[2024-01-24 11:48:21,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,281] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf28b33c-f134-40fd-9884-8078f0e39e44/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,567] [INFO] Running command: gunzip -c /var/lib/cwl/stga634decb-f816-43dd-bfc6-ee2559452451/GCF_902832905.1_ASM90283290v1_genomic.fna.gz | prodigal -d GCF_902832905.1_ASM90283290v1_genomic.fna/cds.fna -a GCF_902832905.1_ASM90283290v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:50,010] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:50,011] [INFO] Task started: HMMsearch
[2024-01-24 11:48:50,011] [INFO] Running command: hmmsearch --tblout GCF_902832905.1_ASM90283290v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf28b33c-f134-40fd-9884-8078f0e39e44/dqc_reference/reference_markers.hmm GCF_902832905.1_ASM90283290v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:50,357] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:50,358] [INFO] Found 6/6 markers.
[2024-01-24 11:48:50,439] [INFO] Query marker FASTA was written to GCF_902832905.1_ASM90283290v1_genomic.fna/markers.fasta
[2024-01-24 11:48:50,440] [INFO] Task started: Blastn
[2024-01-24 11:48:50,440] [INFO] Running command: blastn -query GCF_902832905.1_ASM90283290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf28b33c-f134-40fd-9884-8078f0e39e44/dqc_reference/reference_markers.fasta -out GCF_902832905.1_ASM90283290v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:51,554] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:51,567] [INFO] Selected 9 target genomes.
[2024-01-24 11:48:51,568] [INFO] Target genome list was writen to GCF_902832905.1_ASM90283290v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:51,573] [INFO] Task started: fastANI
[2024-01-24 11:48:51,573] [INFO] Running command: fastANI --query /var/lib/cwl/stga634decb-f816-43dd-bfc6-ee2559452451/GCF_902832905.1_ASM90283290v1_genomic.fna.gz --refList GCF_902832905.1_ASM90283290v1_genomic.fna/target_genomes.txt --output GCF_902832905.1_ASM90283290v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:49:12,427] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:12,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf28b33c-f134-40fd-9884-8078f0e39e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:49:12,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf28b33c-f134-40fd-9884-8078f0e39e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:49:12,442] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:49:12,442] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:49:12,442] [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
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	100.0	2649	2653	95	inconclusive
Burkholderia plantarii	strain=ATCC 43733	GCA_001411805.1	41899	41899	type	True	99.9855	2649	2653	95	inconclusive
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	95.9976	2217	2653	95	inconclusive
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	92.4203	1714	2653	95	below_threshold
Burkholderia glumae	strain=ATCC 33617	GCA_000960995.1	337	337	type	True	92.3805	1741	2653	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	83.6225	1356	2653	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	83.5995	1399	2653	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	83.3038	1401	2653	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	80.9591	1116	2653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:49:12,444] [INFO] DFAST Taxonomy check result was written to GCF_902832905.1_ASM90283290v1_genomic.fna/tc_result.tsv
[2024-01-24 11:49:12,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:49:12,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:49:12,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf28b33c-f134-40fd-9884-8078f0e39e44/dqc_reference/checkm_data
[2024-01-24 11:49:12,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:49:12,537] [INFO] Task started: CheckM
[2024-01-24 11:49:12,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902832905.1_ASM90283290v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902832905.1_ASM90283290v1_genomic.fna/checkm_input GCF_902832905.1_ASM90283290v1_genomic.fna/checkm_result
[2024-01-24 11:50:38,775] [INFO] Task succeeded: CheckM
[2024-01-24 11:50:38,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:50:38,803] [INFO] ===== Completeness check finished =====
[2024-01-24 11:50:38,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:50:38,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902832905.1_ASM90283290v1_genomic.fna/markers.fasta)
[2024-01-24 11:50:38,805] [INFO] Task started: Blastn
[2024-01-24 11:50:38,805] [INFO] Running command: blastn -query GCF_902832905.1_ASM90283290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf28b33c-f134-40fd-9884-8078f0e39e44/dqc_reference/reference_markers_gtdb.fasta -out GCF_902832905.1_ASM90283290v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:50:41,058] [INFO] Task succeeded: Blastn
[2024-01-24 11:50:41,063] [INFO] Selected 11 target genomes.
[2024-01-24 11:50:41,063] [INFO] Target genome list was writen to GCF_902832905.1_ASM90283290v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:50:41,073] [INFO] Task started: fastANI
[2024-01-24 11:50:41,074] [INFO] Running command: fastANI --query /var/lib/cwl/stga634decb-f816-43dd-bfc6-ee2559452451/GCF_902832905.1_ASM90283290v1_genomic.fna.gz --refList GCF_902832905.1_ASM90283290v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902832905.1_ASM90283290v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:02,831] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:02,846] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:02,846] [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_001411805.1	s__Burkholderia plantarii	99.9855	2649	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.45	95.52	0.94	0.88	5	conclusive
GCF_000960995.1	s__Burkholderia glumae	92.4227	1736	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.66	99.30	0.96	0.92	18	-
GCA_009914575.1	s__Burkholderia gladioli_B	87.8614	411	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000959725.1	s__Burkholderia gladioli	87.2658	1877	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.34	97.08	0.90	0.82	265	-
GCF_017104645.1	s__Burkholderia sp017104645	86.9034	1441	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687455.2	s__Burkholderia sp000687455	83.7521	1066	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902830275.1	s__Burkholderia stagnalis	83.5687	1413	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.76	95.48	0.93	0.80	113	-
GCF_003854275.1	s__Burkholderia sp003854275	83.4037	1303	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	95.08	95.08	0.74	0.74	2	-
GCF_000959525.1	s__Burkholderia multivorans	83.2104	1357	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.58	96.90	0.90	0.85	326	-
GCF_000959365.1	s__Burkholderia oklahomensis	83.1738	1352	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.42	95.09	0.95	0.85	15	-
GCF_000732615.1	s__Burkholderia paludis	82.9934	1390	2653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.34	99.33	0.95	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:02,848] [INFO] GTDB search result was written to GCF_902832905.1_ASM90283290v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:02,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:02,851] [INFO] DFAST_QC result json was written to GCF_902832905.1_ASM90283290v1_genomic.fna/dqc_result.json
[2024-01-24 11:51:02,852] [INFO] DFAST_QC completed!
[2024-01-24 11:51:02,852] [INFO] Total running time: 0h2m42s