[2024-01-24 11:22:49,341] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,343] [INFO] DQC Reference Directory: /var/lib/cwl/stg111e478d-0881-44df-95d4-759fae07bca4/dqc_reference
[2024-01-24 11:22:50,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,530] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,531] [INFO] Running command: gunzip -c /var/lib/cwl/stg020fb2e8-85b3-4f64-a85e-a9624ac5836b/GCF_900446245.1_58116_D01_genomic.fna.gz | prodigal -d GCF_900446245.1_58116_D01_genomic.fna/cds.fna -a GCF_900446245.1_58116_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:07,579] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:07,580] [INFO] Task started: HMMsearch
[2024-01-24 11:23:07,580] [INFO] Running command: hmmsearch --tblout GCF_900446245.1_58116_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg111e478d-0881-44df-95d4-759fae07bca4/dqc_reference/reference_markers.hmm GCF_900446245.1_58116_D01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:07,879] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:07,881] [INFO] Found 6/6 markers.
[2024-01-24 11:23:07,930] [INFO] Query marker FASTA was written to GCF_900446245.1_58116_D01_genomic.fna/markers.fasta
[2024-01-24 11:23:07,930] [INFO] Task started: Blastn
[2024-01-24 11:23:07,931] [INFO] Running command: blastn -query GCF_900446245.1_58116_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg111e478d-0881-44df-95d4-759fae07bca4/dqc_reference/reference_markers.fasta -out GCF_900446245.1_58116_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:08,958] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:08,962] [INFO] Selected 10 target genomes.
[2024-01-24 11:23:08,962] [INFO] Target genome list was writen to GCF_900446245.1_58116_D01_genomic.fna/target_genomes.txt
[2024-01-24 11:23:08,968] [INFO] Task started: fastANI
[2024-01-24 11:23:08,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg020fb2e8-85b3-4f64-a85e-a9624ac5836b/GCF_900446245.1_58116_D01_genomic.fna.gz --refList GCF_900446245.1_58116_D01_genomic.fna/target_genomes.txt --output GCF_900446245.1_58116_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:39,825] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:39,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg111e478d-0881-44df-95d4-759fae07bca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:39,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg111e478d-0881-44df-95d4-759fae07bca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:39,844] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:23:39,844] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:23:39,845] [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 mallei	strain=NCTC12938	GCA_900446245.1	13373	13373	type	True	100.0	1947	1949	95	inconclusive
Burkholderia mallei	strain=ATCC 23344	GCA_000011705.1	13373	13373	type	True	99.9958	1939	1949	95	inconclusive
Burkholderia pseudomallei	strain=WRAIR 286	GCA_006538545.1	28450	28450	type	True	99.2956	1801	1949	95	inconclusive
Burkholderia pseudomallei	strain=ATCC 23343	GCA_001182285.1	28450	28450	type	True	99.2891	1850	1949	95	inconclusive
Burkholderia thailandensis	strain=E264; ATCC 700388	GCA_000012365.1	57975	57975	type	True	92.8609	1628	1949	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	85.6923	1349	1949	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	85.6469	1307	1949	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	84.6504	1274	1949	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	83.4657	1206	1949	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	81.751	1010	1949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:39,847] [INFO] DFAST Taxonomy check result was written to GCF_900446245.1_58116_D01_genomic.fna/tc_result.tsv
[2024-01-24 11:23:39,847] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:39,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:39,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg111e478d-0881-44df-95d4-759fae07bca4/dqc_reference/checkm_data
[2024-01-24 11:23:39,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:39,904] [INFO] Task started: CheckM
[2024-01-24 11:23:39,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900446245.1_58116_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900446245.1_58116_D01_genomic.fna/checkm_input GCF_900446245.1_58116_D01_genomic.fna/checkm_result
[2024-01-24 11:24:40,378] [INFO] Task succeeded: CheckM
[2024-01-24 11:24:40,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 11:24:40,405] [INFO] ===== Completeness check finished =====
[2024-01-24 11:24:40,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:24:40,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900446245.1_58116_D01_genomic.fna/markers.fasta)
[2024-01-24 11:24:40,406] [INFO] Task started: Blastn
[2024-01-24 11:24:40,406] [INFO] Running command: blastn -query GCF_900446245.1_58116_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stg111e478d-0881-44df-95d4-759fae07bca4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900446245.1_58116_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:24:42,506] [INFO] Task succeeded: Blastn
[2024-01-24 11:24:42,510] [INFO] Selected 5 target genomes.
[2024-01-24 11:24:42,510] [INFO] Target genome list was writen to GCF_900446245.1_58116_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:24:42,514] [INFO] Task started: fastANI
[2024-01-24 11:24:42,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg020fb2e8-85b3-4f64-a85e-a9624ac5836b/GCF_900446245.1_58116_D01_genomic.fna.gz --refList GCF_900446245.1_58116_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900446245.1_58116_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:58,486] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:58,493] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:58,493] [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_000011705.1	s__Burkholderia mallei	99.9958	1939	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.31	98.71	0.94	0.78	1780	conclusive
GCF_001462435.1	s__Burkholderia humptydooensis	93.1098	1556	1949	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	92.8249	1631	1949	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.58	98.83	0.96	0.93	53	-
GCF_001524625.2	s__Burkholderia sp001524625	91.255	1626	1949	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	90.985	1646	1949	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 11:24:58,549] [INFO] GTDB search result was written to GCF_900446245.1_58116_D01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:58,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:58,553] [INFO] DFAST_QC result json was written to GCF_900446245.1_58116_D01_genomic.fna/dqc_result.json
[2024-01-24 11:24:58,554] [INFO] DFAST_QC completed!
[2024-01-24 11:24:58,554] [INFO] Total running time: 0h2m9s