[2024-01-24 14:19:59,550] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgc199664a-ce9e-40a9-b7e1-027844d566fd/dqc_reference
[2024-01-24 14:20:01,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:01,027] [INFO] Task started: Prodigal
[2024-01-24 14:20:01,028] [INFO] Running command: gunzip -c /var/lib/cwl/stga3b7961c-be6b-435a-9b40-486ee4012265/GCF_008632125.1_ASM863212v1_genomic.fna.gz | prodigal -d GCF_008632125.1_ASM863212v1_genomic.fna/cds.fna -a GCF_008632125.1_ASM863212v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:18,798] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:18,798] [INFO] Task started: HMMsearch
[2024-01-24 14:20:18,798] [INFO] Running command: hmmsearch --tblout GCF_008632125.1_ASM863212v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc199664a-ce9e-40a9-b7e1-027844d566fd/dqc_reference/reference_markers.hmm GCF_008632125.1_ASM863212v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:19,146] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:19,148] [INFO] Found 6/6 markers.
[2024-01-24 14:20:19,198] [INFO] Query marker FASTA was written to GCF_008632125.1_ASM863212v1_genomic.fna/markers.fasta
[2024-01-24 14:20:19,198] [INFO] Task started: Blastn
[2024-01-24 14:20:19,198] [INFO] Running command: blastn -query GCF_008632125.1_ASM863212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc199664a-ce9e-40a9-b7e1-027844d566fd/dqc_reference/reference_markers.fasta -out GCF_008632125.1_ASM863212v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:20,411] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:20,414] [INFO] Selected 13 target genomes.
[2024-01-24 14:20:20,414] [INFO] Target genome list was writen to GCF_008632125.1_ASM863212v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:20,424] [INFO] Task started: fastANI
[2024-01-24 14:20:20,424] [INFO] Running command: fastANI --query /var/lib/cwl/stga3b7961c-be6b-435a-9b40-486ee4012265/GCF_008632125.1_ASM863212v1_genomic.fna.gz --refList GCF_008632125.1_ASM863212v1_genomic.fna/target_genomes.txt --output GCF_008632125.1_ASM863212v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:43,704] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:43,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc199664a-ce9e-40a9-b7e1-027844d566fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:43,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc199664a-ce9e-40a9-b7e1-027844d566fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:43,716] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:43,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:43,717] [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 cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	100.0	1876	1880	95	conclusive
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	93.0032	1630	1880	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	92.9838	1604	1880	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	84.8081	1211	1880	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	84.4147	1193	1880	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	84.2436	1148	1880	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	84.1868	1156	1880	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	83.617	1108	1880	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	82.5369	1030	1880	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.8124	697	1880	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.8015	729	1880	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.7738	786	1880	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.3291	630	1880	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:43,719] [INFO] DFAST Taxonomy check result was written to GCF_008632125.1_ASM863212v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:43,719] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:43,719] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:43,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc199664a-ce9e-40a9-b7e1-027844d566fd/dqc_reference/checkm_data
[2024-01-24 14:20:43,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:43,778] [INFO] Task started: CheckM
[2024-01-24 14:20:43,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008632125.1_ASM863212v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008632125.1_ASM863212v1_genomic.fna/checkm_input GCF_008632125.1_ASM863212v1_genomic.fna/checkm_result
[2024-01-24 14:21:39,629] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:39,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:39,651] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:39,651] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:39,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008632125.1_ASM863212v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:39,652] [INFO] Task started: Blastn
[2024-01-24 14:21:39,653] [INFO] Running command: blastn -query GCF_008632125.1_ASM863212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc199664a-ce9e-40a9-b7e1-027844d566fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_008632125.1_ASM863212v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:41,930] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:41,934] [INFO] Selected 9 target genomes.
[2024-01-24 14:21:41,935] [INFO] Target genome list was writen to GCF_008632125.1_ASM863212v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:41,956] [INFO] Task started: fastANI
[2024-01-24 14:21:41,956] [INFO] Running command: fastANI --query /var/lib/cwl/stga3b7961c-be6b-435a-9b40-486ee4012265/GCF_008632125.1_ASM863212v1_genomic.fna.gz --refList GCF_008632125.1_ASM863212v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008632125.1_ASM863212v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:56,430] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:56,449] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:56,449] [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_008632125.1	s__Cupriavidus cauae	100.0	1876	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.88	98.88	0.93	0.93	2	conclusive
GCF_008801915.1	s__Cupriavidus gilardii	93.0032	1630	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.02	95.33	0.92	0.88	7	-
GCF_013314895.1	s__Cupriavidus gilardii_C	92.6248	1587	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.09	95.09	0.91	0.91	2	-
GCF_007829435.1	s__Cupriavidus gilardii_D	84.91	1149	1880	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	84.8086	1211	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.73	95.73	0.81	0.78	3	-
GCF_900249755.1	s__Cupriavidus taiwanensis_D	84.7093	1233	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.80	98.80	0.92	0.92	2	-
GCF_000372525.1	s__Cupriavidus neocaledonicus	84.2546	1148	1880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.97	99.97	0.99	0.98	3	-
GCF_000876015.1	s__Cupriavidus basilensis_B	83.8309	1132	1880	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	82.9322	1043	1880	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 14:21:56,451] [INFO] GTDB search result was written to GCF_008632125.1_ASM863212v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:56,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:56,455] [INFO] DFAST_QC result json was written to GCF_008632125.1_ASM863212v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:56,455] [INFO] DFAST_QC completed!
[2024-01-24 14:21:56,455] [INFO] Total running time: 0h1m57s