[2024-01-24 14:06:44,134] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:44,136] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:44,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg07ce4217-7203-4f9f-8bec-b55e323684b3/dqc_reference
[2024-01-24 14:06:45,433] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:45,434] [INFO] Task started: Prodigal
[2024-01-24 14:06:45,434] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a90e4ab-db49-4db6-9516-dff74a4c3f30/GCF_000266985.1_ASM26698v1_genomic.fna.gz | prodigal -d GCF_000266985.1_ASM26698v1_genomic.fna/cds.fna -a GCF_000266985.1_ASM26698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:06,693] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:06,694] [INFO] Task started: HMMsearch
[2024-01-24 14:07:06,694] [INFO] Running command: hmmsearch --tblout GCF_000266985.1_ASM26698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07ce4217-7203-4f9f-8bec-b55e323684b3/dqc_reference/reference_markers.hmm GCF_000266985.1_ASM26698v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:07,104] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:07,105] [INFO] Found 6/6 markers.
[2024-01-24 14:07:07,158] [INFO] Query marker FASTA was written to GCF_000266985.1_ASM26698v1_genomic.fna/markers.fasta
[2024-01-24 14:07:07,159] [INFO] Task started: Blastn
[2024-01-24 14:07:07,159] [INFO] Running command: blastn -query GCF_000266985.1_ASM26698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07ce4217-7203-4f9f-8bec-b55e323684b3/dqc_reference/reference_markers.fasta -out GCF_000266985.1_ASM26698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:08,186] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:08,200] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:08,201] [INFO] Target genome list was writen to GCF_000266985.1_ASM26698v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:08,222] [INFO] Task started: fastANI
[2024-01-24 14:07:08,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a90e4ab-db49-4db6-9516-dff74a4c3f30/GCF_000266985.1_ASM26698v1_genomic.fna.gz --refList GCF_000266985.1_ASM26698v1_genomic.fna/target_genomes.txt --output GCF_000266985.1_ASM26698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:36,645] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:36,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07ce4217-7203-4f9f-8bec-b55e323684b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:36,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07ce4217-7203-4f9f-8bec-b55e323684b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:36,658] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:07:36,658] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:07:36,659] [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 thailandensis	strain=E264	GCA_003568605.1	57975	57975	type	True	93.6136	1783	2388	95	below_threshold
Burkholderia thailandensis	strain=E264; ATCC 700388	GCA_000012365.1	57975	57975	type	True	93.5456	1789	2388	95	below_threshold
Burkholderia thailandensis	strain=ATCC 700388	GCA_000152285.1	57975	57975	type	True	93.4784	1684	2388	95	below_threshold
Burkholderia pseudomallei	strain=ATCC 23343	GCA_001182285.1	28450	28450	type	True	93.006	1809	2388	95	below_threshold
Burkholderia pseudomallei	strain=WRAIR 286	GCA_006538545.1	28450	28450	type	True	92.9859	1753	2388	95	below_threshold
Burkholderia mallei	strain=NCTC12938	GCA_900446245.1	13373	13373	type	True	92.7809	1591	2388	95	below_threshold
Burkholderia mallei	strain=ATCC 23344	GCA_000011705.1	13373	13373	type	True	92.7693	1604	2388	95	below_threshold
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	91.8333	1793	2388	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	86.0925	1424	2388	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	86.0319	1478	2388	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	85.2322	1383	2388	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.5548	1304	2388	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	81.3524	1087	2388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:36,660] [INFO] DFAST Taxonomy check result was written to GCF_000266985.1_ASM26698v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:36,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:36,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:36,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07ce4217-7203-4f9f-8bec-b55e323684b3/dqc_reference/checkm_data
[2024-01-24 14:07:36,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:36,728] [INFO] Task started: CheckM
[2024-01-24 14:07:36,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000266985.1_ASM26698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000266985.1_ASM26698v1_genomic.fna/checkm_input GCF_000266985.1_ASM26698v1_genomic.fna/checkm_result
[2024-01-24 14:08:50,643] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:50,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:50,670] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:50,670] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:50,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000266985.1_ASM26698v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:50,671] [INFO] Task started: Blastn
[2024-01-24 14:08:50,671] [INFO] Running command: blastn -query GCF_000266985.1_ASM26698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07ce4217-7203-4f9f-8bec-b55e323684b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000266985.1_ASM26698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:52,719] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:52,723] [INFO] Selected 5 target genomes.
[2024-01-24 14:08:52,723] [INFO] Target genome list was writen to GCF_000266985.1_ASM26698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:52,727] [INFO] Task started: fastANI
[2024-01-24 14:08:52,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a90e4ab-db49-4db6-9516-dff74a4c3f30/GCF_000266985.1_ASM26698v1_genomic.fna.gz --refList GCF_000266985.1_ASM26698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000266985.1_ASM26698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:05,442] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:05,453] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:05,453] [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_001462435.1	s__Burkholderia humptydooensis	99.1682	2086	2388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.52	99.18	0.95	0.92	12	conclusive
GCF_000012365.1	s__Burkholderia thailandensis	93.5718	1786	2388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.58	98.83	0.96	0.93	53	-
GCF_000011705.1	s__Burkholderia mallei	92.7573	1606	2388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.31	98.71	0.94	0.78	1780	-
GCF_001524625.2	s__Burkholderia sp001524625	91.9892	1793	2388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.38	99.33	0.93	0.91	11	-
GCF_000959365.1	s__Burkholderia oklahomensis	91.8455	1775	2388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.42	95.09	0.95	0.85	15	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:05,456] [INFO] GTDB search result was written to GCF_000266985.1_ASM26698v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:05,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:05,460] [INFO] DFAST_QC result json was written to GCF_000266985.1_ASM26698v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:05,460] [INFO] DFAST_QC completed!
[2024-01-24 14:09:05,461] [INFO] Total running time: 0h2m21s