[2024-01-24 14:31:30,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:30,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:30,076] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb36b4fe-021e-4b15-8cf6-621756f73a4e/dqc_reference
[2024-01-24 14:31:31,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:31,458] [INFO] Task started: Prodigal
[2024-01-24 14:31:31,458] [INFO] Running command: gunzip -c /var/lib/cwl/stg43a13adc-ed4d-49ee-8487-7850678866b6/GCF_002934455.1_ASM293445v1_genomic.fna.gz | prodigal -d GCF_002934455.1_ASM293445v1_genomic.fna/cds.fna -a GCF_002934455.1_ASM293445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:52,304] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:52,304] [INFO] Task started: HMMsearch
[2024-01-24 14:31:52,305] [INFO] Running command: hmmsearch --tblout GCF_002934455.1_ASM293445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb36b4fe-021e-4b15-8cf6-621756f73a4e/dqc_reference/reference_markers.hmm GCF_002934455.1_ASM293445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:52,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:52,653] [INFO] Found 6/6 markers.
[2024-01-24 14:31:52,711] [INFO] Query marker FASTA was written to GCF_002934455.1_ASM293445v1_genomic.fna/markers.fasta
[2024-01-24 14:31:52,712] [INFO] Task started: Blastn
[2024-01-24 14:31:52,712] [INFO] Running command: blastn -query GCF_002934455.1_ASM293445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb36b4fe-021e-4b15-8cf6-621756f73a4e/dqc_reference/reference_markers.fasta -out GCF_002934455.1_ASM293445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:53,714] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:53,719] [INFO] Selected 24 target genomes.
[2024-01-24 14:31:53,719] [INFO] Target genome list was writen to GCF_002934455.1_ASM293445v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:53,734] [INFO] Task started: fastANI
[2024-01-24 14:31:53,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg43a13adc-ed4d-49ee-8487-7850678866b6/GCF_002934455.1_ASM293445v1_genomic.fna.gz --refList GCF_002934455.1_ASM293445v1_genomic.fna/target_genomes.txt --output GCF_002934455.1_ASM293445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:27,781] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:27,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb36b4fe-021e-4b15-8cf6-621756f73a4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:27,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb36b4fe-021e-4b15-8cf6-621756f73a4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:27,804] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:32:27,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:32:27,804] [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
Trinickia symbiotica	strain=JPY-345	GCA_002934455.1	863227	863227	type	True	100.0	2203	2206	95	conclusive
Trinickia caryophylli	strain=LMG 2155	GCA_902833925.1	28094	28094	type	True	80.8713	995	2206	95	below_threshold
Trinickia caryophylli	strain=HAMBI_2159	GCA_003350265.1	28094	28094	type	True	80.8665	971	2206	95	below_threshold
Trinickia caryophylli	strain=DSM 50341	GCA_007097545.1	28094	28094	type	True	80.8403	980	2206	95	below_threshold
Trinickia caryophylli	strain=Ballard 720	GCA_002879875.1	28094	28094	type	True	80.8164	971	2206	95	below_threshold
Trinickia dinghuensis	strain=DHOM06	GCA_003367175.1	2291023	2291023	type	True	80.8122	953	2206	95	below_threshold
Trinickia soli	strain=LMG 24076	GCA_902859815.1	380675	380675	type	True	80.401	827	2206	95	below_threshold
Burkholderia mallei	strain=ATCC 23344	GCA_000011705.1	13373	13373	type	True	80.3888	774	2206	95	below_threshold
Trinickia soli	strain=GP25-8	GCA_002879855.1	380675	380675	type	True	80.3753	832	2206	95	below_threshold
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	80.315	825	2206	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	80.1818	842	2206	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	80.1752	836	2206	95	below_threshold
Burkholderia seminalis	strain=LMG 24067	GCA_902832885.1	488731	488731	type	True	80.0515	831	2206	95	below_threshold
Paraburkholderia caballeronis	strain=TNe-841	GCA_900104845.1	416943	416943	type	True	79.9652	847	2206	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	79.9479	936	2206	95	below_threshold
Burkholderia pyrrocinia	strain=LMG 14191	GCA_902832895.1	60550	60550	suspected-type	True	79.9014	859	2206	95	below_threshold
Paraburkholderia caballeronis	strain=LMG 26416	GCA_900109675.1	416943	416943	type	True	79.8934	863	2206	95	below_threshold
Burkholderia pyrrocinia	strain=DSM 10685	GCA_001028665.1	60550	60550	suspected-type	True	79.8899	864	2206	95	below_threshold
Paraburkholderia franconis	strain=CNPSo 3157	GCA_009362735.1	2654983	2654983	type	True	79.887	903	2206	95	below_threshold
Paraburkholderia phosphatilytica	strain=7QSK02	GCA_003443895.1	2282883	2282883	type	True	79.8659	934	2206	95	below_threshold
Paraburkholderia tuberum	strain=LMG 21444	GCA_902833905.1	157910	157910	type	True	79.8045	923	2206	95	below_threshold
Paraburkholderia youngii	strain=JPY169	GCA_013366925.1	2782701	2782701	type	True	79.7171	948	2206	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	79.567	868	2206	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	79.4703	716	2206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:27,806] [INFO] DFAST Taxonomy check result was written to GCF_002934455.1_ASM293445v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:27,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:27,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:27,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb36b4fe-021e-4b15-8cf6-621756f73a4e/dqc_reference/checkm_data
[2024-01-24 14:32:27,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:27,871] [INFO] Task started: CheckM
[2024-01-24 14:32:27,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002934455.1_ASM293445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002934455.1_ASM293445v1_genomic.fna/checkm_input GCF_002934455.1_ASM293445v1_genomic.fna/checkm_result
[2024-01-24 14:33:24,573] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:24,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:24,596] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:24,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:24,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002934455.1_ASM293445v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:24,597] [INFO] Task started: Blastn
[2024-01-24 14:33:24,597] [INFO] Running command: blastn -query GCF_002934455.1_ASM293445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb36b4fe-021e-4b15-8cf6-621756f73a4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002934455.1_ASM293445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:26,542] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:26,547] [INFO] Selected 17 target genomes.
[2024-01-24 14:33:26,547] [INFO] Target genome list was writen to GCF_002934455.1_ASM293445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:26,563] [INFO] Task started: fastANI
[2024-01-24 14:33:26,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg43a13adc-ed4d-49ee-8487-7850678866b6/GCF_002934455.1_ASM293445v1_genomic.fna.gz --refList GCF_002934455.1_ASM293445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002934455.1_ASM293445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:52,053] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:52,067] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:52,068] [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_002934455.1	s__Trinickia symbiotica	100.0	2203	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	98.34	95.03	0.94	0.86	4	conclusive
GCF_003628145.1	s__Trinickia fusca	81.0961	847	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097545.1	s__Trinickia caryophylli	80.8467	979	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_003367175.1	s__Trinickia dinghuensis	80.8055	954	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144415.1	s__Trinickia sp005144415	80.7359	971	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017315705.1	s__Trinickia sp017315705	80.7117	851	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282575.1	s__Trinickia sp013282575	80.6846	915	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017315725.1	s__Trinickia sp017315725	80.6451	880	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001524625.2	s__Burkholderia sp001524625	80.5102	849	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.38	99.33	0.93	0.91	11	-
GCF_000959525.1	s__Burkholderia multivorans	80.4442	830	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.58	96.90	0.90	0.85	326	-
GCF_002879855.1	s__Trinickia soli	80.3895	830	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	99.68	99.37	0.95	0.90	3	-
GCA_004322045.1	s__Trinickia sp004322045	80.3648	775	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	96.62	96.62	0.93	0.93	2	-
GCF_003854275.1	s__Burkholderia sp003854275	79.9908	850	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	95.08	95.08	0.74	0.74	2	-
GCF_900104845.1	s__Paraburkholderia caballeronis	79.9775	847	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.48	98.95	0.97	0.92	9	-
GCF_001522585.2	s__Burkholderia sp001522585	79.9678	830	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.44	95.03	0.88	0.83	18	-
GCF_902833905.1	s__Paraburkholderia tuberum	79.7933	925	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.72	96.26	0.82	0.75	13	-
GCF_013366925.1	s__Paraburkholderia youngii	79.6978	952	2206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.48	97.40	0.88	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:52,070] [INFO] GTDB search result was written to GCF_002934455.1_ASM293445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:52,070] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:52,075] [INFO] DFAST_QC result json was written to GCF_002934455.1_ASM293445v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:52,075] [INFO] DFAST_QC completed!
[2024-01-24 14:33:52,075] [INFO] Total running time: 0h2m22s