[2024-01-24 13:32:56,102] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:56,104] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:56,104] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0c31195-f827-4a2e-9f55-155450448770/dqc_reference
[2024-01-24 13:32:57,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:57,356] [INFO] Task started: Prodigal
[2024-01-24 13:32:57,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg98ee9085-d46f-4cf8-a79c-106aee257a39/GCF_003182235.1_ASM318223v1_genomic.fna.gz | prodigal -d GCF_003182235.1_ASM318223v1_genomic.fna/cds.fna -a GCF_003182235.1_ASM318223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:15,893] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:15,894] [INFO] Task started: HMMsearch
[2024-01-24 13:33:15,894] [INFO] Running command: hmmsearch --tblout GCF_003182235.1_ASM318223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0c31195-f827-4a2e-9f55-155450448770/dqc_reference/reference_markers.hmm GCF_003182235.1_ASM318223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:16,195] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:16,196] [INFO] Found 6/6 markers.
[2024-01-24 13:33:16,246] [INFO] Query marker FASTA was written to GCF_003182235.1_ASM318223v1_genomic.fna/markers.fasta
[2024-01-24 13:33:16,246] [INFO] Task started: Blastn
[2024-01-24 13:33:16,246] [INFO] Running command: blastn -query GCF_003182235.1_ASM318223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c31195-f827-4a2e-9f55-155450448770/dqc_reference/reference_markers.fasta -out GCF_003182235.1_ASM318223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:17,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:17,178] [INFO] Selected 17 target genomes.
[2024-01-24 13:33:17,178] [INFO] Target genome list was writen to GCF_003182235.1_ASM318223v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:17,191] [INFO] Task started: fastANI
[2024-01-24 13:33:17,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg98ee9085-d46f-4cf8-a79c-106aee257a39/GCF_003182235.1_ASM318223v1_genomic.fna.gz --refList GCF_003182235.1_ASM318223v1_genomic.fna/target_genomes.txt --output GCF_003182235.1_ASM318223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:35,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:35,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0c31195-f827-4a2e-9f55-155450448770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:35,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0c31195-f827-4a2e-9f55-155450448770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:35,257] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:33:35,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:35,258] [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
Phyllobacterium myrsinacearum	strain=IAM 13584	GCA_003182235.1	28101	28101	type	True	100.0	1789	1793	95	conclusive
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	99.9994	1788	1793	95	conclusive
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_004217385.1	28101	28101	type	True	99.9987	1790	1793	95	conclusive
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	92.6322	1506	1793	95	below_threshold
Phyllobacterium zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	80.7683	892	1793	95	below_threshold
Phyllobacterium sophorae	strain=CCBAU 03422	GCA_003010965.1	1520277	1520277	type	True	80.2689	838	1793	95	below_threshold
Phyllobacterium brassicacearum	strain=STM 196	GCA_003010955.1	314235	314235	type	True	79.9955	813	1793	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.9716	435	1793	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.88	493	1793	95	below_threshold
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	77.7831	249	1793	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.7091	369	1793	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.3648	282	1793	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.3141	315	1793	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	77.204	330	1793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,259] [INFO] DFAST Taxonomy check result was written to GCF_003182235.1_ASM318223v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:35,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:35,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:35,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0c31195-f827-4a2e-9f55-155450448770/dqc_reference/checkm_data
[2024-01-24 13:33:35,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:35,310] [INFO] Task started: CheckM
[2024-01-24 13:33:35,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003182235.1_ASM318223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003182235.1_ASM318223v1_genomic.fna/checkm_input GCF_003182235.1_ASM318223v1_genomic.fna/checkm_result
[2024-01-24 13:34:24,720] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:24,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:24,739] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:24,740] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:24,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003182235.1_ASM318223v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:24,740] [INFO] Task started: Blastn
[2024-01-24 13:34:24,740] [INFO] Running command: blastn -query GCF_003182235.1_ASM318223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c31195-f827-4a2e-9f55-155450448770/dqc_reference/reference_markers_gtdb.fasta -out GCF_003182235.1_ASM318223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:26,191] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:26,194] [INFO] Selected 10 target genomes.
[2024-01-24 13:34:26,194] [INFO] Target genome list was writen to GCF_003182235.1_ASM318223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:26,212] [INFO] Task started: fastANI
[2024-01-24 13:34:26,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg98ee9085-d46f-4cf8-a79c-106aee257a39/GCF_003182235.1_ASM318223v1_genomic.fna.gz --refList GCF_003182235.1_ASM318223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003182235.1_ASM318223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:38,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:38,011] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:38,011] [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_002980555.1	s__Phyllobacterium myrsinacearum	99.9994	1788	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.64	98.56	0.99	0.97	5	conclusive
GCA_900539805.1	s__Phyllobacterium sp900539805	92.6566	1441	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	96.69	96.69	0.93	0.93	2	-
GCF_014138285.1	s__Phyllobacterium myrsinacearum_A	85.5922	1355	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104355.1	s__Phyllobacterium sp900104355	84.1373	1274	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472835.1	s__Phyllobacterium sp900472835	84.0403	1249	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	99.91	98.56	0.99	0.96	30	-
GCF_014189505.1	s__Phyllobacterium sp014189505	82.745	1133	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Phyllobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252525.1	s__Ochrobactrum_A pseudogrignonensis	77.7969	248	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.50	96.15	0.90	0.81	34	-
GCF_002294995.1	s__Mesorhizobium sp002294995	77.7186	440	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018798825.1	s__Ochrobactrum_A sp018798825	77.5518	253	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993735.1	s__Chelativorans alearense	77.2056	332	1793	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:38,013] [INFO] GTDB search result was written to GCF_003182235.1_ASM318223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:38,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:38,017] [INFO] DFAST_QC result json was written to GCF_003182235.1_ASM318223v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:38,017] [INFO] DFAST_QC completed!
[2024-01-24 13:34:38,017] [INFO] Total running time: 0h1m42s