[2024-01-25 18:05:50,632] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:50,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:50,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg57768bfd-debb-448f-a1d9-e5f520a7128a/dqc_reference
[2024-01-25 18:05:51,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:51,784] [INFO] Task started: Prodigal
[2024-01-25 18:05:51,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg788080c1-91b9-4faa-91f5-6fcd184d71ee/GCF_015905305.1_ASM1590530v1_genomic.fna.gz | prodigal -d GCF_015905305.1_ASM1590530v1_genomic.fna/cds.fna -a GCF_015905305.1_ASM1590530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:07,892] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:07,893] [INFO] Task started: HMMsearch
[2024-01-25 18:06:07,893] [INFO] Running command: hmmsearch --tblout GCF_015905305.1_ASM1590530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57768bfd-debb-448f-a1d9-e5f520a7128a/dqc_reference/reference_markers.hmm GCF_015905305.1_ASM1590530v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:08,129] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:08,130] [INFO] Found 6/6 markers.
[2024-01-25 18:06:08,166] [INFO] Query marker FASTA was written to GCF_015905305.1_ASM1590530v1_genomic.fna/markers.fasta
[2024-01-25 18:06:08,167] [INFO] Task started: Blastn
[2024-01-25 18:06:08,167] [INFO] Running command: blastn -query GCF_015905305.1_ASM1590530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57768bfd-debb-448f-a1d9-e5f520a7128a/dqc_reference/reference_markers.fasta -out GCF_015905305.1_ASM1590530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:09,091] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:09,094] [INFO] Selected 21 target genomes.
[2024-01-25 18:06:09,094] [INFO] Target genome list was writen to GCF_015905305.1_ASM1590530v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:09,100] [INFO] Task started: fastANI
[2024-01-25 18:06:09,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg788080c1-91b9-4faa-91f5-6fcd184d71ee/GCF_015905305.1_ASM1590530v1_genomic.fna.gz --refList GCF_015905305.1_ASM1590530v1_genomic.fna/target_genomes.txt --output GCF_015905305.1_ASM1590530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:26,375] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:26,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57768bfd-debb-448f-a1d9-e5f520a7128a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:26,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57768bfd-debb-448f-a1d9-e5f520a7128a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:26,388] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:06:26,388] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:06:26,388] [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
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	80.3001	607	1459	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	80.2324	570	1459	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	79.8251	570	1459	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	79.7068	546	1459	95	below_threshold
Luteibacter pinisoli	strain=MAH-14	GCA_006385595.1	2589080	2589080	type	True	79.6427	619	1459	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	79.6338	529	1459	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	79.6118	531	1459	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	79.5906	560	1459	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	79.5823	563	1459	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.5687	588	1459	95	below_threshold
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	79.5556	542	1459	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.5101	512	1459	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	79.4983	596	1459	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	79.4956	539	1459	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.4846	458	1459	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	79.1672	507	1459	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	78.6732	445	1459	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	78.2959	281	1459	95	below_threshold
Xanthomonas citri	strain=CFBP 2913	GCA_002688625.1	346	346	pathovar	True	77.4305	272	1459	95	below_threshold
Xanthomonas citri	strain=LMG867	GCA_020011255.1	346	346	pathovar	True	77.1928	256	1459	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	77.1046	269	1459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:26,390] [INFO] DFAST Taxonomy check result was written to GCF_015905305.1_ASM1590530v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:26,390] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:26,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:26,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57768bfd-debb-448f-a1d9-e5f520a7128a/dqc_reference/checkm_data
[2024-01-25 18:06:26,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:26,431] [INFO] Task started: CheckM
[2024-01-25 18:06:26,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015905305.1_ASM1590530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015905305.1_ASM1590530v1_genomic.fna/checkm_input GCF_015905305.1_ASM1590530v1_genomic.fna/checkm_result
[2024-01-25 18:07:13,807] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:13,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:13,831] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:13,831] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:13,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015905305.1_ASM1590530v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:13,832] [INFO] Task started: Blastn
[2024-01-25 18:07:13,832] [INFO] Running command: blastn -query GCF_015905305.1_ASM1590530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57768bfd-debb-448f-a1d9-e5f520a7128a/dqc_reference/reference_markers_gtdb.fasta -out GCF_015905305.1_ASM1590530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:15,718] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:15,720] [INFO] Selected 23 target genomes.
[2024-01-25 18:07:15,721] [INFO] Target genome list was writen to GCF_015905305.1_ASM1590530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:15,739] [INFO] Task started: fastANI
[2024-01-25 18:07:15,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg788080c1-91b9-4faa-91f5-6fcd184d71ee/GCF_015905305.1_ASM1590530v1_genomic.fna.gz --refList GCF_015905305.1_ASM1590530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015905305.1_ASM1590530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:36,119] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:36,134] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:36,134] [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_015905245.1	s__Luteibacter sp015905245	98.8171	1369	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	98.85	98.84	0.95	0.94	3	conclusive
GCF_012275375.1	s__Dyella sp012275375	80.2811	689	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_003148905.1	s__Fulvimonas soli	80.2624	611	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900112865.1	s__Dyella marensis	80.2129	624	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001428405.1	s__Frateuria_A sp001428405	80.0974	614	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201105.1	s__Dyella jiangningensis_B	79.9943	625	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001617365.1	s__Rhodanobacter sp001617365	79.8924	548	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.98	99.98	0.98	0.97	3	-
GCF_011742875.1	s__Luteibacter yeojuensis	79.8251	570	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332825.1	s__Dyella sp003332825	79.8133	575	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745005.1	s__Luteibacter sp000745005	79.7406	594	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842975.1	s__Rhodanobacter sp014842975	79.704	560	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759365.1	s__Luteibacter anthropi	79.6928	547	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264855.1	s__Dyella jiangningensis_C	79.645	588	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912395.1	s__Luteibacter sp009912395	79.6333	553	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115705.1	s__Frateuria_A terrea	79.6281	530	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016586165.1	s__Dyella sp016586165	79.5949	587	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297575.1	s__Dyella sp014297575	79.5689	588	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742555.1	s__Luteibacter jiangsuensis	79.5561	542	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362045.1	s__Frateuria_A sp013362045	79.5508	472	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000632805.1	s__Dyella jiangningensis	79.3709	575	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121485.1	s__Dyella sp003121485	79.2521	534	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114325.1	s__Rhodanobacter glycinis	79.227	523	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	97.24	96.89	0.85	0.82	5	-
GCF_000953855.2	s__Mizugakiibacter sediminis	78.9312	428	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:36,136] [INFO] GTDB search result was written to GCF_015905305.1_ASM1590530v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:36,136] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:36,140] [INFO] DFAST_QC result json was written to GCF_015905305.1_ASM1590530v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:36,140] [INFO] DFAST_QC completed!
[2024-01-25 18:07:36,140] [INFO] Total running time: 0h1m46s