[2024-01-24 15:26:39,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,533] [INFO] DQC Reference Directory: /var/lib/cwl/stgac1f0a21-bb3d-47ea-bda4-d9ea1de5d4b8/dqc_reference
[2024-01-24 15:26:40,884] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,885] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,885] [INFO] Running command: gunzip -c /var/lib/cwl/stg33b62c28-9bd4-4723-9250-a22408d7c07a/GCF_902833715.1_ASM90283371v1_genomic.fna.gz | prodigal -d GCF_902833715.1_ASM90283371v1_genomic.fna/cds.fna -a GCF_902833715.1_ASM90283371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:04,363] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:04,363] [INFO] Task started: HMMsearch
[2024-01-24 15:27:04,364] [INFO] Running command: hmmsearch --tblout GCF_902833715.1_ASM90283371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac1f0a21-bb3d-47ea-bda4-d9ea1de5d4b8/dqc_reference/reference_markers.hmm GCF_902833715.1_ASM90283371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:04,759] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:04,760] [INFO] Found 6/6 markers.
[2024-01-24 15:27:04,823] [INFO] Query marker FASTA was written to GCF_902833715.1_ASM90283371v1_genomic.fna/markers.fasta
[2024-01-24 15:27:04,823] [INFO] Task started: Blastn
[2024-01-24 15:27:04,823] [INFO] Running command: blastn -query GCF_902833715.1_ASM90283371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac1f0a21-bb3d-47ea-bda4-d9ea1de5d4b8/dqc_reference/reference_markers.fasta -out GCF_902833715.1_ASM90283371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:05,856] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:05,860] [INFO] Selected 12 target genomes.
[2024-01-24 15:27:05,860] [INFO] Target genome list was writen to GCF_902833715.1_ASM90283371v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:05,866] [INFO] Task started: fastANI
[2024-01-24 15:27:05,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg33b62c28-9bd4-4723-9250-a22408d7c07a/GCF_902833715.1_ASM90283371v1_genomic.fna.gz --refList GCF_902833715.1_ASM90283371v1_genomic.fna/target_genomes.txt --output GCF_902833715.1_ASM90283371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:31,103] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:31,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac1f0a21-bb3d-47ea-bda4-d9ea1de5d4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:31,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac1f0a21-bb3d-47ea-bda4-d9ea1de5d4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:31,121] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:31,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:31,122] [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
Paraburkholderia sacchari	strain=LMG 19450	GCA_902833715.1	159450	159450	type	True	100.0	2398	2402	95	conclusive
Paraburkholderia sacchari	strain=LMG 19450	GCA_000785435.2	159450	159450	type	True	99.9948	2396	2402	95	conclusive
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	88.9014	1677	2402	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	88.753	1735	2402	95	below_threshold
Paraburkholderia oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	88.7237	1690	2402	95	below_threshold
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	85.1209	1507	2402	95	below_threshold
Paraburkholderia mimosarum	strain=LMG 23256	GCA_902833725.1	312026	312026	type	True	85.0506	1451	2402	95	below_threshold
Paraburkholderia mimosarum	strain=NBRC 106338	GCA_000739815.1	312026	312026	type	True	85.0229	1438	2402	95	below_threshold
Paraburkholderia mimosarum	strain=LMG 23256	GCA_000472825.1	312026	312026	type	True	84.9724	1469	2402	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.1218	1137	2402	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.1044	1223	2402	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	81.0491	1048	2402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:31,129] [INFO] DFAST Taxonomy check result was written to GCF_902833715.1_ASM90283371v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:31,130] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:31,130] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:31,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac1f0a21-bb3d-47ea-bda4-d9ea1de5d4b8/dqc_reference/checkm_data
[2024-01-24 15:27:31,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:31,213] [INFO] Task started: CheckM
[2024-01-24 15:27:31,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833715.1_ASM90283371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833715.1_ASM90283371v1_genomic.fna/checkm_input GCF_902833715.1_ASM90283371v1_genomic.fna/checkm_result
[2024-01-24 15:28:37,169] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:37,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:37,191] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:37,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:37,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833715.1_ASM90283371v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:37,193] [INFO] Task started: Blastn
[2024-01-24 15:28:37,193] [INFO] Running command: blastn -query GCF_902833715.1_ASM90283371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac1f0a21-bb3d-47ea-bda4-d9ea1de5d4b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833715.1_ASM90283371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:39,155] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:39,159] [INFO] Selected 12 target genomes.
[2024-01-24 15:28:39,159] [INFO] Target genome list was writen to GCF_902833715.1_ASM90283371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:39,169] [INFO] Task started: fastANI
[2024-01-24 15:28:39,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg33b62c28-9bd4-4723-9250-a22408d7c07a/GCF_902833715.1_ASM90283371v1_genomic.fna.gz --refList GCF_902833715.1_ASM90283371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902833715.1_ASM90283371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:02,746] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:02,762] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:02,762] [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_000785435.2	s__Paraburkholderia sacchari	99.9948	2396	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.05	96.11	0.93	0.86	3	conclusive
GCF_902859945.1	s__Paraburkholderia caffeinitolerans	92.5688	1793	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.86	99.86	0.95	0.95	2	-
GCF_004353915.1	s__Paraburkholderia sp004353915	88.8854	1680	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685075.1	s__Paraburkholderia oxyphila	88.7199	1692	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.32	95.32	0.74	0.74	2	-
GCF_900109265.1	s__Paraburkholderia tropica	85.7566	1440	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.07	95.97	0.93	0.85	14	-
GCF_900096975.1	s__Paraburkholderia lycopersici	85.3366	1323	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096715.1	s__Paraburkholderia silvatlantica	85.2299	1417	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.5542	99.65	99.23	0.96	0.92	5	-
GCF_000519185.1	s__Paraburkholderia nodosa	85.0966	1510	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739815.1	s__Paraburkholderia mimosarum	85.0772	1429	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.63	98.93	0.95	0.86	4	-
GCF_001718195.1	s__Paraburkholderia nodosa_A	85.0372	1446	2402	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353905.1	s__Paraburkholderia guartelaensis	85.0265	1518	2402	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	84.7077	1378	2402	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 15:29:02,763] [INFO] GTDB search result was written to GCF_902833715.1_ASM90283371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:02,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:02,767] [INFO] DFAST_QC result json was written to GCF_902833715.1_ASM90283371v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:02,768] [INFO] DFAST_QC completed!
[2024-01-24 15:29:02,768] [INFO] Total running time: 0h2m23s