[2024-01-24 13:17:34,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b6e2ac3-6b0b-4231-96e8-860ef3b10035/dqc_reference
[2024-01-24 13:17:35,987] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,987] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,988] [INFO] Running command: gunzip -c /var/lib/cwl/stg7de92fea-f392-4de5-b4d2-8d6cf48ffe7a/GCF_001522135.2_ASM152213v2_genomic.fna.gz | prodigal -d GCF_001522135.2_ASM152213v2_genomic.fna/cds.fna -a GCF_001522135.2_ASM152213v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:57,419] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:57,419] [INFO] Task started: HMMsearch
[2024-01-24 13:17:57,420] [INFO] Running command: hmmsearch --tblout GCF_001522135.2_ASM152213v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b6e2ac3-6b0b-4231-96e8-860ef3b10035/dqc_reference/reference_markers.hmm GCF_001522135.2_ASM152213v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:57,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:57,773] [INFO] Found 6/6 markers.
[2024-01-24 13:17:57,833] [INFO] Query marker FASTA was written to GCF_001522135.2_ASM152213v2_genomic.fna/markers.fasta
[2024-01-24 13:17:57,833] [INFO] Task started: Blastn
[2024-01-24 13:17:57,833] [INFO] Running command: blastn -query GCF_001522135.2_ASM152213v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b6e2ac3-6b0b-4231-96e8-860ef3b10035/dqc_reference/reference_markers.fasta -out GCF_001522135.2_ASM152213v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:58,858] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:58,861] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:58,861] [INFO] Target genome list was writen to GCF_001522135.2_ASM152213v2_genomic.fna/target_genomes.txt
[2024-01-24 13:17:58,864] [INFO] Task started: fastANI
[2024-01-24 13:17:58,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg7de92fea-f392-4de5-b4d2-8d6cf48ffe7a/GCF_001522135.2_ASM152213v2_genomic.fna.gz --refList GCF_001522135.2_ASM152213v2_genomic.fna/target_genomes.txt --output GCF_001522135.2_ASM152213v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:22,335] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:22,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b6e2ac3-6b0b-4231-96e8-860ef3b10035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:22,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b6e2ac3-6b0b-4231-96e8-860ef3b10035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:22,345] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:18:22,345] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:22,345] [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 oklahomensis	strain=C6786	GCA_001522135.2	342113	342113	type	True	100.0	2377	2378	95	conclusive
Burkholderia oklahomensis	strain=C6786	GCA_000959365.1	342113	342113	type	True	99.9996	2376	2378	95	conclusive
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	99.9996	2375	2378	95	conclusive
Burkholderia oklahomensis	strain=LMG 23618	GCA_902829515.1	342113	342113	type	True	99.9852	2334	2378	95	conclusive
Burkholderia oklahomensis	strain=C6786	GCA_000170375.1	342113	342113	type	True	99.8244	1998	2378	95	conclusive
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	86.0134	1496	2378	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	86.0086	1443	2378	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	84.8105	1410	2378	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.4887	1333	2378	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	81.0607	1096	2378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:22,347] [INFO] DFAST Taxonomy check result was written to GCF_001522135.2_ASM152213v2_genomic.fna/tc_result.tsv
[2024-01-24 13:18:22,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:22,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:22,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b6e2ac3-6b0b-4231-96e8-860ef3b10035/dqc_reference/checkm_data
[2024-01-24 13:18:22,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:22,421] [INFO] Task started: CheckM
[2024-01-24 13:18:22,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001522135.2_ASM152213v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001522135.2_ASM152213v2_genomic.fna/checkm_input GCF_001522135.2_ASM152213v2_genomic.fna/checkm_result
[2024-01-24 13:19:36,967] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:36,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:36,993] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:36,993] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:36,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001522135.2_ASM152213v2_genomic.fna/markers.fasta)
[2024-01-24 13:19:36,994] [INFO] Task started: Blastn
[2024-01-24 13:19:36,994] [INFO] Running command: blastn -query GCF_001522135.2_ASM152213v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b6e2ac3-6b0b-4231-96e8-860ef3b10035/dqc_reference/reference_markers_gtdb.fasta -out GCF_001522135.2_ASM152213v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:39,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:39,106] [INFO] Selected 5 target genomes.
[2024-01-24 13:19:39,106] [INFO] Target genome list was writen to GCF_001522135.2_ASM152213v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:39,107] [INFO] Task started: fastANI
[2024-01-24 13:19:39,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg7de92fea-f392-4de5-b4d2-8d6cf48ffe7a/GCF_001522135.2_ASM152213v2_genomic.fna.gz --refList GCF_001522135.2_ASM152213v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001522135.2_ASM152213v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:52,437] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:52,442] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:52,443] [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_000959365.1	s__Burkholderia oklahomensis	99.9996	2375	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.42	95.09	0.95	0.85	15	conclusive
GCF_001524625.2	s__Burkholderia sp001524625	92.0129	1941	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.38	99.33	0.93	0.91	11	-
GCF_001462435.1	s__Burkholderia humptydooensis	91.8536	1799	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.52	99.18	0.95	0.92	12	-
GCF_000012365.1	s__Burkholderia thailandensis	91.2241	1842	2378	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	90.9558	1663	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.31	98.71	0.94	0.78	1780	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:52,445] [INFO] GTDB search result was written to GCF_001522135.2_ASM152213v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:52,445] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:52,449] [INFO] DFAST_QC result json was written to GCF_001522135.2_ASM152213v2_genomic.fna/dqc_result.json
[2024-01-24 13:19:52,449] [INFO] DFAST_QC completed!
[2024-01-24 13:19:52,450] [INFO] Total running time: 0h2m18s