[2024-01-24 13:19:11,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:11,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:11,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg09ed1885-2013-4b25-9178-9220448eda3f/dqc_reference
[2024-01-24 13:19:13,204] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:13,205] [INFO] Task started: Prodigal
[2024-01-24 13:19:13,205] [INFO] Running command: gunzip -c /var/lib/cwl/stg25660d27-f56c-4861-9d76-2b36dc627be8/GCF_001865575.2_ASM186557v2_genomic.fna.gz | prodigal -d GCF_001865575.2_ASM186557v2_genomic.fna/cds.fna -a GCF_001865575.2_ASM186557v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:39,316] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:39,317] [INFO] Task started: HMMsearch
[2024-01-24 13:19:39,317] [INFO] Running command: hmmsearch --tblout GCF_001865575.2_ASM186557v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09ed1885-2013-4b25-9178-9220448eda3f/dqc_reference/reference_markers.hmm GCF_001865575.2_ASM186557v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:39,829] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:39,830] [INFO] Found 6/6 markers.
[2024-01-24 13:19:39,899] [INFO] Query marker FASTA was written to GCF_001865575.2_ASM186557v2_genomic.fna/markers.fasta
[2024-01-24 13:19:39,899] [INFO] Task started: Blastn
[2024-01-24 13:19:39,900] [INFO] Running command: blastn -query GCF_001865575.2_ASM186557v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ed1885-2013-4b25-9178-9220448eda3f/dqc_reference/reference_markers.fasta -out GCF_001865575.2_ASM186557v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:41,147] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:41,150] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:41,150] [INFO] Target genome list was writen to GCF_001865575.2_ASM186557v2_genomic.fna/target_genomes.txt
[2024-01-24 13:19:41,155] [INFO] Task started: fastANI
[2024-01-24 13:19:41,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg25660d27-f56c-4861-9d76-2b36dc627be8/GCF_001865575.2_ASM186557v2_genomic.fna.gz --refList GCF_001865575.2_ASM186557v2_genomic.fna/target_genomes.txt --output GCF_001865575.2_ASM186557v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:04,985] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:04,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09ed1885-2013-4b25-9178-9220448eda3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:04,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09ed1885-2013-4b25-9178-9220448eda3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:04,996] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:20:04,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:20:04,997] [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 sprentiae	strain=WSM5005	GCA_001865575.2	948107	948107	type	True	100.0	2608	2611	95	conclusive
Paraburkholderia sprentiae	strain=WSM5005	GCA_000473465.1	948107	948107	type	True	99.9679	2562	2611	95	conclusive
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	93.1491	2002	2611	95	below_threshold
Paraburkholderia tuberum	strain=LMG 21444	GCA_902833905.1	157910	157910	type	True	91.6633	1902	2611	95	below_threshold
Paraburkholderia atlantica	strain=CNPSo 3155	GCA_009362785.1	2654982	2654982	type	True	90.8049	1833	2611	95	below_threshold
Paraburkholderia youngii	strain=JPY169	GCA_013366925.1	2782701	2782701	type	True	90.7356	1886	2611	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	90.6528	1680	2611	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	83.9802	1320	2611	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	83.8877	1375	2611	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	83.8696	1410	2611	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	83.5847	1204	2611	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:04,999] [INFO] DFAST Taxonomy check result was written to GCF_001865575.2_ASM186557v2_genomic.fna/tc_result.tsv
[2024-01-24 13:20:04,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:04,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:05,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09ed1885-2013-4b25-9178-9220448eda3f/dqc_reference/checkm_data
[2024-01-24 13:20:05,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:05,077] [INFO] Task started: CheckM
[2024-01-24 13:20:05,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001865575.2_ASM186557v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001865575.2_ASM186557v2_genomic.fna/checkm_input GCF_001865575.2_ASM186557v2_genomic.fna/checkm_result
[2024-01-24 13:21:18,528] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:18,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:18,556] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:18,556] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:18,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001865575.2_ASM186557v2_genomic.fna/markers.fasta)
[2024-01-24 13:21:18,557] [INFO] Task started: Blastn
[2024-01-24 13:21:18,557] [INFO] Running command: blastn -query GCF_001865575.2_ASM186557v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ed1885-2013-4b25-9178-9220448eda3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001865575.2_ASM186557v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:20,695] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:20,699] [INFO] Selected 8 target genomes.
[2024-01-24 13:21:20,700] [INFO] Target genome list was writen to GCF_001865575.2_ASM186557v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:20,726] [INFO] Task started: fastANI
[2024-01-24 13:21:20,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg25660d27-f56c-4861-9d76-2b36dc627be8/GCF_001865575.2_ASM186557v2_genomic.fna.gz --refList GCF_001865575.2_ASM186557v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001865575.2_ASM186557v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:38,661] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:38,673] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:38,674] [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_001865575.1	s__Paraburkholderia sprentiae	99.9965	2590	2611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.96	99.96	0.99	0.99	2	conclusive
GCF_014397785.1	s__Paraburkholderia sp014397785	93.1422	2003	2611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902833905.1	s__Paraburkholderia tuberum	91.6858	1900	2611	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	91.0995	1786	2611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009362785.1	s__Paraburkholderia atlantica	90.7931	1833	2611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.68	97.45	0.92	0.86	7	-
GCF_013366925.1	s__Paraburkholderia youngii	90.724	1888	2611	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.48	97.40	0.88	0.87	5	-
GCF_001580545.1	s__Paraburkholderia monticola	90.6594	1679	2611	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	90.3794	1572	2611	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 13:21:38,675] [INFO] GTDB search result was written to GCF_001865575.2_ASM186557v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:38,676] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:38,681] [INFO] DFAST_QC result json was written to GCF_001865575.2_ASM186557v2_genomic.fna/dqc_result.json
[2024-01-24 13:21:38,681] [INFO] DFAST_QC completed!
[2024-01-24 13:21:38,681] [INFO] Total running time: 0h2m27s