[2024-01-24 12:06:11,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:11,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:11,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg50697f55-9109-485e-93a5-7b52453d76a9/dqc_reference
[2024-01-24 12:06:13,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,246] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,247] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd065985-a321-4c96-a860-17add83f8a63/GCF_902859825.1_LMG_22037_genomic.fna.gz | prodigal -d GCF_902859825.1_LMG_22037_genomic.fna/cds.fna -a GCF_902859825.1_LMG_22037_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:37,193] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:37,193] [INFO] Task started: HMMsearch
[2024-01-24 12:06:37,194] [INFO] Running command: hmmsearch --tblout GCF_902859825.1_LMG_22037_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50697f55-9109-485e-93a5-7b52453d76a9/dqc_reference/reference_markers.hmm GCF_902859825.1_LMG_22037_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:37,640] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:37,641] [INFO] Found 6/6 markers.
[2024-01-24 12:06:37,704] [INFO] Query marker FASTA was written to GCF_902859825.1_LMG_22037_genomic.fna/markers.fasta
[2024-01-24 12:06:37,705] [INFO] Task started: Blastn
[2024-01-24 12:06:37,705] [INFO] Running command: blastn -query GCF_902859825.1_LMG_22037_genomic.fna/markers.fasta -db /var/lib/cwl/stg50697f55-9109-485e-93a5-7b52453d76a9/dqc_reference/reference_markers.fasta -out GCF_902859825.1_LMG_22037_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:38,665] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:38,668] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:38,668] [INFO] Target genome list was writen to GCF_902859825.1_LMG_22037_genomic.fna/target_genomes.txt
[2024-01-24 12:06:38,676] [INFO] Task started: fastANI
[2024-01-24 12:06:38,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd065985-a321-4c96-a860-17add83f8a63/GCF_902859825.1_LMG_22037_genomic.fna.gz --refList GCF_902859825.1_LMG_22037_genomic.fna/target_genomes.txt --output GCF_902859825.1_LMG_22037_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:06,023] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:06,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50697f55-9109-485e-93a5-7b52453d76a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:06,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50697f55-9109-485e-93a5-7b52453d76a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:06,037] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:07:06,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:06,037] [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 phenoliruptrix	strain=LMG 22037	GCA_902859825.1	252970	252970	suspected-type	True	100.0	2352	2358	95	conclusive
Paraburkholderia phenoliruptrix	strain=LMG 22037	GCA_902833655.1	252970	252970	suspected-type	True	99.9972	2358	2358	95	conclusive
Paraburkholderia graminis	strain=LMG 18924	GCA_902859785.1	60548	60548	type	True	88.8922	1714	2358	95	below_threshold
Paraburkholderia graminis	strain=C4D1M	GCA_000172415.1	60548	60548	type	True	88.7951	1692	2358	95	below_threshold
Paraburkholderia dilworthii	strain=WSM3556	GCA_000472525.1	948106	948106	type	True	87.1833	1669	2358	95	below_threshold
Paraburkholderia kirstenboschensis	strain=LMG 28727	GCA_904848585.1	1245436	1245436	type	True	86.959	1703	2358	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	86.6753	1360	2358	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	85.4421	1376	2358	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	84.7574	1313	2358	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	84.2759	1349	2358	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	84.2689	1447	2358	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	84.238	1474	2358	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	84.1979	1404	2358	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.0443	1365	2358	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.3263	1091	2358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:06,039] [INFO] DFAST Taxonomy check result was written to GCF_902859825.1_LMG_22037_genomic.fna/tc_result.tsv
[2024-01-24 12:07:06,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:06,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:06,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50697f55-9109-485e-93a5-7b52453d76a9/dqc_reference/checkm_data
[2024-01-24 12:07:06,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:06,113] [INFO] Task started: CheckM
[2024-01-24 12:07:06,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859825.1_LMG_22037_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859825.1_LMG_22037_genomic.fna/checkm_input GCF_902859825.1_LMG_22037_genomic.fna/checkm_result
[2024-01-24 12:08:13,480] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:13,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:13,511] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:13,512] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:13,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859825.1_LMG_22037_genomic.fna/markers.fasta)
[2024-01-24 12:08:13,513] [INFO] Task started: Blastn
[2024-01-24 12:08:13,513] [INFO] Running command: blastn -query GCF_902859825.1_LMG_22037_genomic.fna/markers.fasta -db /var/lib/cwl/stg50697f55-9109-485e-93a5-7b52453d76a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859825.1_LMG_22037_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:15,094] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:15,099] [INFO] Selected 11 target genomes.
[2024-01-24 12:08:15,099] [INFO] Target genome list was writen to GCF_902859825.1_LMG_22037_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:15,137] [INFO] Task started: fastANI
[2024-01-24 12:08:15,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd065985-a321-4c96-a860-17add83f8a63/GCF_902859825.1_LMG_22037_genomic.fna.gz --refList GCF_902859825.1_LMG_22037_genomic.fna/target_genomes_gtdb.txt --output GCF_902859825.1_LMG_22037_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:36,098] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:36,115] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:36,115] [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_902859825.1	s__Paraburkholderia phenoliruptrix	100.0	2352	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.08	98.23	0.90	0.84	7	conclusive
GCF_000472445.1	s__Paraburkholderia sp000472445	89.2611	1675	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172415.1	s__Paraburkholderia graminis	88.7782	1694	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.52	98.23	0.90	0.89	12	-
GCF_000472545.1	s__Paraburkholderia sp000472545	88.0657	1721	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000148685.1	s__Paraburkholderia sp000148685	87.969	1752	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.01	98.00	0.91	0.91	4	-
GCF_000472525.1	s__Paraburkholderia dilworthii	87.1847	1669	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904848585.1	s__Paraburkholderia kirstenboschensis	86.9618	1702	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.97	99.97	1.00	1.00	2	-
GCF_009690905.1	s__Paraburkholderia madseniana	84.2669	1447	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_900230185.1	s__Paraburkholderia sp900230185	84.0855	1491	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142905.1	s__Paraburkholderia sp900142905	84.0707	1426	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCA_003153455.1	s__PALSA-1004 sp003153455	75.356	116	2358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__PALSA-1004	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:36,117] [INFO] GTDB search result was written to GCF_902859825.1_LMG_22037_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:36,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:36,121] [INFO] DFAST_QC result json was written to GCF_902859825.1_LMG_22037_genomic.fna/dqc_result.json
[2024-01-24 12:08:36,121] [INFO] DFAST_QC completed!
[2024-01-24 12:08:36,122] [INFO] Total running time: 0h2m25s