[2024-01-24 13:23:11,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:11,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:11,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e69b508-fd74-4b34-829d-e22923355104/dqc_reference
[2024-01-24 13:23:12,945] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:12,946] [INFO] Task started: Prodigal
[2024-01-24 13:23:12,946] [INFO] Running command: gunzip -c /var/lib/cwl/stgcebec6ea-1b3e-4a7c-b3a7-f0aef887ed6c/GCF_010093345.1_ASM1009334v1_genomic.fna.gz | prodigal -d GCF_010093345.1_ASM1009334v1_genomic.fna/cds.fna -a GCF_010093345.1_ASM1009334v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:26,437] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:26,438] [INFO] Task started: HMMsearch
[2024-01-24 13:23:26,438] [INFO] Running command: hmmsearch --tblout GCF_010093345.1_ASM1009334v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e69b508-fd74-4b34-829d-e22923355104/dqc_reference/reference_markers.hmm GCF_010093345.1_ASM1009334v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:26,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:26,707] [INFO] Found 6/6 markers.
[2024-01-24 13:23:26,750] [INFO] Query marker FASTA was written to GCF_010093345.1_ASM1009334v1_genomic.fna/markers.fasta
[2024-01-24 13:23:26,750] [INFO] Task started: Blastn
[2024-01-24 13:23:26,751] [INFO] Running command: blastn -query GCF_010093345.1_ASM1009334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e69b508-fd74-4b34-829d-e22923355104/dqc_reference/reference_markers.fasta -out GCF_010093345.1_ASM1009334v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:27,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:27,727] [INFO] Selected 16 target genomes.
[2024-01-24 13:23:27,727] [INFO] Target genome list was writen to GCF_010093345.1_ASM1009334v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:27,733] [INFO] Task started: fastANI
[2024-01-24 13:23:27,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgcebec6ea-1b3e-4a7c-b3a7-f0aef887ed6c/GCF_010093345.1_ASM1009334v1_genomic.fna.gz --refList GCF_010093345.1_ASM1009334v1_genomic.fna/target_genomes.txt --output GCF_010093345.1_ASM1009334v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:41,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:41,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e69b508-fd74-4b34-829d-e22923355104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:41,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e69b508-fd74-4b34-829d-e22923355104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:41,481] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:41,481] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:41,481] [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 yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	100.0	1300	1302	95	conclusive
Pseudoxanthomonas sacheonensis	strain=DSM 19373	GCA_010093305.1	443615	443615	type	True	84.7589	888	1302	95	below_threshold
Pseudoxanthomonas gei	strain=KCTC 32298	GCA_010119615.1	1383030	1383030	type	True	84.318	839	1302	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	82.3553	702	1302	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	82.1874	721	1302	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	82.0396	775	1302	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	81.9544	777	1302	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	81.8737	684	1302	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	81.3836	614	1302	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	81.206	658	1302	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.151	641	1302	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.6827	659	1302	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	80.506	612	1302	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	80.264	610	1302	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	79.3223	439	1302	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	79.2052	459	1302	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:41,483] [INFO] DFAST Taxonomy check result was written to GCF_010093345.1_ASM1009334v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:41,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:41,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:41,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e69b508-fd74-4b34-829d-e22923355104/dqc_reference/checkm_data
[2024-01-24 13:23:41,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:41,552] [INFO] Task started: CheckM
[2024-01-24 13:23:41,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093345.1_ASM1009334v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093345.1_ASM1009334v1_genomic.fna/checkm_input GCF_010093345.1_ASM1009334v1_genomic.fna/checkm_result
[2024-01-24 13:24:21,845] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:21,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:21,868] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:21,869] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:21,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093345.1_ASM1009334v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:21,869] [INFO] Task started: Blastn
[2024-01-24 13:24:21,870] [INFO] Running command: blastn -query GCF_010093345.1_ASM1009334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e69b508-fd74-4b34-829d-e22923355104/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093345.1_ASM1009334v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:23,678] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:23,682] [INFO] Selected 9 target genomes.
[2024-01-24 13:24:23,682] [INFO] Target genome list was writen to GCF_010093345.1_ASM1009334v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:23,702] [INFO] Task started: fastANI
[2024-01-24 13:24:23,702] [INFO] Running command: fastANI --query /var/lib/cwl/stgcebec6ea-1b3e-4a7c-b3a7-f0aef887ed6c/GCF_010093345.1_ASM1009334v1_genomic.fna.gz --refList GCF_010093345.1_ASM1009334v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093345.1_ASM1009334v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:32,325] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:32,340] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:32,340] [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_010093345.1	s__Pseudoxanthomonas_A yeongjuensis	100.0	1300	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010093305.1	s__Pseudoxanthomonas_A sacheonensis	84.7421	890	1302	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_900104085.1	s__Pseudoxanthomonas_A sp900104085	84.3864	926	1302	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_010119615.1	s__Pseudoxanthomonas_A gei	84.318	839	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173415.1	s__Pseudoxanthomonas_A sp004173415	84.067	572	1302	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_010211755.1	s__Pseudoxanthomonas_A sangjuensis	82.3591	702	1302	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_900215535.1	s__Pseudoxanthomonas_A wuyuanensis	82.0187	777	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014852005.1	s__Pseudoxanthomonas_A sp014852005	81.4779	707	1302	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_001431505.1	s__Stenotrophomonas daejeonensis	81.3977	613	1302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:32,342] [INFO] GTDB search result was written to GCF_010093345.1_ASM1009334v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:32,343] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:32,346] [INFO] DFAST_QC result json was written to GCF_010093345.1_ASM1009334v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:32,346] [INFO] DFAST_QC completed!
[2024-01-24 13:24:32,347] [INFO] Total running time: 0h1m21s