[2024-01-24 14:32:30,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:30,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:30,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg7584270f-c8c1-4b43-a3cc-21bf725247f3/dqc_reference
[2024-01-24 14:32:31,876] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:31,877] [INFO] Task started: Prodigal
[2024-01-24 14:32:31,877] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b299341-45b2-40ea-8c56-65d8b3d8a4c5/GCF_025717065.2_ASM2571706v2_genomic.fna.gz | prodigal -d GCF_025717065.2_ASM2571706v2_genomic.fna/cds.fna -a GCF_025717065.2_ASM2571706v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:52,085] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:52,086] [INFO] Task started: HMMsearch
[2024-01-24 14:32:52,086] [INFO] Running command: hmmsearch --tblout GCF_025717065.2_ASM2571706v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7584270f-c8c1-4b43-a3cc-21bf725247f3/dqc_reference/reference_markers.hmm GCF_025717065.2_ASM2571706v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:52,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:52,411] [INFO] Found 6/6 markers.
[2024-01-24 14:32:52,469] [INFO] Query marker FASTA was written to GCF_025717065.2_ASM2571706v2_genomic.fna/markers.fasta
[2024-01-24 14:32:52,469] [INFO] Task started: Blastn
[2024-01-24 14:32:52,469] [INFO] Running command: blastn -query GCF_025717065.2_ASM2571706v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7584270f-c8c1-4b43-a3cc-21bf725247f3/dqc_reference/reference_markers.fasta -out GCF_025717065.2_ASM2571706v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:53,474] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:53,477] [INFO] Selected 17 target genomes.
[2024-01-24 14:32:53,478] [INFO] Target genome list was writen to GCF_025717065.2_ASM2571706v2_genomic.fna/target_genomes.txt
[2024-01-24 14:32:53,484] [INFO] Task started: fastANI
[2024-01-24 14:32:53,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b299341-45b2-40ea-8c56-65d8b3d8a4c5/GCF_025717065.2_ASM2571706v2_genomic.fna.gz --refList GCF_025717065.2_ASM2571706v2_genomic.fna/target_genomes.txt --output GCF_025717065.2_ASM2571706v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:33:10,290] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:10,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7584270f-c8c1-4b43-a3cc-21bf725247f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:33:10,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7584270f-c8c1-4b43-a3cc-21bf725247f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:33:10,313] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:33:10,314] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:33:10,314] [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
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	81.9428	959	2207	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	79.8885	1052	2207	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	78.9272	828	2207	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	78.5394	591	2207	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	78.3268	702	2207	95	below_threshold
Lysobacter gilvus	strain=HX-5-24	GCA_009740395.1	2682097	2682097	type	True	78.0797	447	2207	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	77.9622	445	2207	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	77.905	571	2207	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	77.8995	598	2207	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.6808	370	2207	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	77.6548	398	2207	95	below_threshold
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	77.6082	461	2207	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.5585	327	2207	95	below_threshold
Lysobacter lacus	strain=UKS-15	GCA_008274655.1	1643323	1643323	type	True	77.4855	345	2207	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	77.2029	520	2207	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	77.1706	444	2207	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	77.1235	534	2207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:33:10,316] [INFO] DFAST Taxonomy check result was written to GCF_025717065.2_ASM2571706v2_genomic.fna/tc_result.tsv
[2024-01-24 14:33:10,316] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:33:10,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:33:10,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7584270f-c8c1-4b43-a3cc-21bf725247f3/dqc_reference/checkm_data
[2024-01-24 14:33:10,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:33:10,378] [INFO] Task started: CheckM
[2024-01-24 14:33:10,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025717065.2_ASM2571706v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025717065.2_ASM2571706v2_genomic.fna/checkm_input GCF_025717065.2_ASM2571706v2_genomic.fna/checkm_result
[2024-01-24 14:34:13,911] [INFO] Task succeeded: CheckM
[2024-01-24 14:34:13,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:34:13,937] [INFO] ===== Completeness check finished =====
[2024-01-24 14:34:13,938] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:34:13,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025717065.2_ASM2571706v2_genomic.fna/markers.fasta)
[2024-01-24 14:34:13,939] [INFO] Task started: Blastn
[2024-01-24 14:34:13,939] [INFO] Running command: blastn -query GCF_025717065.2_ASM2571706v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7584270f-c8c1-4b43-a3cc-21bf725247f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_025717065.2_ASM2571706v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:34:15,937] [INFO] Task succeeded: Blastn
[2024-01-24 14:34:15,941] [INFO] Selected 16 target genomes.
[2024-01-24 14:34:15,941] [INFO] Target genome list was writen to GCF_025717065.2_ASM2571706v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:34:15,978] [INFO] Task started: fastANI
[2024-01-24 14:34:15,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b299341-45b2-40ea-8c56-65d8b3d8a4c5/GCF_025717065.2_ASM2571706v2_genomic.fna.gz --refList GCF_025717065.2_ASM2571706v2_genomic.fna/target_genomes_gtdb.txt --output GCF_025717065.2_ASM2571706v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:32,525] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:32,549] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:34:32,549] [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
GCA_001725155.1	s__Tahibacter sp001725155	81.0327	1089	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	99.99	99.99	0.99	0.98	4	-
GCA_013298265.1	s__Tahibacter sp013298265	79.9922	643	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363655.1	s__Tahibacter aquaticus	79.9343	1043	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138265.1	s__Dokdonella_A fugitiva_A	78.9845	912	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342425.1	s__Dokdonella_A fugitiva	78.8973	834	2207	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_000953855.2	s__Mizugakiibacter sediminis	78.8812	624	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302215.1	s__Dokdonella sp017302215	78.873	577	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	78.7443	643	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCA_003241385.1	s__Dokdonella denitrificans_A	78.6472	767	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790075.1	s__Tahibacter sp016790075	78.5699	588	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	77.996	509	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367355.1	s__Lysobacter sp003367355	77.9768	449	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	77.9248	593	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001182895.1	s__Frateuria_B defendens	77.9001	517	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109915.1	s__Luteibacter sp900109915	77.7029	471	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018847975.1	s__Lysobacter sp018847975	77.299	756	2207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:34:32,551] [INFO] GTDB search result was written to GCF_025717065.2_ASM2571706v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:32,551] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:32,555] [INFO] DFAST_QC result json was written to GCF_025717065.2_ASM2571706v2_genomic.fna/dqc_result.json
[2024-01-24 14:34:32,556] [INFO] DFAST_QC completed!
[2024-01-24 14:34:32,556] [INFO] Total running time: 0h2m2s