[2024-01-24 14:22:01,775] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fea6d80-6a08-46e0-9e1a-f2ded60c35c6/dqc_reference
[2024-01-24 14:22:03,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:03,045] [INFO] Task started: Prodigal
[2024-01-24 14:22:03,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg97cfad61-f3c1-455e-8cce-8999e82123d4/GCF_900446175.1_52223_E01_genomic.fna.gz | prodigal -d GCF_900446175.1_52223_E01_genomic.fna/cds.fna -a GCF_900446175.1_52223_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:29,681] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:29,682] [INFO] Task started: HMMsearch
[2024-01-24 14:22:29,682] [INFO] Running command: hmmsearch --tblout GCF_900446175.1_52223_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fea6d80-6a08-46e0-9e1a-f2ded60c35c6/dqc_reference/reference_markers.hmm GCF_900446175.1_52223_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:30,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:30,064] [INFO] Found 6/6 markers.
[2024-01-24 14:22:30,130] [INFO] Query marker FASTA was written to GCF_900446175.1_52223_E01_genomic.fna/markers.fasta
[2024-01-24 14:22:30,131] [INFO] Task started: Blastn
[2024-01-24 14:22:30,131] [INFO] Running command: blastn -query GCF_900446175.1_52223_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fea6d80-6a08-46e0-9e1a-f2ded60c35c6/dqc_reference/reference_markers.fasta -out GCF_900446175.1_52223_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:31,274] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:31,278] [INFO] Selected 10 target genomes.
[2024-01-24 14:22:31,279] [INFO] Target genome list was writen to GCF_900446175.1_52223_E01_genomic.fna/target_genomes.txt
[2024-01-24 14:22:31,282] [INFO] Task started: fastANI
[2024-01-24 14:22:31,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg97cfad61-f3c1-455e-8cce-8999e82123d4/GCF_900446175.1_52223_E01_genomic.fna.gz --refList GCF_900446175.1_52223_E01_genomic.fna/target_genomes.txt --output GCF_900446175.1_52223_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:57,467] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:57,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fea6d80-6a08-46e0-9e1a-f2ded60c35c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:57,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fea6d80-6a08-46e0-9e1a-f2ded60c35c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:57,478] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:22:57,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:57,478] [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 cepacia	strain=UCB 717	GCA_001411495.1	292	292	type	True	99.9995	2844	2845	95	conclusive
Burkholderia cepacia	strain=ATCC 25416	GCA_006094315.1	292	292	type	True	99.9972	2837	2845	95	conclusive
Burkholderia cepacia	strain=ATCC 25416	GCA_003546465.1	292	292	type	True	99.9919	2838	2845	95	conclusive
Burkholderia cepacia	strain=ATCC 25416	GCA_000473485.1	292	292	type	True	99.9892	2831	2845	95	conclusive
Burkholderia cepacia	strain=NBRC 14074	GCA_001528845.1	292	292	type	True	99.9775	2752	2845	95	conclusive
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	90.6628	1906	2845	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	88.6125	1771	2845	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	88.585	1841	2845	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.1921	1457	2845	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	81.0785	1300	2845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:57,480] [INFO] DFAST Taxonomy check result was written to GCF_900446175.1_52223_E01_genomic.fna/tc_result.tsv
[2024-01-24 14:22:57,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:57,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:57,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fea6d80-6a08-46e0-9e1a-f2ded60c35c6/dqc_reference/checkm_data
[2024-01-24 14:22:57,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:57,560] [INFO] Task started: CheckM
[2024-01-24 14:22:57,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900446175.1_52223_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900446175.1_52223_E01_genomic.fna/checkm_input GCF_900446175.1_52223_E01_genomic.fna/checkm_result
[2024-01-24 14:24:27,207] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:27,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:27,228] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:27,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:27,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900446175.1_52223_E01_genomic.fna/markers.fasta)
[2024-01-24 14:24:27,229] [INFO] Task started: Blastn
[2024-01-24 14:24:27,229] [INFO] Running command: blastn -query GCF_900446175.1_52223_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fea6d80-6a08-46e0-9e1a-f2ded60c35c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900446175.1_52223_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:29,219] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:29,222] [INFO] Selected 15 target genomes.
[2024-01-24 14:24:29,222] [INFO] Target genome list was writen to GCF_900446175.1_52223_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:29,248] [INFO] Task started: fastANI
[2024-01-24 14:24:29,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg97cfad61-f3c1-455e-8cce-8999e82123d4/GCF_900446175.1_52223_E01_genomic.fna.gz --refList GCF_900446175.1_52223_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900446175.1_52223_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:05,121] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:05,133] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:05,133] [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_001411495.1	s__Burkholderia cepacia	99.9995	2843	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.84	96.33	0.89	0.79	182	conclusive
GCF_011605345.1	s__Burkholderia sp011605345	94.7506	2303	2845	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	94.622	1840	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499335.1	s__Burkholderia lata_B	93.7481	2253	2845	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	93.7282	2215	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.50	95.00	0.89	0.80	3	-
GCF_000012945.1	s__Burkholderia lata	93.7113	2234	2845	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	93.6414	2105	2845	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	93.4164	2091	2845	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	93.2814	2214	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.97	95.20	0.90	0.82	86	-
GCF_902832845.1	s__Burkholderia metallica	93.0207	2083	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.19	98.00	0.94	0.86	6	-
GCF_001028665.1	s__Burkholderia pyrrocinia	92.7968	2146	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	95.68	95.03	0.81	0.77	21	-
GCF_902499125.1	s__Burkholderia arboris	92.4145	2173	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.82	96.20	0.94	0.91	3	-
GCF_016899425.1	s__Burkholderia sp002223185	91.7181	2081	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.86	95.32	0.94	0.84	68	-
GCF_000292915.1	s__Burkholderia cepacia_D	91.1733	1786	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003853415.1	s__Burkholderia sp003853415	91.0387	1900	2845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.32	99.32	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:05,135] [INFO] GTDB search result was written to GCF_900446175.1_52223_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:05,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:05,141] [INFO] DFAST_QC result json was written to GCF_900446175.1_52223_E01_genomic.fna/dqc_result.json
[2024-01-24 14:25:05,141] [INFO] DFAST_QC completed!
[2024-01-24 14:25:05,141] [INFO] Total running time: 0h3m3s