[2024-01-24 13:09:49,359] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg00cfc683-19bc-4e6a-b3c0-e6168ecdf6b0/dqc_reference
[2024-01-24 13:09:50,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,681] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,682] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6a450d9-27a1-4c2a-9a5d-85d9dc0157f4/GCF_000170495.1_ASM17049v1_genomic.fna.gz | prodigal -d GCF_000170495.1_ASM17049v1_genomic.fna/cds.fna -a GCF_000170495.1_ASM17049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:07,282] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:07,282] [INFO] Task started: HMMsearch
[2024-01-24 13:10:07,282] [INFO] Running command: hmmsearch --tblout GCF_000170495.1_ASM17049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00cfc683-19bc-4e6a-b3c0-e6168ecdf6b0/dqc_reference/reference_markers.hmm GCF_000170495.1_ASM17049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:07,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:07,631] [INFO] Found 6/6 markers.
[2024-01-24 13:10:07,690] [INFO] Query marker FASTA was written to GCF_000170495.1_ASM17049v1_genomic.fna/markers.fasta
[2024-01-24 13:10:07,690] [INFO] Task started: Blastn
[2024-01-24 13:10:07,690] [INFO] Running command: blastn -query GCF_000170495.1_ASM17049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00cfc683-19bc-4e6a-b3c0-e6168ecdf6b0/dqc_reference/reference_markers.fasta -out GCF_000170495.1_ASM17049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:08,731] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:08,734] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:08,735] [INFO] Target genome list was writen to GCF_000170495.1_ASM17049v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:08,741] [INFO] Task started: fastANI
[2024-01-24 13:10:08,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6a450d9-27a1-4c2a-9a5d-85d9dc0157f4/GCF_000170495.1_ASM17049v1_genomic.fna.gz --refList GCF_000170495.1_ASM17049v1_genomic.fna/target_genomes.txt --output GCF_000170495.1_ASM17049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:30,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:30,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00cfc683-19bc-4e6a-b3c0-e6168ecdf6b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:30,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00cfc683-19bc-4e6a-b3c0-e6168ecdf6b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:30,032] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:30,032] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:30,032] [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; ATCC 700388	GCA_000012365.1	57975	57975	type	True	93.1513	1297	1722	95	below_threshold
Burkholderia thailandensis	strain=E264	GCA_003568605.1	57975	57975	type	True	93.133	1303	1722	95	below_threshold
Burkholderia thailandensis	strain=ATCC 700388	GCA_000152285.1	57975	57975	type	True	92.9528	1241	1722	95	below_threshold
Burkholderia pseudomallei	strain=WRAIR 286	GCA_006538545.1	28450	28450	type	True	92.6468	1295	1722	95	below_threshold
Burkholderia pseudomallei	strain=ATCC 23343	GCA_001182285.1	28450	28450	type	True	92.5938	1317	1722	95	below_threshold
Burkholderia mallei	strain=NCTC12938	GCA_900446245.1	13373	13373	type	True	92.1718	1164	1722	95	below_threshold
Burkholderia mallei	strain=ATCC 23344	GCA_000011705.1	13373	13373	type	True	92.0769	1170	1722	95	below_threshold
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	91.4904	1304	1722	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	85.8776	1094	1722	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	85.786	1075	1722	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	84.9662	1031	1722	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.5368	976	1722	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	81.4986	806	1722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:30,034] [INFO] DFAST Taxonomy check result was written to GCF_000170495.1_ASM17049v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:30,034] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:30,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:30,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00cfc683-19bc-4e6a-b3c0-e6168ecdf6b0/dqc_reference/checkm_data
[2024-01-24 13:10:30,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:30,105] [INFO] Task started: CheckM
[2024-01-24 13:10:30,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000170495.1_ASM17049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000170495.1_ASM17049v1_genomic.fna/checkm_input GCF_000170495.1_ASM17049v1_genomic.fna/checkm_result
[2024-01-24 13:11:19,470] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:19,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:19,496] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:19,496] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:19,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000170495.1_ASM17049v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:19,497] [INFO] Task started: Blastn
[2024-01-24 13:11:19,497] [INFO] Running command: blastn -query GCF_000170495.1_ASM17049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00cfc683-19bc-4e6a-b3c0-e6168ecdf6b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000170495.1_ASM17049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:21,505] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:21,509] [INFO] Selected 5 target genomes.
[2024-01-24 13:11:21,509] [INFO] Target genome list was writen to GCF_000170495.1_ASM17049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:21,558] [INFO] Task started: fastANI
[2024-01-24 13:11:21,558] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6a450d9-27a1-4c2a-9a5d-85d9dc0157f4/GCF_000170495.1_ASM17049v1_genomic.fna.gz --refList GCF_000170495.1_ASM17049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000170495.1_ASM17049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:30,677] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:30,687] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:30,687] [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	98.9486	1495	1722	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	93.1688	1296	1722	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	92.1525	1165	1722	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	91.5527	1307	1722	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	91.5225	1297	1722	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 13:11:30,689] [INFO] GTDB search result was written to GCF_000170495.1_ASM17049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:30,689] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:30,692] [INFO] DFAST_QC result json was written to GCF_000170495.1_ASM17049v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:30,692] [INFO] DFAST_QC completed!
[2024-01-24 13:11:30,693] [INFO] Total running time: 0h1m41s