[2024-01-24 14:55:08,414] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg532de91f-3d4e-47c9-83a0-21b784a26bd6/dqc_reference
[2024-01-24 14:55:10,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,043] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,043] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bf6a8b5-0145-4b2e-8832-35b17d819ddc/GCF_009906855.1_ASM990685v1_genomic.fna.gz | prodigal -d GCF_009906855.1_ASM990685v1_genomic.fna/cds.fna -a GCF_009906855.1_ASM990685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:28,795] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:28,796] [INFO] Task started: HMMsearch
[2024-01-24 14:55:28,796] [INFO] Running command: hmmsearch --tblout GCF_009906855.1_ASM990685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg532de91f-3d4e-47c9-83a0-21b784a26bd6/dqc_reference/reference_markers.hmm GCF_009906855.1_ASM990685v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:29,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:29,121] [INFO] Found 6/6 markers.
[2024-01-24 14:55:29,170] [INFO] Query marker FASTA was written to GCF_009906855.1_ASM990685v1_genomic.fna/markers.fasta
[2024-01-24 14:55:29,170] [INFO] Task started: Blastn
[2024-01-24 14:55:29,170] [INFO] Running command: blastn -query GCF_009906855.1_ASM990685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg532de91f-3d4e-47c9-83a0-21b784a26bd6/dqc_reference/reference_markers.fasta -out GCF_009906855.1_ASM990685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:30,265] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:30,269] [INFO] Selected 20 target genomes.
[2024-01-24 14:55:30,269] [INFO] Target genome list was writen to GCF_009906855.1_ASM990685v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:30,299] [INFO] Task started: fastANI
[2024-01-24 14:55:30,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf6a8b5-0145-4b2e-8832-35b17d819ddc/GCF_009906855.1_ASM990685v1_genomic.fna.gz --refList GCF_009906855.1_ASM990685v1_genomic.fna/target_genomes.txt --output GCF_009906855.1_ASM990685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:53,559] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:53,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg532de91f-3d4e-47c9-83a0-21b784a26bd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:53,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg532de91f-3d4e-47c9-83a0-21b784a26bd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:53,580] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:53,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:53,580] [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
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	100.0	1957	1957	95	conclusive
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	82.2265	776	1957	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	82.1841	781	1957	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.1698	845	1957	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	80.7374	646	1957	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	80.5819	886	1957	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	80.5656	389	1957	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.4755	741	1957	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	80.264	561	1957	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.1501	945	1957	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.0484	565	1957	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.9811	669	1957	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	79.9631	942	1957	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	79.8391	576	1957	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	79.8256	777	1957	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	79.7738	692	1957	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.6559	821	1957	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.5205	591	1957	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	79.1794	494	1957	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	78.8621	566	1957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:53,582] [INFO] DFAST Taxonomy check result was written to GCF_009906855.1_ASM990685v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:53,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:53,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:53,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg532de91f-3d4e-47c9-83a0-21b784a26bd6/dqc_reference/checkm_data
[2024-01-24 14:55:53,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:53,637] [INFO] Task started: CheckM
[2024-01-24 14:55:53,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009906855.1_ASM990685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009906855.1_ASM990685v1_genomic.fna/checkm_input GCF_009906855.1_ASM990685v1_genomic.fna/checkm_result
[2024-01-24 14:57:26,182] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:26,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:26,205] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:26,206] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:26,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009906855.1_ASM990685v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:26,207] [INFO] Task started: Blastn
[2024-01-24 14:57:26,207] [INFO] Running command: blastn -query GCF_009906855.1_ASM990685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg532de91f-3d4e-47c9-83a0-21b784a26bd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009906855.1_ASM990685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:28,519] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:28,523] [INFO] Selected 16 target genomes.
[2024-01-24 14:57:28,523] [INFO] Target genome list was writen to GCF_009906855.1_ASM990685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:28,536] [INFO] Task started: fastANI
[2024-01-24 14:57:28,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf6a8b5-0145-4b2e-8832-35b17d819ddc/GCF_009906855.1_ASM990685v1_genomic.fna.gz --refList GCF_009906855.1_ASM990685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009906855.1_ASM990685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:48,597] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:48,616] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:48,616] [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_009906855.1	s__Xylophilus rhododendri	100.0	1957	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001421705.1	s__Xylophilus sp001421705	82.4986	896	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428875.1	s__Xylophilus sp016428875	82.3733	805	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217575.1	s__Xylophilus ampelinus	82.2493	774	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113035.1	s__Acidovorax_A wautersii	81.2005	842	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476815.1	s__Pseudacidovorax intermedius_A	81.0104	855	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002397315.1	s__Acidovorax_A sp002397315	80.5825	783	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003604195.1	s__Giesbergeria lacusdiani	80.5798	638	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001955695.1	s__Rhodoferax_B koreense	80.4191	824	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207955.1	s__Acidovorax soli_A	80.1482	878	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770955.1	s__Giesbergeria sp001770955	80.0583	507	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	80.0522	664	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCA_003208485.1	s__Acidovorax sp003208485	80.0153	789	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381265.1	s__Curvibacter lanceolatus	79.8399	774	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.6079	99.38	99.38	0.94	0.94	2	-
GCF_002157145.1	s__Acidovorax carolinensis	79.8237	579	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.15	97.05	0.89	0.88	4	-
GCF_001571325.1	s__Comamonas tsuruhatensis	79.7807	796	1957	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	98.55	98.21	0.90	0.80	27	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:48,618] [INFO] GTDB search result was written to GCF_009906855.1_ASM990685v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:48,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:48,623] [INFO] DFAST_QC result json was written to GCF_009906855.1_ASM990685v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:48,624] [INFO] DFAST_QC completed!
[2024-01-24 14:57:48,624] [INFO] Total running time: 0h2m40s