[2024-01-24 11:51:36,704] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:36,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:36,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fe9061a-ee06-4334-9736-121e6025960a/dqc_reference
[2024-01-24 11:51:38,001] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,001] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg99520a82-f94d-4cb8-bf46-06ab8a8272ae/GCF_905397285.1_LMG_26296_genomic.fna.gz | prodigal -d GCF_905397285.1_LMG_26296_genomic.fna/cds.fna -a GCF_905397285.1_LMG_26296_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:58,961] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:58,962] [INFO] Task started: HMMsearch
[2024-01-24 11:51:58,962] [INFO] Running command: hmmsearch --tblout GCF_905397285.1_LMG_26296_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fe9061a-ee06-4334-9736-121e6025960a/dqc_reference/reference_markers.hmm GCF_905397285.1_LMG_26296_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:59,299] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:59,300] [INFO] Found 6/6 markers.
[2024-01-24 11:51:59,348] [INFO] Query marker FASTA was written to GCF_905397285.1_LMG_26296_genomic.fna/markers.fasta
[2024-01-24 11:51:59,348] [INFO] Task started: Blastn
[2024-01-24 11:51:59,348] [INFO] Running command: blastn -query GCF_905397285.1_LMG_26296_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fe9061a-ee06-4334-9736-121e6025960a/dqc_reference/reference_markers.fasta -out GCF_905397285.1_LMG_26296_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:00,356] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:00,360] [INFO] Selected 22 target genomes.
[2024-01-24 11:52:00,361] [INFO] Target genome list was writen to GCF_905397285.1_LMG_26296_genomic.fna/target_genomes.txt
[2024-01-24 11:52:00,371] [INFO] Task started: fastANI
[2024-01-24 11:52:00,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg99520a82-f94d-4cb8-bf46-06ab8a8272ae/GCF_905397285.1_LMG_26296_genomic.fna.gz --refList GCF_905397285.1_LMG_26296_genomic.fna/target_genomes.txt --output GCF_905397285.1_LMG_26296_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:29,292] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:29,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fe9061a-ee06-4334-9736-121e6025960a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:29,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fe9061a-ee06-4334-9736-121e6025960a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:29,316] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:29,316] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:29,317] [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
Cupriavidus plantarum	strain=LMG 26296	GCA_905397285.1	942865	942865	type	True	100.0	2061	2062	95	conclusive
Cupriavidus campinensis	strain=LMG 19282	GCA_905397395.1	151783	151783	type	True	83.1193	1145	2062	95	below_threshold
Cupriavidus agavae	strain=ASC-9842	GCA_004217045.1	1001822	1001822	type	True	82.7271	1170	2062	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	82.3135	1029	2062	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	82.2918	1016	2062	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	82.2602	1064	2062	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	82.2023	1052	2062	95	below_threshold
Cupriavidus metallidurans	strain=CH34	GCA_000196015.1	119219	119219	type	True	82.1786	1027	2062	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	82.1601	1047	2062	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	82.1014	1066	2062	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	82.0782	1042	2062	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	82.0557	1038	2062	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	81.9448	940	2062	95	below_threshold
Cupriavidus pauculus	strain=FDAARGOS_1472	GCA_019931045.1	82633	82633	type	True	81.906	1114	2062	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	81.8872	939	2062	95	below_threshold
Cupriavidus pauculus	strain=CCUG 12507	GCA_008801835.1	82633	82633	type	True	81.8538	1127	2062	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	81.8379	972	2062	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	81.8055	961	2062	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.2924	709	2062	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.0451	568	2062	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	77.8275	398	2062	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	77.7546	461	2062	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:29,318] [INFO] DFAST Taxonomy check result was written to GCF_905397285.1_LMG_26296_genomic.fna/tc_result.tsv
[2024-01-24 11:52:29,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:29,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:29,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fe9061a-ee06-4334-9736-121e6025960a/dqc_reference/checkm_data
[2024-01-24 11:52:29,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:29,377] [INFO] Task started: CheckM
[2024-01-24 11:52:29,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_905397285.1_LMG_26296_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_905397285.1_LMG_26296_genomic.fna/checkm_input GCF_905397285.1_LMG_26296_genomic.fna/checkm_result
[2024-01-24 11:53:29,034] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:29,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:29,057] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:29,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:29,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_905397285.1_LMG_26296_genomic.fna/markers.fasta)
[2024-01-24 11:53:29,058] [INFO] Task started: Blastn
[2024-01-24 11:53:29,059] [INFO] Running command: blastn -query GCF_905397285.1_LMG_26296_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fe9061a-ee06-4334-9736-121e6025960a/dqc_reference/reference_markers_gtdb.fasta -out GCF_905397285.1_LMG_26296_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:31,003] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:31,008] [INFO] Selected 20 target genomes.
[2024-01-24 11:53:31,008] [INFO] Target genome list was writen to GCF_905397285.1_LMG_26296_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:31,044] [INFO] Task started: fastANI
[2024-01-24 11:53:31,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg99520a82-f94d-4cb8-bf46-06ab8a8272ae/GCF_905397285.1_LMG_26296_genomic.fna.gz --refList GCF_905397285.1_LMG_26296_genomic.fna/target_genomes_gtdb.txt --output GCF_905397285.1_LMG_26296_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:57,418] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:57,440] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:57,441] [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_905397285.1	s__Cupriavidus plantarum	100.0	2061	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.10	99.08	0.96	0.96	5	conclusive
GCF_008693385.1	s__Cupriavidus pauculus_D	88.7769	1854	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905397395.1	s__Cupriavidus campinensis	83.1172	1145	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.28	95.05	0.89	0.86	6	-
GCF_003854935.1	s__Cupriavidus pauculus_C	83.0077	1227	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009663685.1	s__Cupriavidus necator_C	82.664	1172	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104095.1	s__Cupriavidus sp900104095	82.6514	1185	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101625.1	s__Cupriavidus sp900101625	82.5918	1143	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292345.1	s__Cupriavidus sp000292345	82.5472	969	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001652915.1	s__Cupriavidus sp001652915	82.4828	1198	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598055.1	s__Cupriavidus nantongensis	82.2641	1063	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.73	95.73	0.81	0.78	3	-
GCF_900250075.1	s__Cupriavidus taiwanensis_C	82.2049	1074	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.42	95.79	0.88	0.85	6	-
GCF_900094595.1	s__Cupriavidus alkaliphilus	82.1929	1043	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	-
GCF_000426345.1	s__Cupriavidus sp000426345	82.0516	1017	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.93	98.88	0.87	0.86	3	-
GCF_000876015.1	s__Cupriavidus basilensis_B	82.0316	1166	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.55	98.55	0.88	0.88	2	-
GCF_000812465.1	s__Cupriavidus sp000812465	81.9681	1003	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801915.1	s__Cupriavidus gilardii	81.9513	940	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.02	95.33	0.92	0.88	7	-
GCF_017814975.1	s__Cupriavidus sp017814975	81.8729	1057	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013314895.1	s__Cupriavidus gilardii_C	81.8646	935	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.09	95.09	0.91	0.91	2	-
GCF_008801835.1	s__Cupriavidus pauculus	81.8551	1126	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.57	98.49	0.87	0.84	3	-
GCA_019236395.1	s__Cupriavidus sp019236395	81.6836	476	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:57,443] [INFO] GTDB search result was written to GCF_905397285.1_LMG_26296_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:57,444] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:57,451] [INFO] DFAST_QC result json was written to GCF_905397285.1_LMG_26296_genomic.fna/dqc_result.json
[2024-01-24 11:53:57,451] [INFO] DFAST_QC completed!
[2024-01-24 11:53:57,452] [INFO] Total running time: 0h2m21s