[2024-01-24 13:32:30,605] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:30,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:30,608] [INFO] DQC Reference Directory: /var/lib/cwl/stgc83413f7-740c-4923-aaa9-8dfa577dbf43/dqc_reference
[2024-01-24 13:32:32,002] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:32,003] [INFO] Task started: Prodigal
[2024-01-24 13:32:32,003] [INFO] Running command: gunzip -c /var/lib/cwl/stgacfd11df-060d-4622-8dc1-1e9ec9bdef0e/GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/cds.fna -a GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:46,101] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:46,101] [INFO] Task started: HMMsearch
[2024-01-24 13:32:46,102] [INFO] Running command: hmmsearch --tblout GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc83413f7-740c-4923-aaa9-8dfa577dbf43/dqc_reference/reference_markers.hmm GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:46,514] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:46,515] [INFO] Found 6/6 markers.
[2024-01-24 13:32:46,567] [INFO] Query marker FASTA was written to GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:32:46,567] [INFO] Task started: Blastn
[2024-01-24 13:32:46,567] [INFO] Running command: blastn -query GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc83413f7-740c-4923-aaa9-8dfa577dbf43/dqc_reference/reference_markers.fasta -out GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:47,647] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:47,651] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:47,651] [INFO] Target genome list was writen to GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:32:47,657] [INFO] Task started: fastANI
[2024-01-24 13:32:47,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgacfd11df-060d-4622-8dc1-1e9ec9bdef0e/GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna.gz --refList GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:03,323] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:03,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc83413f7-740c-4923-aaa9-8dfa577dbf43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:03,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc83413f7-740c-4923-aaa9-8dfa577dbf43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:03,338] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:03,339] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:03,339] [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
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	100.0	1498	1501	95	conclusive
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	79.262	562	1501	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	78.9196	514	1501	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.5986	492	1501	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	78.3048	287	1501	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.2383	314	1501	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	78.1587	380	1501	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	78.1557	321	1501	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.1392	361	1501	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	78.1163	358	1501	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	78.0913	339	1501	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	78.0814	331	1501	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	78.046	350	1501	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	78.0039	382	1501	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	77.9513	459	1501	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.9277	251	1501	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	77.6559	301	1501	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	77.6513	353	1501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:03,340] [INFO] DFAST Taxonomy check result was written to GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:33:03,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:03,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:03,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc83413f7-740c-4923-aaa9-8dfa577dbf43/dqc_reference/checkm_data
[2024-01-24 13:33:03,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:03,391] [INFO] Task started: CheckM
[2024-01-24 13:33:03,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/checkm_input GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:33:53,362] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:53,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:53,387] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:53,387] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:53,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:33:53,388] [INFO] Task started: Blastn
[2024-01-24 13:33:53,388] [INFO] Running command: blastn -query GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc83413f7-740c-4923-aaa9-8dfa577dbf43/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:55,214] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:55,217] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:55,218] [INFO] Target genome list was writen to GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:55,237] [INFO] Task started: fastANI
[2024-01-24 13:33:55,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgacfd11df-060d-4622-8dc1-1e9ec9bdef0e/GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna.gz --refList GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:05,054] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:05,067] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:05,067] [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_900115085.1	s__Dokdonella immobilis	100.0	1498	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001899855.1	s__Dokdonella sp001899855	81.2802	730	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707485.1	s__Dokdonella sp016707485	80.9966	725	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	99.34	99.18	0.96	0.94	4	-
GCA_017302215.1	s__Dokdonella sp017302215	80.6251	591	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721015.1	s__Dokdonella sp016721015	80.5037	750	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	79.3938	558	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295005.1	s__Dokdonella sp004295005	79.2519	493	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712865.1	s__Dokdonella sp016712865	79.2124	572	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	99.46	99.45	0.98	0.98	3	-
GCF_004342425.1	s__Dokdonella_A fugitiva	78.9195	514	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.45	99.45	0.96	0.96	2	-
GCF_014138265.1	s__Dokdonella_A fugitiva_A	78.7986	529	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004143945.1	s__Dokdonella_A sp004143945	78.7664	484	1501	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:05,069] [INFO] GTDB search result was written to GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:05,069] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:05,073] [INFO] DFAST_QC result json was written to GCF_900115085.1_IMG-taxon_2667527410_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:34:05,073] [INFO] DFAST_QC completed!
[2024-01-24 13:34:05,073] [INFO] Total running time: 0h1m34s