[2024-01-24 12:29:28,376] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg350df008-92dd-4a04-82fd-a6e84a8d12ff/dqc_reference
[2024-01-24 12:29:29,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:29,904] [INFO] Task started: Prodigal
[2024-01-24 12:29:29,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a213a34-d881-483a-951f-d16cdecdc8db/GCF_023078455.1_ASM2307845v1_genomic.fna.gz | prodigal -d GCF_023078455.1_ASM2307845v1_genomic.fna/cds.fna -a GCF_023078455.1_ASM2307845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:50,854] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:50,854] [INFO] Task started: HMMsearch
[2024-01-24 12:29:50,854] [INFO] Running command: hmmsearch --tblout GCF_023078455.1_ASM2307845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg350df008-92dd-4a04-82fd-a6e84a8d12ff/dqc_reference/reference_markers.hmm GCF_023078455.1_ASM2307845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:51,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:51,254] [INFO] Found 6/6 markers.
[2024-01-24 12:29:51,303] [INFO] Query marker FASTA was written to GCF_023078455.1_ASM2307845v1_genomic.fna/markers.fasta
[2024-01-24 12:29:51,304] [INFO] Task started: Blastn
[2024-01-24 12:29:51,304] [INFO] Running command: blastn -query GCF_023078455.1_ASM2307845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg350df008-92dd-4a04-82fd-a6e84a8d12ff/dqc_reference/reference_markers.fasta -out GCF_023078455.1_ASM2307845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:52,250] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:52,253] [INFO] Selected 18 target genomes.
[2024-01-24 12:29:52,254] [INFO] Target genome list was writen to GCF_023078455.1_ASM2307845v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:52,261] [INFO] Task started: fastANI
[2024-01-24 12:29:52,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a213a34-d881-483a-951f-d16cdecdc8db/GCF_023078455.1_ASM2307845v1_genomic.fna.gz --refList GCF_023078455.1_ASM2307845v1_genomic.fna/target_genomes.txt --output GCF_023078455.1_ASM2307845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:09,235] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:09,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg350df008-92dd-4a04-82fd-a6e84a8d12ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:09,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg350df008-92dd-4a04-82fd-a6e84a8d12ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:09,251] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:09,251] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:09,252] [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
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	83.6191	969	1585	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	83.3368	930	1585	95	below_threshold
Luteibacter pinisoli	strain=MAH-14	GCA_006385595.1	2589080	2589080	type	True	82.7949	967	1585	95	below_threshold
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	82.7155	931	1585	95	below_threshold
Luteibacter rhizovicinus	strain=LJ96	GCA_001887595.1	242606	242606	type	True	81.9536	946	1585	95	below_threshold
Luteibacter rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	81.9021	822	1585	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.0977	622	1585	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	80.083	585	1585	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.7884	516	1585	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.7752	576	1585	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	79.4432	516	1585	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	79.3249	538	1585	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.9981	378	1585	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.9625	405	1585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:09,253] [INFO] DFAST Taxonomy check result was written to GCF_023078455.1_ASM2307845v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:09,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:09,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:09,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg350df008-92dd-4a04-82fd-a6e84a8d12ff/dqc_reference/checkm_data
[2024-01-24 12:30:09,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:09,307] [INFO] Task started: CheckM
[2024-01-24 12:30:09,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023078455.1_ASM2307845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023078455.1_ASM2307845v1_genomic.fna/checkm_input GCF_023078455.1_ASM2307845v1_genomic.fna/checkm_result
[2024-01-24 12:31:17,713] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:17,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:17,738] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:17,738] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:17,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023078455.1_ASM2307845v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:17,739] [INFO] Task started: Blastn
[2024-01-24 12:31:17,739] [INFO] Running command: blastn -query GCF_023078455.1_ASM2307845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg350df008-92dd-4a04-82fd-a6e84a8d12ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_023078455.1_ASM2307845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:19,366] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:19,369] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:19,370] [INFO] Target genome list was writen to GCF_023078455.1_ASM2307845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:19,398] [INFO] Task started: fastANI
[2024-01-24 12:31:19,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a213a34-d881-483a-951f-d16cdecdc8db/GCF_023078455.1_ASM2307845v1_genomic.fna.gz --refList GCF_023078455.1_ASM2307845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023078455.1_ASM2307845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:35,459] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:35,471] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:31:35,472] [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_007829075.1	s__Luteibacter yeojuensis_B	93.9843	1311	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009912395.1	s__Luteibacter sp009912395	84.0361	985	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759365.1	s__Luteibacter anthropi	83.5959	972	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742875.1	s__Luteibacter yeojuensis	83.311	933	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110505.1	s__Luteibacter sp900110505	83.1846	968	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	97.58	97.58	0.93	0.93	2	-
GCF_000964085.1	s__Luteibacter yeojuensis_A	83.1099	940	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018889975.1	s__Luteibacter sp018889975	83.0335	949	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385595.1	s__Luteibacter pinisoli	82.7885	968	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742555.1	s__Luteibacter jiangsuensis	82.7039	933	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745005.1	s__Luteibacter sp000745005	82.59	922	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050935.1	s__Luteibacter sp003050935	81.9973	905	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449605.1	s__Luteibacter sp018449605	81.8913	873	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483055.1	s__Dokdonella sp002483055	78.1058	339	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632775.1	s__Dokdonella koreensis	77.9994	403	1585	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:35,473] [INFO] GTDB search result was written to GCF_023078455.1_ASM2307845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:35,474] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:35,477] [INFO] DFAST_QC result json was written to GCF_023078455.1_ASM2307845v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:35,477] [INFO] DFAST_QC completed!
[2024-01-24 12:31:35,478] [INFO] Total running time: 0h2m7s