[2024-01-24 13:27:58,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b843e19-2222-4e5b-929a-5aa7935326cf/dqc_reference
[2024-01-24 13:27:59,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,949] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg8444711c-b25c-45a5-b9c8-92ef6193ce1e/GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna.gz | prodigal -d GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/cds.fna -a GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:25,202] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:25,202] [INFO] Task started: HMMsearch
[2024-01-24 13:28:25,202] [INFO] Running command: hmmsearch --tblout GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b843e19-2222-4e5b-929a-5aa7935326cf/dqc_reference/reference_markers.hmm GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:25,636] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:25,637] [INFO] Found 6/6 markers.
[2024-01-24 13:28:25,704] [INFO] Query marker FASTA was written to GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/markers.fasta
[2024-01-24 13:28:25,704] [INFO] Task started: Blastn
[2024-01-24 13:28:25,704] [INFO] Running command: blastn -query GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b843e19-2222-4e5b-929a-5aa7935326cf/dqc_reference/reference_markers.fasta -out GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:26,706] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:26,710] [INFO] Selected 19 target genomes.
[2024-01-24 13:28:26,710] [INFO] Target genome list was writen to GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/target_genomes.txt
[2024-01-24 13:28:26,720] [INFO] Task started: fastANI
[2024-01-24 13:28:26,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg8444711c-b25c-45a5-b9c8-92ef6193ce1e/GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna.gz --refList GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/target_genomes.txt --output GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:00,926] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:00,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b843e19-2222-4e5b-929a-5aa7935326cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:00,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b843e19-2222-4e5b-929a-5aa7935326cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:00,942] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:29:00,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:00,942] [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
Paraburkholderia kururiensis	strain=LMG 19447	GCA_902833705.1	984307	984307	type	True	100.0	2468	2470	95	conclusive
Paraburkholderia kururiensis	strain=KP23	GCA_003986935.1	984307	984307	type	True	99.9884	2440	2470	95	conclusive
Paraburkholderia kururiensis subsp. thiooxydans	strain=NBRC 107107	GCA_000739795.1	445708	984307	type	True	96.0109	2021	2470	95	conclusive
Paraburkholderia caballeronis	strain=TNe-841	GCA_900104845.1	416943	416943	type	True	82.1294	1128	2470	95	below_threshold
Paraburkholderia ferrariae	strain=NBRC 106233	GCA_000685035.1	386056	386056	type	True	82.1204	1151	2470	95	below_threshold
Paraburkholderia lycopersici	strain=TNe-862	GCA_900096975.1	416944	416944	type	True	82.0221	1143	2470	95	below_threshold
Paraburkholderia acidipaludis	strain=NBRC 101816	GCA_000684975.1	660537	660537	type	True	81.976	1106	2470	95	below_threshold
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	81.8846	1208	2470	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_000785435.2	159450	159450	type	True	81.7854	1072	2470	95	below_threshold
Paraburkholderia sacchari	strain=LMG 19450	GCA_902833715.1	159450	159450	type	True	81.7362	1071	2470	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	81.6822	1140	2470	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	81.6304	1193	2470	95	below_threshold
Paraburkholderia dinghuensis	strain=DHOA04	GCA_003837865.1	2305225	2305225	type	True	81.6086	943	2470	95	below_threshold
Paraburkholderia oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	81.5748	1180	2470	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	81.2024	1004	2470	95	below_threshold
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	81.1212	1119	2470	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.0738	1145	2470	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	80.7003	1069	2470	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	80.64	987	2470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:00,944] [INFO] DFAST Taxonomy check result was written to GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/tc_result.tsv
[2024-01-24 13:29:00,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:00,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:00,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b843e19-2222-4e5b-929a-5aa7935326cf/dqc_reference/checkm_data
[2024-01-24 13:29:00,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:01,022] [INFO] Task started: CheckM
[2024-01-24 13:29:01,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/checkm_input GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/checkm_result
[2024-01-24 13:30:15,531] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:15,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:15,554] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:15,554] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:15,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/markers.fasta)
[2024-01-24 13:30:15,555] [INFO] Task started: Blastn
[2024-01-24 13:30:15,555] [INFO] Running command: blastn -query GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b843e19-2222-4e5b-929a-5aa7935326cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:17,393] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:17,399] [INFO] Selected 18 target genomes.
[2024-01-24 13:30:17,399] [INFO] Target genome list was writen to GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:17,419] [INFO] Task started: fastANI
[2024-01-24 13:30:17,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg8444711c-b25c-45a5-b9c8-92ef6193ce1e/GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna.gz --refList GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/target_genomes_gtdb.txt --output GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:44,760] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:44,779] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:44,780] [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_003986935.1	s__Paraburkholderia kururiensis	99.9884	2440	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.16	96.06	0.93	0.91	5	conclusive
GCF_003350035.1	s__Paraburkholderia kururiensis_A	92.1886	1937	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104845.1	s__Paraburkholderia caballeronis	82.1458	1126	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.48	98.95	0.97	0.92	9	-
GCF_000685035.1	s__Paraburkholderia ferrariae	82.1425	1147	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298475.1	s__Paraburkholderia sp004298475	82.0649	863	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.94	99.94	0.88	0.88	2	-
GCF_900096975.1	s__Paraburkholderia lycopersici	82.0322	1140	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000684975.1	s__Paraburkholderia acidipaludis	81.9994	1102	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752995.1	s__Paraburkholderia sp011752995	81.9226	1115	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCF_000519185.1	s__Paraburkholderia nodosa	81.9042	1206	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785435.2	s__Paraburkholderia sacchari	81.7804	1074	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.05	96.11	0.93	0.86	3	-
GCF_009789655.1	s__Paraburkholderia acidiphila	81.7587	1194	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109265.1	s__Paraburkholderia tropica	81.7395	1250	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.07	95.97	0.93	0.85	14	-
GCF_002870125.1	s__Paraburkholderia sp002870125	81.7049	894	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789675.1	s__Paraburkholderia acidisoli	81.6982	1188	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003837865.1	s__Paraburkholderia dinghuensis	81.6236	941	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253405.1	s__Paraburkholderia sp003253405	81.6007	1061	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859935.1	s__Paraburkholderia fynbosensis	81.1356	1117	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.83	96.83	0.79	0.79	2	-
GCF_000472545.1	s__Paraburkholderia sp000472545	80.8684	1140	2470	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:44,781] [INFO] GTDB search result was written to GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:44,782] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:44,786] [INFO] DFAST_QC result json was written to GCF_902833705.1_Paraburkholderia_kururiensis_LMG_19447_genomic.fna/dqc_result.json
[2024-01-24 13:30:44,787] [INFO] DFAST_QC completed!
[2024-01-24 13:30:44,787] [INFO] Total running time: 0h2m46s