[2024-01-24 12:22:48,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,410] [INFO] DQC Reference Directory: /var/lib/cwl/stgb659e53a-e22c-4ffe-817a-03dbbba6dd88/dqc_reference
[2024-01-24 12:22:49,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,701] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,702] [INFO] Running command: gunzip -c /var/lib/cwl/stg89b9d778-8d4c-4e78-b78e-af0eb3b89ad5/GCF_010093225.1_ASM1009322v1_genomic.fna.gz | prodigal -d GCF_010093225.1_ASM1009322v1_genomic.fna/cds.fna -a GCF_010093225.1_ASM1009322v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:58,958] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:58,959] [INFO] Task started: HMMsearch
[2024-01-24 12:22:58,959] [INFO] Running command: hmmsearch --tblout GCF_010093225.1_ASM1009322v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb659e53a-e22c-4ffe-817a-03dbbba6dd88/dqc_reference/reference_markers.hmm GCF_010093225.1_ASM1009322v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:59,229] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:59,231] [INFO] Found 6/6 markers.
[2024-01-24 12:22:59,265] [INFO] Query marker FASTA was written to GCF_010093225.1_ASM1009322v1_genomic.fna/markers.fasta
[2024-01-24 12:22:59,265] [INFO] Task started: Blastn
[2024-01-24 12:22:59,265] [INFO] Running command: blastn -query GCF_010093225.1_ASM1009322v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb659e53a-e22c-4ffe-817a-03dbbba6dd88/dqc_reference/reference_markers.fasta -out GCF_010093225.1_ASM1009322v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:00,195] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:00,199] [INFO] Selected 14 target genomes.
[2024-01-24 12:23:00,199] [INFO] Target genome list was writen to GCF_010093225.1_ASM1009322v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:00,206] [INFO] Task started: fastANI
[2024-01-24 12:23:00,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg89b9d778-8d4c-4e78-b78e-af0eb3b89ad5/GCF_010093225.1_ASM1009322v1_genomic.fna.gz --refList GCF_010093225.1_ASM1009322v1_genomic.fna/target_genomes.txt --output GCF_010093225.1_ASM1009322v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:13,272] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:13,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb659e53a-e22c-4ffe-817a-03dbbba6dd88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:13,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb659e53a-e22c-4ffe-817a-03dbbba6dd88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:13,284] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:13,284] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:13,284] [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
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	100.0	970	974	95	conclusive
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	87.8895	771	974	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	87.6828	763	974	95	below_threshold
Pseudoxanthomonas daejeonensis	strain=DSM 17801	GCA_010093205.1	266062	266062	type	True	87.1468	809	974	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	86.7746	718	974	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	86.7655	713	974	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	86.0781	725	974	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	85.8671	679	974	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	83.3606	685	974	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	82.8709	669	974	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	82.2387	507	974	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.1386	615	974	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	81.1272	543	974	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	80.6523	557	974	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:13,286] [INFO] DFAST Taxonomy check result was written to GCF_010093225.1_ASM1009322v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:13,287] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:13,287] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:13,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb659e53a-e22c-4ffe-817a-03dbbba6dd88/dqc_reference/checkm_data
[2024-01-24 12:23:13,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:13,321] [INFO] Task started: CheckM
[2024-01-24 12:23:13,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093225.1_ASM1009322v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093225.1_ASM1009322v1_genomic.fna/checkm_input GCF_010093225.1_ASM1009322v1_genomic.fna/checkm_result
[2024-01-24 12:23:45,709] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:45,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:45,733] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:45,733] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:45,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093225.1_ASM1009322v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:45,734] [INFO] Task started: Blastn
[2024-01-24 12:23:45,734] [INFO] Running command: blastn -query GCF_010093225.1_ASM1009322v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb659e53a-e22c-4ffe-817a-03dbbba6dd88/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093225.1_ASM1009322v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:47,372] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:47,379] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:47,380] [INFO] Target genome list was writen to GCF_010093225.1_ASM1009322v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:47,391] [INFO] Task started: fastANI
[2024-01-24 12:23:47,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg89b9d778-8d4c-4e78-b78e-af0eb3b89ad5/GCF_010093225.1_ASM1009322v1_genomic.fna.gz --refList GCF_010093225.1_ASM1009322v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093225.1_ASM1009322v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:00,835] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:00,861] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:00,861] [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_010093225.1	s__Pseudoxanthomonas koreensis	100.0	970	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000972865.1	s__Pseudoxanthomonas suwonensis_B	88.6734	791	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	87.9781	748	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	87.9489	776	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_010211765.1	s__Pseudoxanthomonas kaohsiungensis	87.8895	771	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	87.6999	762	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302035.1	s__Pseudoxanthomonas sp017302035	87.441	640	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.26	99.26	0.94	0.94	2	-
GCA_017745195.1	s__Pseudoxanthomonas sp017745195	87.292	718	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093205.1	s__Pseudoxanthomonas daejeonensis	87.131	810	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018060215.1	s__Pseudoxanthomonas sp018060215	86.8932	535	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.22	98.87	0.83	0.81	6	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	86.7745	718	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000185965.1	s__Pseudoxanthomonas suwonensis_A	86.2989	731	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093235.1	s__Pseudoxanthomonas suwonensis	86.1097	723	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769165.1	s__Xanthomonas_A hyacinthi	83.3081	689	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	81.9006	670	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:00,867] [INFO] GTDB search result was written to GCF_010093225.1_ASM1009322v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:00,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:00,873] [INFO] DFAST_QC result json was written to GCF_010093225.1_ASM1009322v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:00,873] [INFO] DFAST_QC completed!
[2024-01-24 12:24:00,874] [INFO] Total running time: 0h1m12s