GCF_902833225.1	s__Burkholderia sp902833225	92.4035	2097	2886	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	92.3245	1770	2886	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292915.1	s__Burkholderia cepacia_D	91.1399	1775	2886	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 13:48:55,306] [INFO] GTDB search result was written to GCF_902499175.1_ASM90249917v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:55,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:55,311] [INFO] DFAST_QC result json was written to GCF_902499175.1_ASM90249917v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:55,311] [INFO] DFAST_QC completed!
[2024-01-24 13:48:55,311] [INFO] Total running time: 0h3m9s