[2024-01-24 12:30:05,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg17e2d838-1dad-42aa-b74b-d54fc25f6cf7/dqc_reference
[2024-01-24 12:30:07,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,249] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,249] [INFO] Running command: gunzip -c /var/lib/cwl/stga65405fc-cb93-41fb-a733-2784e72ec97a/GCF_010211765.1_ASM1021176v1_genomic.fna.gz | prodigal -d GCF_010211765.1_ASM1021176v1_genomic.fna/cds.fna -a GCF_010211765.1_ASM1021176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:17,116] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:17,117] [INFO] Task started: HMMsearch
[2024-01-24 12:30:17,117] [INFO] Running command: hmmsearch --tblout GCF_010211765.1_ASM1021176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17e2d838-1dad-42aa-b74b-d54fc25f6cf7/dqc_reference/reference_markers.hmm GCF_010211765.1_ASM1021176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:17,377] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:17,378] [INFO] Found 6/6 markers.
[2024-01-24 12:30:17,407] [INFO] Query marker FASTA was written to GCF_010211765.1_ASM1021176v1_genomic.fna/markers.fasta
[2024-01-24 12:30:17,408] [INFO] Task started: Blastn
[2024-01-24 12:30:17,408] [INFO] Running command: blastn -query GCF_010211765.1_ASM1021176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17e2d838-1dad-42aa-b74b-d54fc25f6cf7/dqc_reference/reference_markers.fasta -out GCF_010211765.1_ASM1021176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:18,321] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:18,324] [INFO] Selected 22 target genomes.
[2024-01-24 12:30:18,324] [INFO] Target genome list was writen to GCF_010211765.1_ASM1021176v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:18,330] [INFO] Task started: fastANI
[2024-01-24 12:30:18,331] [INFO] Running command: fastANI --query /var/lib/cwl/stga65405fc-cb93-41fb-a733-2784e72ec97a/GCF_010211765.1_ASM1021176v1_genomic.fna.gz --refList GCF_010211765.1_ASM1021176v1_genomic.fna/target_genomes.txt --output GCF_010211765.1_ASM1021176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:37,087] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:37,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17e2d838-1dad-42aa-b74b-d54fc25f6cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:37,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17e2d838-1dad-42aa-b74b-d54fc25f6cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:37,100] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:37,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:37,101] [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 kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	100.0	1225	1226	95	conclusive
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	87.815	783	1226	95	below_threshold
Pseudoxanthomonas daejeonensis	strain=DSM 17801	GCA_010093205.1	266062	266062	type	True	87.5092	954	1226	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	87.2343	906	1226	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	86.1727	806	1226	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	86.1498	798	1226	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	85.7909	818	1226	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	85.4977	736	1226	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	82.6501	757	1226	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.6497	638	1226	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	82.046	700	1226	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.7734	734	1226	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	81.7197	446	1226	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.7153	533	1226	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.6986	653	1226	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.4744	701	1226	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	81.3399	564	1226	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	81.1879	649	1226	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	80.9627	596	1226	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	80.9454	641	1226	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	80.9189	594	1226	95	below_threshold
Pseudoxanthomonas dokdonensis	strain=DSM 21858	GCA_001431405.1	344882	344882	type	True	80.1969	608	1226	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:37,102] [INFO] DFAST Taxonomy check result was written to GCF_010211765.1_ASM1021176v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:37,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:37,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:37,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17e2d838-1dad-42aa-b74b-d54fc25f6cf7/dqc_reference/checkm_data
[2024-01-24 12:30:37,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:37,143] [INFO] Task started: CheckM
[2024-01-24 12:30:37,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010211765.1_ASM1021176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010211765.1_ASM1021176v1_genomic.fna/checkm_input GCF_010211765.1_ASM1021176v1_genomic.fna/checkm_result
[2024-01-24 12:31:11,713] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:11,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:11,728] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:11,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:11,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010211765.1_ASM1021176v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:11,729] [INFO] Task started: Blastn
[2024-01-24 12:31:11,729] [INFO] Running command: blastn -query GCF_010211765.1_ASM1021176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17e2d838-1dad-42aa-b74b-d54fc25f6cf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_010211765.1_ASM1021176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:13,330] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:13,333] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:13,334] [INFO] Target genome list was writen to GCF_010211765.1_ASM1021176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:13,339] [INFO] Task started: fastANI
[2024-01-24 12:31:13,339] [INFO] Running command: fastANI --query /var/lib/cwl/stga65405fc-cb93-41fb-a733-2784e72ec97a/GCF_010211765.1_ASM1021176v1_genomic.fna.gz --refList GCF_010211765.1_ASM1021176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010211765.1_ASM1021176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:27,990] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:28,000] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:28,001] [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_010211765.1	s__Pseudoxanthomonas kaohsiungensis	100.0	1225	1226	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	88.3702	932	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093225.1	s__Pseudoxanthomonas koreensis	87.8432	781	1226	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	87.5114	954	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745195.1	s__Pseudoxanthomonas sp017745195	87.2958	815	1226	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	87.2712	888	1226	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	87.2293	907	1226	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	87.0539	875	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	86.1746	805	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017302035.1	s__Pseudoxanthomonas sp017302035	86.1664	675	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.26	99.26	0.94	0.94	2	-
GCF_002940085.1	s__Xanthomonas_A sacchari	82.6881	754	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.45	95.41	0.95	0.91	6	-
GCF_000472505.1	s__Luteimonas sp000472505	82.2116	707	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_007859305.1	s__Luteimonas wenzhouensis	82.0285	701	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_003586305.1	s__Lysobacter tabacisoli	81.46	639	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923255.1	s__Lysobacter thermophilus	80.9303	601	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	-
GCF_001431405.1	s__Pseudoxanthomonas_A dokdonensis	80.162	611	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017755.1	s__VRTS01 sp008017755	79.6045	439	1226	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__VRTS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:28,003] [INFO] GTDB search result was written to GCF_010211765.1_ASM1021176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:28,003] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:28,007] [INFO] DFAST_QC result json was written to GCF_010211765.1_ASM1021176v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:28,007] [INFO] DFAST_QC completed!
[2024-01-24 12:31:28,007] [INFO] Total running time: 0h1m23s