[2024-01-24 12:15:04,189] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,190] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg576e6a1c-dbbd-4279-9763-9f69473d27c9/dqc_reference
[2024-01-24 12:15:05,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,504] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,504] [INFO] Running command: gunzip -c /var/lib/cwl/stgef337377-4c3f-47df-b1b1-13f81e766159/GCF_004322705.1_ASM432270v1_genomic.fna.gz | prodigal -d GCF_004322705.1_ASM432270v1_genomic.fna/cds.fna -a GCF_004322705.1_ASM432270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:20,302] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:20,303] [INFO] Task started: HMMsearch
[2024-01-24 12:15:20,303] [INFO] Running command: hmmsearch --tblout GCF_004322705.1_ASM432270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg576e6a1c-dbbd-4279-9763-9f69473d27c9/dqc_reference/reference_markers.hmm GCF_004322705.1_ASM432270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:20,615] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:20,617] [INFO] Found 6/6 markers.
[2024-01-24 12:15:20,658] [INFO] Query marker FASTA was written to GCF_004322705.1_ASM432270v1_genomic.fna/markers.fasta
[2024-01-24 12:15:20,658] [INFO] Task started: Blastn
[2024-01-24 12:15:20,658] [INFO] Running command: blastn -query GCF_004322705.1_ASM432270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg576e6a1c-dbbd-4279-9763-9f69473d27c9/dqc_reference/reference_markers.fasta -out GCF_004322705.1_ASM432270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:21,692] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:21,696] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:21,696] [INFO] Target genome list was writen to GCF_004322705.1_ASM432270v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:21,702] [INFO] Task started: fastANI
[2024-01-24 12:15:21,702] [INFO] Running command: fastANI --query /var/lib/cwl/stgef337377-4c3f-47df-b1b1-13f81e766159/GCF_004322705.1_ASM432270v1_genomic.fna.gz --refList GCF_004322705.1_ASM432270v1_genomic.fna/target_genomes.txt --output GCF_004322705.1_ASM432270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:33,163] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:33,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg576e6a1c-dbbd-4279-9763-9f69473d27c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:33,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg576e6a1c-dbbd-4279-9763-9f69473d27c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:33,176] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:33,176] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:33,176] [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
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	81.3191	589	1404	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	81.3148	753	1404	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	81.2923	750	1404	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	81.244	705	1404	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	81.2287	722	1404	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	80.4056	687	1404	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	80.4056	626	1404	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.2673	569	1404	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	80.187	573	1404	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	80.1067	568	1404	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	80.0705	573	1404	95	below_threshold
Rhodanobacter panaciterrae	strain=KCTC 22232	GCA_014651895.1	490572	490572	type	True	79.7828	576	1404	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	79.3259	467	1404	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.8661	295	1404	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:33,178] [INFO] DFAST Taxonomy check result was written to GCF_004322705.1_ASM432270v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:33,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:33,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:33,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg576e6a1c-dbbd-4279-9763-9f69473d27c9/dqc_reference/checkm_data
[2024-01-24 12:15:33,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:33,219] [INFO] Task started: CheckM
[2024-01-24 12:15:33,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004322705.1_ASM432270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004322705.1_ASM432270v1_genomic.fna/checkm_input GCF_004322705.1_ASM432270v1_genomic.fna/checkm_result
[2024-01-24 12:16:20,270] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:20,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:20,299] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:20,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:20,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004322705.1_ASM432270v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:20,301] [INFO] Task started: Blastn
[2024-01-24 12:16:20,301] [INFO] Running command: blastn -query GCF_004322705.1_ASM432270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg576e6a1c-dbbd-4279-9763-9f69473d27c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004322705.1_ASM432270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:22,122] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:22,127] [INFO] Selected 15 target genomes.
[2024-01-24 12:16:22,127] [INFO] Target genome list was writen to GCF_004322705.1_ASM432270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:22,139] [INFO] Task started: fastANI
[2024-01-24 12:16:22,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgef337377-4c3f-47df-b1b1-13f81e766159/GCF_004322705.1_ASM432270v1_genomic.fna.gz --refList GCF_004322705.1_ASM432270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004322705.1_ASM432270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:36,035] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:36,050] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:36,051] [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_004322705.1	s__Dyella terrae	100.0	1404	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012275375.1	s__Dyella sp012275375	82.3138	820	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_900112865.1	s__Dyella marensis	82.2549	797	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003332825.1	s__Dyella sp003332825	81.5136	701	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201105.1	s__Dyella jiangningensis_B	81.4886	725	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003264855.1	s__Dyella jiangningensis_C	81.3963	742	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	81.3668	726	1404	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	81.3122	753	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725385.1	s__Dyella japonica_C	81.2786	734	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004296575.1	s__Dyella sp004296575	81.2738	752	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351225.1	s__Dyella solisilvae	81.2539	704	1404	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	81.2362	699	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016905005.1	s__Dyella kyungheensis	81.2255	722	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000632805.1	s__Dyella jiangningensis	81.1379	755	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	80.0161	603	1404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:36,052] [INFO] GTDB search result was written to GCF_004322705.1_ASM432270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:36,053] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:36,057] [INFO] DFAST_QC result json was written to GCF_004322705.1_ASM432270v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:36,057] [INFO] DFAST_QC completed!
[2024-01-24 12:16:36,057] [INFO] Total running time: 0h1m32s