[2024-01-24 13:25:31,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,292] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,292] [INFO] DQC Reference Directory: /var/lib/cwl/stgc477960f-8900-475d-bca3-6d28f23f18eb/dqc_reference
[2024-01-24 13:25:32,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,599] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,599] [INFO] Running command: gunzip -c /var/lib/cwl/stgc239e1c1-6ca6-4acf-9ce5-2a857d2e81db/GCF_009362785.1_ASM936278v1_genomic.fna.gz | prodigal -d GCF_009362785.1_ASM936278v1_genomic.fna/cds.fna -a GCF_009362785.1_ASM936278v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:59,235] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:59,235] [INFO] Task started: HMMsearch
[2024-01-24 13:25:59,235] [INFO] Running command: hmmsearch --tblout GCF_009362785.1_ASM936278v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc477960f-8900-475d-bca3-6d28f23f18eb/dqc_reference/reference_markers.hmm GCF_009362785.1_ASM936278v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:59,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:59,636] [INFO] Found 6/6 markers.
[2024-01-24 13:25:59,711] [INFO] Query marker FASTA was written to GCF_009362785.1_ASM936278v1_genomic.fna/markers.fasta
[2024-01-24 13:25:59,711] [INFO] Task started: Blastn
[2024-01-24 13:25:59,712] [INFO] Running command: blastn -query GCF_009362785.1_ASM936278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc477960f-8900-475d-bca3-6d28f23f18eb/dqc_reference/reference_markers.fasta -out GCF_009362785.1_ASM936278v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:00,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:00,785] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:00,785] [INFO] Target genome list was writen to GCF_009362785.1_ASM936278v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:00,793] [INFO] Task started: fastANI
[2024-01-24 13:26:00,793] [INFO] Running command: fastANI --query /var/lib/cwl/stgc239e1c1-6ca6-4acf-9ce5-2a857d2e81db/GCF_009362785.1_ASM936278v1_genomic.fna.gz --refList GCF_009362785.1_ASM936278v1_genomic.fna/target_genomes.txt --output GCF_009362785.1_ASM936278v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:21,989] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:21,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc477960f-8900-475d-bca3-6d28f23f18eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:21,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc477960f-8900-475d-bca3-6d28f23f18eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:22,001] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:22,001] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:22,001] [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
Paraburkholderia atlantica	strain=CNPSo 3155	GCA_009362785.1	2654982	2654982	type	True	100.0	2867	2873	95	conclusive
Paraburkholderia youngii	strain=JPY169	GCA_013366925.1	2782701	2782701	type	True	94.6992	2339	2873	95	below_threshold
Paraburkholderia tuberum	strain=LMG 21444	GCA_902833905.1	157910	157910	type	True	92.454	1918	2873	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	91.0388	1856	2873	95	below_threshold
Paraburkholderia sprentiae	strain=WSM5005	GCA_000473465.1	948107	948107	type	True	90.8036	1836	2873	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	90.648	1846	2873	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	83.9636	1366	2873	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	83.95	1470	2873	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	83.7781	1404	2873	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	83.3866	1197	2873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:22,003] [INFO] DFAST Taxonomy check result was written to GCF_009362785.1_ASM936278v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:22,004] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:22,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:22,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc477960f-8900-475d-bca3-6d28f23f18eb/dqc_reference/checkm_data
[2024-01-24 13:26:22,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:22,087] [INFO] Task started: CheckM
[2024-01-24 13:26:22,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009362785.1_ASM936278v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009362785.1_ASM936278v1_genomic.fna/checkm_input GCF_009362785.1_ASM936278v1_genomic.fna/checkm_result
[2024-01-24 13:27:34,340] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:34,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:34,367] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:34,367] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:34,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009362785.1_ASM936278v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:34,368] [INFO] Task started: Blastn
[2024-01-24 13:27:34,368] [INFO] Running command: blastn -query GCF_009362785.1_ASM936278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc477960f-8900-475d-bca3-6d28f23f18eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009362785.1_ASM936278v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:36,373] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:36,377] [INFO] Selected 7 target genomes.
[2024-01-24 13:27:36,377] [INFO] Target genome list was writen to GCF_009362785.1_ASM936278v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:36,398] [INFO] Task started: fastANI
[2024-01-24 13:27:36,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgc239e1c1-6ca6-4acf-9ce5-2a857d2e81db/GCF_009362785.1_ASM936278v1_genomic.fna.gz --refList GCF_009362785.1_ASM936278v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009362785.1_ASM936278v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:53,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:53,078] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:53,078] [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_009362785.1	s__Paraburkholderia atlantica	100.0	2867	2873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.68	97.45	0.92	0.86	7	conclusive
GCF_013366925.1	s__Paraburkholderia youngii	94.6929	2340	2873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.48	97.40	0.88	0.87	5	-
GCF_902833905.1	s__Paraburkholderia tuberum	92.4634	1917	2873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.72	96.26	0.82	0.75	13	-
GCF_004197395.1	s__Paraburkholderia sp004197395	91.9806	2070	2873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397785.1	s__Paraburkholderia sp014397785	91.0575	1854	2873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173575.1	s__Paraburkholderia sp000173575	90.8079	1744	2873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580545.1	s__Paraburkholderia monticola	90.6601	1845	2873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:53,079] [INFO] GTDB search result was written to GCF_009362785.1_ASM936278v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:53,080] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:53,083] [INFO] DFAST_QC result json was written to GCF_009362785.1_ASM936278v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:53,083] [INFO] DFAST_QC completed!
[2024-01-24 13:27:53,083] [INFO] Total running time: 0h2m22s