[2024-01-24 14:12:45,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,594] [INFO] DQC Reference Directory: /var/lib/cwl/stgef25c944-9e52-4a70-ba67-d010b688fc45/dqc_reference
[2024-01-24 14:12:46,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:46,856] [INFO] Task started: Prodigal
[2024-01-24 14:12:46,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg50813b45-35d8-4f34-83e4-d3f41d0a4e80/GCF_025398735.1_ASM2539873v1_genomic.fna.gz | prodigal -d GCF_025398735.1_ASM2539873v1_genomic.fna/cds.fna -a GCF_025398735.1_ASM2539873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:10,909] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:10,910] [INFO] Task started: HMMsearch
[2024-01-24 14:13:10,910] [INFO] Running command: hmmsearch --tblout GCF_025398735.1_ASM2539873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef25c944-9e52-4a70-ba67-d010b688fc45/dqc_reference/reference_markers.hmm GCF_025398735.1_ASM2539873v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:11,260] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:11,262] [INFO] Found 6/6 markers.
[2024-01-24 14:13:11,317] [INFO] Query marker FASTA was written to GCF_025398735.1_ASM2539873v1_genomic.fna/markers.fasta
[2024-01-24 14:13:11,318] [INFO] Task started: Blastn
[2024-01-24 14:13:11,318] [INFO] Running command: blastn -query GCF_025398735.1_ASM2539873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef25c944-9e52-4a70-ba67-d010b688fc45/dqc_reference/reference_markers.fasta -out GCF_025398735.1_ASM2539873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:12,246] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:12,250] [INFO] Selected 21 target genomes.
[2024-01-24 14:13:12,251] [INFO] Target genome list was writen to GCF_025398735.1_ASM2539873v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:12,260] [INFO] Task started: fastANI
[2024-01-24 14:13:12,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg50813b45-35d8-4f34-83e4-d3f41d0a4e80/GCF_025398735.1_ASM2539873v1_genomic.fna.gz --refList GCF_025398735.1_ASM2539873v1_genomic.fna/target_genomes.txt --output GCF_025398735.1_ASM2539873v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:28,656] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:28,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef25c944-9e52-4a70-ba67-d010b688fc45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:28,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef25c944-9e52-4a70-ba67-d010b688fc45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:28,678] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:28,679] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:28,679] [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	80.0519	684	2152	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	79.631	823	2152	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	78.2532	317	2152	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	77.9557	334	2152	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	77.8645	419	2152	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.861	458	2152	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.853	263	2152	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	77.8151	395	2152	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	77.8015	391	2152	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.7919	301	2152	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	77.7743	354	2152	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	77.74	322	2152	95	below_threshold
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	77.6306	367	2152	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	77.5231	436	2152	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	77.5081	336	2152	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	77.5022	345	2152	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	77.4145	315	2152	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	77.3198	276	2152	95	below_threshold
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	77.3192	263	2152	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	77.3145	340	2152	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	77.2023	293	2152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:28,681] [INFO] DFAST Taxonomy check result was written to GCF_025398735.1_ASM2539873v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:28,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:28,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:28,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef25c944-9e52-4a70-ba67-d010b688fc45/dqc_reference/checkm_data
[2024-01-24 14:13:28,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:28,753] [INFO] Task started: CheckM
[2024-01-24 14:13:28,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025398735.1_ASM2539873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025398735.1_ASM2539873v1_genomic.fna/checkm_input GCF_025398735.1_ASM2539873v1_genomic.fna/checkm_result
[2024-01-24 14:14:56,619] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:56,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:56,651] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:56,651] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:56,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025398735.1_ASM2539873v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:56,652] [INFO] Task started: Blastn
[2024-01-24 14:14:56,652] [INFO] Running command: blastn -query GCF_025398735.1_ASM2539873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef25c944-9e52-4a70-ba67-d010b688fc45/dqc_reference/reference_markers_gtdb.fasta -out GCF_025398735.1_ASM2539873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:58,433] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:58,437] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:58,437] [INFO] Target genome list was writen to GCF_025398735.1_ASM2539873v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:58,451] [INFO] Task started: fastANI
[2024-01-24 14:14:58,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg50813b45-35d8-4f34-83e4-d3f41d0a4e80/GCF_025398735.1_ASM2539873v1_genomic.fna.gz --refList GCF_025398735.1_ASM2539873v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025398735.1_ASM2539873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:11,695] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:11,719] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:15:11,719] [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	79.8178	771	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	99.99	99.99	0.99	0.98	4	-
GCF_004363655.1	s__Tahibacter aquaticus	79.6502	821	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298265.1	s__Tahibacter sp013298265	79.0993	494	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790075.1	s__Tahibacter sp016790075	78.8105	534	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	78.425	404	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632775.1	s__Dokdonella koreensis	77.8886	454	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	77.8884	416	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017744955.1	s__Dokdonella_A sp017744955	77.8519	479	2152	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_001182895.1	s__Frateuria_B defendens	77.7941	379	2152	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_013620825.1	s__Rhodanobacter sp001899565	77.7874	371	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCA_002297645.1	s__Dokdonella_A sp002297645	77.742	360	2152	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_017848855.1	s__Rhodanobacter denitrificans_B	77.6979	346	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431665.1	s__Stenotrophomonas maltophilia_K	77.5345	264	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138265.1	s__Dokdonella_A fugitiva_A	77.5287	432	2152	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_000336385.2	s__Lysobacter antibioticus_A	77.495	398	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014171555.1	s__Stenotrophomonas maltophilia_AK	77.4549	275	2152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.10	95.71	0.92	0.85	90	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:11,721] [INFO] GTDB search result was written to GCF_025398735.1_ASM2539873v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:11,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:11,730] [INFO] DFAST_QC result json was written to GCF_025398735.1_ASM2539873v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:11,731] [INFO] DFAST_QC completed!
[2024-01-24 14:15:11,731] [INFO] Total running time: 0h2m26s