[2024-01-25 20:03:05,931] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c77f56a-34bb-4e86-bfdc-d55cfa479cc1/dqc_reference
[2024-01-25 20:03:07,115] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:07,124] [INFO] Task started: Prodigal
[2024-01-25 20:03:07,124] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5714889-85cf-4943-9f0b-71f3cd4ee435/GCF_902499155.1_ASM90249915v1_genomic.fna.gz | prodigal -d GCF_902499155.1_ASM90249915v1_genomic.fna/cds.fna -a GCF_902499155.1_ASM90249915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:27,351] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:27,352] [INFO] Task started: HMMsearch
[2024-01-25 20:03:27,352] [INFO] Running command: hmmsearch --tblout GCF_902499155.1_ASM90249915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c77f56a-34bb-4e86-bfdc-d55cfa479cc1/dqc_reference/reference_markers.hmm GCF_902499155.1_ASM90249915v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:27,655] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:27,656] [INFO] Found 6/6 markers.
[2024-01-25 20:03:27,714] [INFO] Query marker FASTA was written to GCF_902499155.1_ASM90249915v1_genomic.fna/markers.fasta
[2024-01-25 20:03:27,714] [INFO] Task started: Blastn
[2024-01-25 20:03:27,714] [INFO] Running command: blastn -query GCF_902499155.1_ASM90249915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c77f56a-34bb-4e86-bfdc-d55cfa479cc1/dqc_reference/reference_markers.fasta -out GCF_902499155.1_ASM90249915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:28,712] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:28,714] [INFO] Selected 12 target genomes.
[2024-01-25 20:03:28,715] [INFO] Target genome list was writen to GCF_902499155.1_ASM90249915v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:28,721] [INFO] Task started: fastANI
[2024-01-25 20:03:28,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5714889-85cf-4943-9f0b-71f3cd4ee435/GCF_902499155.1_ASM90249915v1_genomic.fna.gz --refList GCF_902499155.1_ASM90249915v1_genomic.fna/target_genomes.txt --output GCF_902499155.1_ASM90249915v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:56,521] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:56,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c77f56a-34bb-4e86-bfdc-d55cfa479cc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:56,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c77f56a-34bb-4e86-bfdc-d55cfa479cc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:56,530] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:03:56,531] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:56,531] [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 stagnalis		GCA_902499155.1	1503054	1503054	type	True	100.0	2508	2521	95	conclusive
Burkholderia stagnalis	strain=CCUG 65686	GCA_008802125.1	1503054	1503054	type	True	99.992	2499	2521	95	conclusive
Burkholderia stagnalis	strain=LMG 28156	GCA_902830275.1	1503054	1503054	type	True	99.9899	2503	2521	95	conclusive
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	91.3056	1822	2521	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	91.2952	1859	2521	95	below_threshold
Burkholderia ubonensis subsp. mesacidophila	strain=ATCC 31433	GCA_002097715.1	265293	101571	type	True	91.2436	1821	2521	95	below_threshold
Burkholderia ubonensis subsp. mesacidophila	strain=ATCC 31433	GCA_002362295.1	265293	101571	type	True	91.1477	1813	2521	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	88.5339	1637	2521	95	below_threshold
Burkholderia contaminans	strain=LMG 23361	GCA_000987075.1	488447	488447	type	True	88.4577	1763	2521	95	below_threshold
Burkholderia contaminans	strain=LMG 23361	GCA_001758385.2	488447	488447	type	True	88.4442	1764	2521	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.9173	1327	2521	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.9094	1096	2521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:56,532] [INFO] DFAST Taxonomy check result was written to GCF_902499155.1_ASM90249915v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:56,533] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:56,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:56,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c77f56a-34bb-4e86-bfdc-d55cfa479cc1/dqc_reference/checkm_data
[2024-01-25 20:03:56,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:56,609] [INFO] Task started: CheckM
[2024-01-25 20:03:56,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902499155.1_ASM90249915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902499155.1_ASM90249915v1_genomic.fna/checkm_input GCF_902499155.1_ASM90249915v1_genomic.fna/checkm_result
[2024-01-25 20:05:14,895] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:14,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:14,915] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:14,916] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:14,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902499155.1_ASM90249915v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:14,917] [INFO] Task started: Blastn
[2024-01-25 20:05:14,917] [INFO] Running command: blastn -query GCF_902499155.1_ASM90249915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c77f56a-34bb-4e86-bfdc-d55cfa479cc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_902499155.1_ASM90249915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:16,973] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:16,976] [INFO] Selected 10 target genomes.
[2024-01-25 20:05:16,976] [INFO] Target genome list was writen to GCF_902499155.1_ASM90249915v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:16,982] [INFO] Task started: fastANI
[2024-01-25 20:05:16,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5714889-85cf-4943-9f0b-71f3cd4ee435/GCF_902499155.1_ASM90249915v1_genomic.fna.gz --refList GCF_902499155.1_ASM90249915v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902499155.1_ASM90249915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:41,313] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:41,321] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:41,321] [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_902830275.1	s__Burkholderia stagnalis	99.9899	2503	2521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.76	95.48	0.93	0.80	113	conclusive
GCF_004343775.1	s__Burkholderia sp004343775	93.7055	2000	2521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000959245.1	s__Burkholderia ubonensis	91.48	1801	2521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.20	95.69	0.89	0.72	308	-
GCF_002097715.1	s__Burkholderia acidophila	91.2175	1824	2521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003854275.1	s__Burkholderia sp003854275	89.941	1666	2521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	95.08	95.08	0.74	0.74	2	-
GCF_003853705.1	s__Burkholderia sp003853705	88.8182	1713	2521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899425.1	s__Burkholderia sp002223185	88.6306	1711	2521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.86	95.32	0.94	0.84	68	-
GCF_902499125.1	s__Burkholderia arboris	88.5913	1713	2521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.82	96.20	0.94	0.91	3	-
GCF_902833045.1	s__Burkholderia sp902833045	88.499	1685	2521	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	88.4611	1763	2521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.97	95.20	0.90	0.82	86	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:41,322] [INFO] GTDB search result was written to GCF_902499155.1_ASM90249915v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:41,323] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:41,325] [INFO] DFAST_QC result json was written to GCF_902499155.1_ASM90249915v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:41,325] [INFO] DFAST_QC completed!
[2024-01-25 20:05:41,325] [INFO] Total running time: 0h2m35s