[2023-06-14 00:33:32,495] [INFO] DFAST_QC pipeline started.
[2023-06-14 00:33:32,497] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 00:33:32,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgea28fee2-440c-475f-be5c-23c33c47667b/dqc_reference
[2023-06-14 00:33:33,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 00:33:33,707] [INFO] Task started: Prodigal
[2023-06-14 00:33:33,707] [INFO] Running command: gunzip -c /var/lib/cwl/stg581ff74b-7230-4684-8f15-a9718c1b82cc/GCA_022482405.1_ASM2248240v1_genomic.fna.gz | prodigal -d GCA_022482405.1_ASM2248240v1_genomic.fna/cds.fna -a GCA_022482405.1_ASM2248240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 00:33:38,568] [INFO] Task succeeded: Prodigal
[2023-06-14 00:33:38,568] [INFO] Task started: HMMsearch
[2023-06-14 00:33:38,568] [INFO] Running command: hmmsearch --tblout GCA_022482405.1_ASM2248240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea28fee2-440c-475f-be5c-23c33c47667b/dqc_reference/reference_markers.hmm GCA_022482405.1_ASM2248240v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 00:33:38,826] [INFO] Task succeeded: HMMsearch
[2023-06-14 00:33:38,827] [INFO] Found 6/6 markers.
[2023-06-14 00:33:38,851] [INFO] Query marker FASTA was written to GCA_022482405.1_ASM2248240v1_genomic.fna/markers.fasta
[2023-06-14 00:33:38,851] [INFO] Task started: Blastn
[2023-06-14 00:33:38,851] [INFO] Running command: blastn -query GCA_022482405.1_ASM2248240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea28fee2-440c-475f-be5c-23c33c47667b/dqc_reference/reference_markers.fasta -out GCA_022482405.1_ASM2248240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:33:39,541] [INFO] Task succeeded: Blastn
[2023-06-14 00:33:39,545] [INFO] Selected 32 target genomes.
[2023-06-14 00:33:39,545] [INFO] Target genome list was writen to GCA_022482405.1_ASM2248240v1_genomic.fna/target_genomes.txt
[2023-06-14 00:33:39,553] [INFO] Task started: fastANI
[2023-06-14 00:33:39,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg581ff74b-7230-4684-8f15-a9718c1b82cc/GCA_022482405.1_ASM2248240v1_genomic.fna.gz --refList GCA_022482405.1_ASM2248240v1_genomic.fna/target_genomes.txt --output GCA_022482405.1_ASM2248240v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 00:34:01,115] [INFO] Task succeeded: fastANI
[2023-06-14 00:34:01,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea28fee2-440c-475f-be5c-23c33c47667b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 00:34:01,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea28fee2-440c-475f-be5c-23c33c47667b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 00:34:01,131] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 00:34:01,131] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 00:34:01,131] [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
Sutterella megalosphaeroides	strain=6FBBBH3	GCA_003609995.1	2494234	2494234	type	True	79.007	87	639	95	below_threshold
Sutterella faecalis	strain=KGMB03119	GCA_006337085.1	2584944	2584944	type	True	78.4509	96	639	95	below_threshold
Burkholderia dolosa	strain=FDAARGOS_1463	GCA_019930785.1	152500	152500	type	True	78.3079	56	639	95	below_threshold
Sutterella wadsworthensis	strain=FDAARGOS_1159	GCA_016724805.1	40545	40545	type	True	78.054	67	639	95	below_threshold
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	77.3157	77	639	95	below_threshold
Sutterella parvirubra	strain=YIT 11816	GCA_000250875.1	437898	437898	type	True	76.9326	91	639	95	below_threshold
Sutterella wadsworthensis	strain=DSM 14016	GCA_003315195.1	40545	40545	type	True	76.9011	60	639	95	below_threshold
Burkholderia pseudomallei	strain=ATCC 23343	GCA_001182285.1	28450	28450	type	True	76.6391	51	639	95	below_threshold
Burkholderia oklahomensis	strain=C6786	GCA_000170375.1	342113	342113	type	True	76.1593	63	639	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 00:34:01,160] [INFO] DFAST Taxonomy check result was written to GCA_022482405.1_ASM2248240v1_genomic.fna/tc_result.tsv
[2023-06-14 00:34:01,161] [INFO] ===== Taxonomy check completed =====
[2023-06-14 00:34:01,161] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 00:34:01,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea28fee2-440c-475f-be5c-23c33c47667b/dqc_reference/checkm_data
[2023-06-14 00:34:01,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 00:34:01,193] [INFO] Task started: CheckM
[2023-06-14 00:34:01,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022482405.1_ASM2248240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022482405.1_ASM2248240v1_genomic.fna/checkm_input GCA_022482405.1_ASM2248240v1_genomic.fna/checkm_result
[2023-06-14 00:34:22,784] [INFO] Task succeeded: CheckM
[2023-06-14 00:34:22,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 00:34:22,850] [INFO] ===== Completeness check finished =====
[2023-06-14 00:34:22,850] [INFO] ===== Start GTDB Search =====
[2023-06-14 00:34:22,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022482405.1_ASM2248240v1_genomic.fna/markers.fasta)
[2023-06-14 00:34:22,851] [INFO] Task started: Blastn
[2023-06-14 00:34:22,851] [INFO] Running command: blastn -query GCA_022482405.1_ASM2248240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea28fee2-440c-475f-be5c-23c33c47667b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022482405.1_ASM2248240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:34:23,816] [INFO] Task succeeded: Blastn
[2023-06-14 00:34:23,821] [INFO] Selected 19 target genomes.
[2023-06-14 00:34:23,821] [INFO] Target genome list was writen to GCA_022482405.1_ASM2248240v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 00:34:23,856] [INFO] Task started: fastANI
[2023-06-14 00:34:23,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg581ff74b-7230-4684-8f15-a9718c1b82cc/GCA_022482405.1_ASM2248240v1_genomic.fna.gz --refList GCA_022482405.1_ASM2248240v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022482405.1_ASM2248240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 00:34:39,887] [INFO] Task succeeded: fastANI
[2023-06-14 00:34:39,903] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 00:34:39,903] [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_003402575.1	s__Mesosutterella multiformis	99.187	602	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mesosutterella	95.0	99.16	98.62	0.94	0.88	11	conclusive
GCF_001182045.1	s__Mesosutterella massiliensis	94.3763	599	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mesosutterella	95.0	99.88	99.78	0.99	0.98	5	-
GCA_902797695.1	s__Mesosutterella sp902797695	79.1372	239	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mesosutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902945.1	s__Paraburkholderia caribensis	78.0422	57	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.86	96.01	0.91	0.80	9	-
GCF_009183815.1	s__Sutterella seckii_A	77.5929	88	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.09	95.34	0.87	0.81	4	-
GCF_001462435.1	s__Burkholderia humptydooensis	77.5278	61	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.52	99.18	0.95	0.92	12	-
GCF_016899755.1	s__Sutterella massiliensis	77.2828	71	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.18	98.18	0.90	0.90	2	-
GCA_905215795.1	s__Sutterella sp905215795	76.9343	59	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315195.1	s__Sutterella wadsworthensis	76.9011	60	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.28	97.53	0.92	0.89	35	-
GCA_905202595.1	s__Sutterella sp905202595	76.8349	72	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403875.1	s__Burkholderia guangdongensis	76.7445	51	639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 00:34:39,905] [INFO] GTDB search result was written to GCA_022482405.1_ASM2248240v1_genomic.fna/result_gtdb.tsv
[2023-06-14 00:34:39,906] [INFO] ===== GTDB Search completed =====
[2023-06-14 00:34:39,912] [INFO] DFAST_QC result json was written to GCA_022482405.1_ASM2248240v1_genomic.fna/dqc_result.json
[2023-06-14 00:34:39,913] [INFO] DFAST_QC completed!
[2023-06-14 00:34:39,913] [INFO] Total running time: 0h1m7s