[2024-01-24 11:19:53,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:53,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:53,681] [INFO] DQC Reference Directory: /var/lib/cwl/stgac5027d0-c98b-4ccd-8023-b2efbb8dd02d/dqc_reference
[2024-01-24 11:19:55,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:55,035] [INFO] Task started: Prodigal
[2024-01-24 11:19:55,035] [INFO] Running command: gunzip -c /var/lib/cwl/stga3778ec1-593a-43ec-982e-0e3c425b5fb2/GCF_004217385.1_ASM421738v1_genomic.fna.gz | prodigal -d GCF_004217385.1_ASM421738v1_genomic.fna/cds.fna -a GCF_004217385.1_ASM421738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:12,404] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:12,404] [INFO] Task started: HMMsearch
[2024-01-24 11:20:12,404] [INFO] Running command: hmmsearch --tblout GCF_004217385.1_ASM421738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac5027d0-c98b-4ccd-8023-b2efbb8dd02d/dqc_reference/reference_markers.hmm GCF_004217385.1_ASM421738v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:12,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:12,713] [INFO] Found 6/6 markers.
[2024-01-24 11:20:12,764] [INFO] Query marker FASTA was written to GCF_004217385.1_ASM421738v1_genomic.fna/markers.fasta
[2024-01-24 11:20:12,765] [INFO] Task started: Blastn
[2024-01-24 11:20:12,765] [INFO] Running command: blastn -query GCF_004217385.1_ASM421738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac5027d0-c98b-4ccd-8023-b2efbb8dd02d/dqc_reference/reference_markers.fasta -out GCF_004217385.1_ASM421738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:13,708] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:13,713] [INFO] Selected 17 target genomes.
[2024-01-24 11:20:13,714] [INFO] Target genome list was writen to GCF_004217385.1_ASM421738v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:13,722] [INFO] Task started: fastANI
[2024-01-24 11:20:13,723] [INFO] Running command: fastANI --query /var/lib/cwl/stga3778ec1-593a-43ec-982e-0e3c425b5fb2/GCF_004217385.1_ASM421738v1_genomic.fna.gz --refList GCF_004217385.1_ASM421738v1_genomic.fna/target_genomes.txt --output GCF_004217385.1_ASM421738v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:33,412] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:33,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac5027d0-c98b-4ccd-8023-b2efbb8dd02d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:33,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac5027d0-c98b-4ccd-8023-b2efbb8dd02d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:33,454] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:20:33,454] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:33,454] [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=DSM 5892	GCA_004217385.1	28101	28101	type	True	100.0	1800	1800	95	conclusive
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	99.9975	1799	1800	95	conclusive
Phyllobacterium myrsinacearum	strain=IAM 13584	GCA_003182235.1	28101	28101	type	True	99.9946	1788	1800	95	conclusive
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	92.6443	1506	1800	95	below_threshold
Phyllobacterium zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	80.7857	884	1800	95	below_threshold
Phyllobacterium sophorae	strain=CCBAU 03422	GCA_003010965.1	1520277	1520277	type	True	80.2411	858	1800	95	below_threshold
Phyllobacterium brassicacearum	strain=STM 196	GCA_003010955.1	314235	314235	type	True	80.0246	808	1800	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.912	431	1800	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.887	494	1800	95	below_threshold
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	77.7184	264	1800	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.5488	370	1800	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.2888	294	1800	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	77.1919	328	1800	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.143	323	1800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:33,456] [INFO] DFAST Taxonomy check result was written to GCF_004217385.1_ASM421738v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:33,457] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:33,457] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:33,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac5027d0-c98b-4ccd-8023-b2efbb8dd02d/dqc_reference/checkm_data
[2024-01-24 11:20:33,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:33,517] [INFO] Task started: CheckM
[2024-01-24 11:20:33,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217385.1_ASM421738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217385.1_ASM421738v1_genomic.fna/checkm_input GCF_004217385.1_ASM421738v1_genomic.fna/checkm_result
[2024-01-24 11:21:27,455] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:27,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:27,483] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:27,483] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:27,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217385.1_ASM421738v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:27,484] [INFO] Task started: Blastn
[2024-01-24 11:21:27,484] [INFO] Running command: blastn -query GCF_004217385.1_ASM421738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac5027d0-c98b-4ccd-8023-b2efbb8dd02d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217385.1_ASM421738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:29,088] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:29,092] [INFO] Selected 10 target genomes.
[2024-01-24 11:21:29,092] [INFO] Target genome list was writen to GCF_004217385.1_ASM421738v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:29,101] [INFO] Task started: fastANI
[2024-01-24 11:21:29,102] [INFO] Running command: fastANI --query /var/lib/cwl/stga3778ec1-593a-43ec-982e-0e3c425b5fb2/GCF_004217385.1_ASM421738v1_genomic.fna.gz --refList GCF_004217385.1_ASM421738v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217385.1_ASM421738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:41,677] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:41,697] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:41,698] [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	99.9975	1799	1800	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	92.6307	1447	1800	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	85.5134	1370	1800	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	84.1438	1257	1800	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	84.0544	1253	1800	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	82.587	1169	1800	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_002294995.1	s__Mesorhizobium sp002294995	77.7401	429	1800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252525.1	s__Ochrobactrum_A pseudogrignonensis	77.7184	264	1800	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_018798825.1	s__Ochrobactrum_A sp018798825	77.5021	257	1800	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	77.1704	333	1800	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 11:21:41,699] [INFO] GTDB search result was written to GCF_004217385.1_ASM421738v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:41,700] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:41,703] [INFO] DFAST_QC result json was written to GCF_004217385.1_ASM421738v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:41,703] [INFO] DFAST_QC completed!
[2024-01-24 11:21:41,704] [INFO] Total running time: 0h1m48s