[2024-01-24 13:55:25,534] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:25,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:25,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg595cb7cd-c850-4027-974e-dea81b4be2ec/dqc_reference
[2024-01-24 13:55:26,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:26,779] [INFO] Task started: Prodigal
[2024-01-24 13:55:26,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg51869726-e287-4250-a02d-0d3a56ed9140/GCF_914271545.1_LMG_21510_genomic.fna.gz | prodigal -d GCF_914271545.1_LMG_21510_genomic.fna/cds.fna -a GCF_914271545.1_LMG_21510_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:44,462] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:44,462] [INFO] Task started: HMMsearch
[2024-01-24 13:55:44,463] [INFO] Running command: hmmsearch --tblout GCF_914271545.1_LMG_21510_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg595cb7cd-c850-4027-974e-dea81b4be2ec/dqc_reference/reference_markers.hmm GCF_914271545.1_LMG_21510_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:44,777] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:44,779] [INFO] Found 6/6 markers.
[2024-01-24 13:55:44,827] [INFO] Query marker FASTA was written to GCF_914271545.1_LMG_21510_genomic.fna/markers.fasta
[2024-01-24 13:55:44,827] [INFO] Task started: Blastn
[2024-01-24 13:55:44,827] [INFO] Running command: blastn -query GCF_914271545.1_LMG_21510_genomic.fna/markers.fasta -db /var/lib/cwl/stg595cb7cd-c850-4027-974e-dea81b4be2ec/dqc_reference/reference_markers.fasta -out GCF_914271545.1_LMG_21510_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:45,767] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:45,778] [INFO] Selected 24 target genomes.
[2024-01-24 13:55:45,778] [INFO] Target genome list was writen to GCF_914271545.1_LMG_21510_genomic.fna/target_genomes.txt
[2024-01-24 13:55:45,885] [INFO] Task started: fastANI
[2024-01-24 13:55:45,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg51869726-e287-4250-a02d-0d3a56ed9140/GCF_914271545.1_LMG_21510_genomic.fna.gz --refList GCF_914271545.1_LMG_21510_genomic.fna/target_genomes.txt --output GCF_914271545.1_LMG_21510_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:16,097] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:16,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg595cb7cd-c850-4027-974e-dea81b4be2ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:16,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg595cb7cd-c850-4027-974e-dea81b4be2ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:16,122] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:16,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:16,122] [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 respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	100.0	1858	1858	95	conclusive
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	84.5556	1192	1858	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	84.4442	1193	1858	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	84.4136	1186	1858	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	84.1053	1162	1858	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	83.8371	1114	1858	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	83.7002	1084	1858	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	83.6905	1129	1858	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	83.6753	1121	1858	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	83.5964	1083	1858	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	83.4139	1090	1858	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	82.834	1088	1858	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	82.5466	1015	1858	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.3704	703	1858	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.176	582	1858	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.1266	513	1858	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	78.0544	566	1858	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	76.1843	300	1858	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	75.5693	197	1858	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	75.349	133	1858	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	75.1152	88	1858	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	75.1143	115	1858	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	74.8937	57	1858	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	74.7917	256	1858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:16,124] [INFO] DFAST Taxonomy check result was written to GCF_914271545.1_LMG_21510_genomic.fna/tc_result.tsv
[2024-01-24 13:56:16,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:16,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:16,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg595cb7cd-c850-4027-974e-dea81b4be2ec/dqc_reference/checkm_data
[2024-01-24 13:56:16,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:16,180] [INFO] Task started: CheckM
[2024-01-24 13:56:16,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_914271545.1_LMG_21510_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_914271545.1_LMG_21510_genomic.fna/checkm_input GCF_914271545.1_LMG_21510_genomic.fna/checkm_result
[2024-01-24 13:57:12,327] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:12,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:12,349] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:12,349] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:12,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_914271545.1_LMG_21510_genomic.fna/markers.fasta)
[2024-01-24 13:57:12,350] [INFO] Task started: Blastn
[2024-01-24 13:57:12,350] [INFO] Running command: blastn -query GCF_914271545.1_LMG_21510_genomic.fna/markers.fasta -db /var/lib/cwl/stg595cb7cd-c850-4027-974e-dea81b4be2ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_914271545.1_LMG_21510_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:14,073] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:14,077] [INFO] Selected 30 target genomes.
[2024-01-24 13:57:14,077] [INFO] Target genome list was writen to GCF_914271545.1_LMG_21510_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:14,280] [INFO] Task started: fastANI
[2024-01-24 13:57:14,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg51869726-e287-4250-a02d-0d3a56ed9140/GCF_914271545.1_LMG_21510_genomic.fna.gz --refList GCF_914271545.1_LMG_21510_genomic.fna/target_genomes_gtdb.txt --output GCF_914271545.1_LMG_21510_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:54,989] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:55,010] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:57:55,010] [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	84.564	1190	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.88	98.88	0.93	0.93	2	-
GCF_008801915.1	s__Cupriavidus gilardii	84.4114	1198	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.02	95.33	0.92	0.88	7	-
GCF_001598055.1	s__Cupriavidus nantongensis	84.1089	1162	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.73	95.73	0.81	0.78	3	-
GCF_013314895.1	s__Cupriavidus gilardii_C	84.102	1201	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.09	95.09	0.91	0.91	2	-
GCF_900249755.1	s__Cupriavidus taiwanensis_D	83.9966	1128	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.80	98.80	0.92	0.92	2	-
GCF_000876015.1	s__Cupriavidus basilensis_B	83.9345	1160	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.55	98.55	0.88	0.88	2	-
GCF_900094595.1	s__Cupriavidus alkaliphilus	83.8153	1118	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	-
GCF_013141915.1	s__Cupriavidus necator_B	83.7882	1125	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900250075.1	s__Cupriavidus taiwanensis_C	83.7586	1143	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.42	95.79	0.88	0.85	6	-
GCF_016894385.1	s__Cupriavidus oxalaticus	83.7418	1079	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.73	98.93	0.98	0.92	5	-
GCF_000372525.1	s__Cupriavidus neocaledonicus	83.6924	1129	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.97	99.97	0.99	0.98	3	-
GCF_004768545.1	s__Cupriavidus oxalaticus_A	83.5527	1117	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.89	98.53	0.88	0.85	3	-
GCA_000471925.1	s__Cupriavidus pickettii_A	83.4878	1141	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402535.1	s__Cupriavidus sp003402535	83.4811	1153	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744095.1	s__Cupriavidus necator_A	83.3861	1154	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219215.1	s__Cupriavidus necator	83.3678	1134	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.10	95.22	0.79	0.76	13	-
GCF_007829435.1	s__Cupriavidus gilardii_D	83.1328	1071	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812465.1	s__Cupriavidus sp000812465	83.0552	1030	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854325.1	s__Cupriavidus malaysiensis	82.8575	1084	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.34	99.30	0.91	0.91	3	-
GCF_900101625.1	s__Cupriavidus sp900101625	82.4001	997	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020205.1	s__Ralstonia pickettii_B	79.9774	617	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.08	96.31	0.87	0.83	22	-
GCF_001424165.1	s__Massilia sp001424165	77.7899	468	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255905.1	s__PBB1 sp002255905	77.4052	272	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PBB1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365205.1	s__CAIWHR01 sp010365205	76.5868	174	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012767755.2	s__Pseudomonas_F sp003234055	76.1941	298	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	75.9062	206	1858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882925.1	s__Chersky-534 sp017882925	74.7809	76	1858	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__Chersky-534;g__Chersky-534	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:55,012] [INFO] GTDB search result was written to GCF_914271545.1_LMG_21510_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:55,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:55,018] [INFO] DFAST_QC result json was written to GCF_914271545.1_LMG_21510_genomic.fna/dqc_result.json
[2024-01-24 13:57:55,018] [INFO] DFAST_QC completed!
[2024-01-24 13:57:55,018] [INFO] Total running time: 0h2m29s