[2024-01-24 13:46:00,859] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:00,861] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:00,861] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf77ff10-452a-480c-a57e-4f9c9f8f2174/dqc_reference
[2024-01-24 13:46:02,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,310] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e8760cb-604e-4d85-b883-246ca555a810/GCF_019931045.1_ASM1993104v1_genomic.fna.gz | prodigal -d GCF_019931045.1_ASM1993104v1_genomic.fna/cds.fna -a GCF_019931045.1_ASM1993104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:24,689] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:24,689] [INFO] Task started: HMMsearch
[2024-01-24 13:46:24,689] [INFO] Running command: hmmsearch --tblout GCF_019931045.1_ASM1993104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf77ff10-452a-480c-a57e-4f9c9f8f2174/dqc_reference/reference_markers.hmm GCF_019931045.1_ASM1993104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:25,061] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:25,063] [INFO] Found 6/6 markers.
[2024-01-24 13:46:25,111] [INFO] Query marker FASTA was written to GCF_019931045.1_ASM1993104v1_genomic.fna/markers.fasta
[2024-01-24 13:46:25,111] [INFO] Task started: Blastn
[2024-01-24 13:46:25,111] [INFO] Running command: blastn -query GCF_019931045.1_ASM1993104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf77ff10-452a-480c-a57e-4f9c9f8f2174/dqc_reference/reference_markers.fasta -out GCF_019931045.1_ASM1993104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:26,211] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:26,213] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:26,214] [INFO] Target genome list was writen to GCF_019931045.1_ASM1993104v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:26,221] [INFO] Task started: fastANI
[2024-01-24 13:46:26,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e8760cb-604e-4d85-b883-246ca555a810/GCF_019931045.1_ASM1993104v1_genomic.fna.gz --refList GCF_019931045.1_ASM1993104v1_genomic.fna/target_genomes.txt --output GCF_019931045.1_ASM1993104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:52,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:52,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf77ff10-452a-480c-a57e-4f9c9f8f2174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:52,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf77ff10-452a-480c-a57e-4f9c9f8f2174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:52,118] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:52,119] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:52,119] [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 pauculus	strain=FDAARGOS_1472	GCA_019931045.1	82633	82633	type	True	100.0	2155	2158	95	conclusive
Cupriavidus pauculus	strain=CCUG 12507	GCA_008801835.1	82633	82633	type	True	99.9709	2071	2158	95	conclusive
Cupriavidus agavae	strain=ASC-9842	GCA_004217045.1	1001822	1001822	type	True	84.5919	1307	2158	95	below_threshold
Cupriavidus metallidurans	strain=CH34	GCA_000196015.1	119219	119219	type	True	84.2962	1318	2158	95	below_threshold
Cupriavidus campinensis	strain=LMG 19282	GCA_905397395.1	151783	151783	type	True	83.7459	1297	2158	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	82.9238	1188	2158	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	82.6467	1137	2158	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	82.509	1120	2158	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	82.4793	1168	2158	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	82.3895	1132	2158	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	82.0471	1101	2158	95	below_threshold
Cupriavidus plantarum	strain=LMG 26296	GCA_905397285.1	942865	942865	type	True	81.8337	1143	2158	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	81.4851	1095	2158	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	80.212	683	2158	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.1222	562	2158	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.0807	578	2158	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	77.9074	564	2158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:52,121] [INFO] DFAST Taxonomy check result was written to GCF_019931045.1_ASM1993104v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:52,121] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:52,122] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:52,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf77ff10-452a-480c-a57e-4f9c9f8f2174/dqc_reference/checkm_data
[2024-01-24 13:46:52,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:52,187] [INFO] Task started: CheckM
[2024-01-24 13:46:52,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019931045.1_ASM1993104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019931045.1_ASM1993104v1_genomic.fna/checkm_input GCF_019931045.1_ASM1993104v1_genomic.fna/checkm_result
[2024-01-24 13:48:00,600] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:00,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:00,622] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:00,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:00,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019931045.1_ASM1993104v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:00,623] [INFO] Task started: Blastn
[2024-01-24 13:48:00,624] [INFO] Running command: blastn -query GCF_019931045.1_ASM1993104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf77ff10-452a-480c-a57e-4f9c9f8f2174/dqc_reference/reference_markers_gtdb.fasta -out GCF_019931045.1_ASM1993104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:02,588] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:02,592] [INFO] Selected 11 target genomes.
[2024-01-24 13:48:02,592] [INFO] Target genome list was writen to GCF_019931045.1_ASM1993104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:02,605] [INFO] Task started: fastANI
[2024-01-24 13:48:02,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e8760cb-604e-4d85-b883-246ca555a810/GCF_019931045.1_ASM1993104v1_genomic.fna.gz --refList GCF_019931045.1_ASM1993104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019931045.1_ASM1993104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:19,812] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:19,826] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:19,826] [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_008801835.1	s__Cupriavidus pauculus	99.9709	2071	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.57	98.49	0.87	0.84	3	conclusive
GCF_003854935.1	s__Cupriavidus pauculus_C	85.5879	1384	2158	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	85.46	1447	2158	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	85.1841	1439	2158	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	85.0354	1459	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858765.1	s__Cupriavidus pauculus_B	85.0029	1447	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217045.1	s__Cupriavidus sp004217045	84.6232	1302	2158	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	84.078	1165	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503625.1	s__Cupriavidus sp005503625	84.0594	1326	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.70	98.70	0.91	0.91	2	-
GCF_000069785.1	s__Cupriavidus taiwanensis	82.5233	1161	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.86	98.78	0.92	0.91	9	-
GCF_000876015.1	s__Cupriavidus basilensis_B	82.2973	1177	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.55	98.55	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:19,828] [INFO] GTDB search result was written to GCF_019931045.1_ASM1993104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:19,828] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:19,832] [INFO] DFAST_QC result json was written to GCF_019931045.1_ASM1993104v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:19,832] [INFO] DFAST_QC completed!
[2024-01-24 13:48:19,832] [INFO] Total running time: 0h2m19s