[2024-01-24 14:23:02,037] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:02,039] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:02,039] [INFO] DQC Reference Directory: /var/lib/cwl/stga64654e0-115a-4b75-a9d8-7dabc5939d12/dqc_reference
[2024-01-24 14:23:03,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:03,677] [INFO] Task started: Prodigal
[2024-01-24 14:23:03,677] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6ef5f9a-97e4-4683-878a-4a60f50513e4/GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/cds.fna -a GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:26,491] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:26,492] [INFO] Task started: HMMsearch
[2024-01-24 14:23:26,492] [INFO] Running command: hmmsearch --tblout GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga64654e0-115a-4b75-a9d8-7dabc5939d12/dqc_reference/reference_markers.hmm GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:27,075] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:27,077] [INFO] Found 6/6 markers.
[2024-01-24 14:23:27,138] [INFO] Query marker FASTA was written to GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:23:27,139] [INFO] Task started: Blastn
[2024-01-24 14:23:27,139] [INFO] Running command: blastn -query GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga64654e0-115a-4b75-a9d8-7dabc5939d12/dqc_reference/reference_markers.fasta -out GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:29,996] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:30,000] [INFO] Selected 22 target genomes.
[2024-01-24 14:23:30,000] [INFO] Target genome list was writen to GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:23:30,009] [INFO] Task started: fastANI
[2024-01-24 14:23:30,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ef5f9a-97e4-4683-878a-4a60f50513e4/GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna.gz --refList GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:24:07,206] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:07,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga64654e0-115a-4b75-a9d8-7dabc5939d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:24:07,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga64654e0-115a-4b75-a9d8-7dabc5939d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:24:07,317] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:24:07,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:24:07,318] [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	99.9861	2059	2067	95	conclusive
Cupriavidus campinensis	strain=LMG 19282	GCA_905397395.1	151783	151783	type	True	82.9924	1167	2067	95	below_threshold
Cupriavidus agavae	strain=ASC-9842	GCA_004217045.1	1001822	1001822	type	True	82.7634	1162	2067	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	82.375	1057	2067	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	82.3347	1034	2067	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	82.2955	1026	2067	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	82.2048	1047	2067	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	82.1965	1053	2067	95	below_threshold
Cupriavidus metallidurans	strain=CH34	GCA_000196015.1	119219	119219	type	True	82.1893	1041	2067	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	82.0958	1033	2067	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	82.0656	1031	2067	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	82.052	1071	2067	95	below_threshold
Cupriavidus pauculus	strain=FDAARGOS_1472	GCA_019931045.1	82633	82633	type	True	81.9817	1118	2067	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	81.961	940	2067	95	below_threshold
Cupriavidus pauculus	strain=CCUG 12507	GCA_008801835.1	82633	82633	type	True	81.914	1121	2067	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	81.8885	949	2067	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	81.8835	989	2067	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	81.8199	936	2067	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.233	718	2067	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.0777	571	2067	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	77.91	390	2067	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	77.7749	454	2067	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:24:07,319] [INFO] DFAST Taxonomy check result was written to GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:24:07,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:24:07,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:24:07,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga64654e0-115a-4b75-a9d8-7dabc5939d12/dqc_reference/checkm_data
[2024-01-24 14:24:07,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:24:07,396] [INFO] Task started: CheckM
[2024-01-24 14:24:07,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/checkm_input GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:25:19,790] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:19,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:19,812] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:19,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:19,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:25:19,813] [INFO] Task started: Blastn
[2024-01-24 14:25:19,813] [INFO] Running command: blastn -query GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga64654e0-115a-4b75-a9d8-7dabc5939d12/dqc_reference/reference_markers_gtdb.fasta -out GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:23,657] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:23,661] [INFO] Selected 20 target genomes.
[2024-01-24 14:25:23,661] [INFO] Target genome list was writen to GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:23,689] [INFO] Task started: fastANI
[2024-01-24 14:25:23,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ef5f9a-97e4-4683-878a-4a60f50513e4/GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna.gz --refList GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:52,865] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:52,954] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:52,954] [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	99.9861	2059	2067	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	88.7746	1866	2067	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	82.9694	1170	2067	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	82.9181	1246	2067	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	82.6717	1181	2067	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	82.6302	1184	2067	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	82.6225	1173	2067	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	82.5901	1176	2067	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	82.5794	966	2067	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	82.3926	1054	2067	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	82.2214	1072	2067	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	82.2206	1045	2067	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	82.0893	1013	2067	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	82.0698	1175	2067	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	81.9592	1005	2067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814975.1	s__Cupriavidus sp017814975	81.9542	1039	2067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801835.1	s__Cupriavidus pauculus	81.9313	1118	2067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.57	98.49	0.87	0.84	3	-
GCF_008801915.1	s__Cupriavidus gilardii	81.8808	951	2067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.02	95.33	0.92	0.88	7	-
GCA_019236395.1	s__Cupriavidus sp019236395	81.8622	471	2067	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	81.8549	929	2067	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.09	95.09	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:52,956] [INFO] GTDB search result was written to GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:52,956] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:52,961] [INFO] DFAST_QC result json was written to GCF_900184175.1_IMG-taxon_2681812959_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:25:52,961] [INFO] DFAST_QC completed!
[2024-01-24 14:25:52,961] [INFO] Total running time: 0h2m51s