[2024-01-24 11:34:40,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:40,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:40,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg90ee8cae-8519-417a-9de6-712fe3a929e5/dqc_reference
[2024-01-24 11:34:42,156] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,157] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,158] [INFO] Running command: gunzip -c /var/lib/cwl/stga3ee0b7d-7204-4f91-bbbe-0f35bc0b3525/GCF_006476605.1_ASM647660v1_genomic.fna.gz | prodigal -d GCF_006476605.1_ASM647660v1_genomic.fna/cds.fna -a GCF_006476605.1_ASM647660v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:53,883] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:53,883] [INFO] Task started: HMMsearch
[2024-01-24 11:34:53,883] [INFO] Running command: hmmsearch --tblout GCF_006476605.1_ASM647660v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90ee8cae-8519-417a-9de6-712fe3a929e5/dqc_reference/reference_markers.hmm GCF_006476605.1_ASM647660v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:54,192] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:54,193] [INFO] Found 6/6 markers.
[2024-01-24 11:34:54,238] [INFO] Query marker FASTA was written to GCF_006476605.1_ASM647660v1_genomic.fna/markers.fasta
[2024-01-24 11:34:54,241] [INFO] Task started: Blastn
[2024-01-24 11:34:54,241] [INFO] Running command: blastn -query GCF_006476605.1_ASM647660v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90ee8cae-8519-417a-9de6-712fe3a929e5/dqc_reference/reference_markers.fasta -out GCF_006476605.1_ASM647660v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:55,029] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:55,033] [INFO] Selected 13 target genomes.
[2024-01-24 11:34:55,033] [INFO] Target genome list was writen to GCF_006476605.1_ASM647660v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:55,038] [INFO] Task started: fastANI
[2024-01-24 11:34:55,039] [INFO] Running command: fastANI --query /var/lib/cwl/stga3ee0b7d-7204-4f91-bbbe-0f35bc0b3525/GCF_006476605.1_ASM647660v1_genomic.fna.gz --refList GCF_006476605.1_ASM647660v1_genomic.fna/target_genomes.txt --output GCF_006476605.1_ASM647660v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:08,226] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:08,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90ee8cae-8519-417a-9de6-712fe3a929e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:08,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90ee8cae-8519-417a-9de6-712fe3a929e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:08,239] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:08,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:08,240] [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
Brucella gallinifaecis	strain=ISO 196	GCA_006476605.1	215590	215590	type	True	100.0	1229	1230	95	conclusive
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	82.9508	816	1230	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	82.5493	756	1230	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_003049685.2	571256	571256	type	True	82.5135	782	1230	95	below_threshold
Brucella thiophenivorans	strain=DSM 7216	GCA_002252445.1	571255	571255	type	True	82.3614	758	1230	95	below_threshold
Brucella grignonensis	strain=OgA9a	GCA_002252505.1	94627	94627	type	True	82.1578	736	1230	95	below_threshold
Brucella rhizosphaerae	strain=PR17	GCA_002252475.1	571254	571254	type	True	81.8707	733	1230	95	below_threshold
[Ochrobactrum] quorumnocens	strain=A44	GCA_002278035.1	271865	271865	type	True	81.5285	743	1230	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	78.3491	246	1230	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	78.3331	247	1230	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.6329	80	1230	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.3795	124	1230	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.281	88	1230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:08,245] [INFO] DFAST Taxonomy check result was written to GCF_006476605.1_ASM647660v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:08,250] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:08,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:08,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90ee8cae-8519-417a-9de6-712fe3a929e5/dqc_reference/checkm_data
[2024-01-24 11:35:08,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:08,290] [INFO] Task started: CheckM
[2024-01-24 11:35:08,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006476605.1_ASM647660v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006476605.1_ASM647660v1_genomic.fna/checkm_input GCF_006476605.1_ASM647660v1_genomic.fna/checkm_result
[2024-01-24 11:35:45,896] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:45,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:45,909] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:45,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:45,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006476605.1_ASM647660v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:45,910] [INFO] Task started: Blastn
[2024-01-24 11:35:45,910] [INFO] Running command: blastn -query GCF_006476605.1_ASM647660v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90ee8cae-8519-417a-9de6-712fe3a929e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_006476605.1_ASM647660v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:47,132] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:47,135] [INFO] Selected 8 target genomes.
[2024-01-24 11:35:47,136] [INFO] Target genome list was writen to GCF_006476605.1_ASM647660v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:47,141] [INFO] Task started: fastANI
[2024-01-24 11:35:47,141] [INFO] Running command: fastANI --query /var/lib/cwl/stga3ee0b7d-7204-4f91-bbbe-0f35bc0b3525/GCF_006476605.1_ASM647660v1_genomic.fna.gz --refList GCF_006476605.1_ASM647660v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006476605.1_ASM647660v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:55,796] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:55,805] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:55,805] [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_006476605.1	s__Ochrobactrum_A gallinifaecis	100.0	1229	1230	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	conclusive
GCF_002252525.1	s__Ochrobactrum_A pseudogrignonensis	82.9407	817	1230	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_014397025.1	s__Ochrobactrum_A sp014397025	82.7082	797	1230	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_018798825.1	s__Ochrobactrum_A sp018798825	82.694	768	1230	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_003049685.1	s__Ochrobactrum_A pituitosa	82.5033	783	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	98.27	97.05	0.91	0.82	14	-
GCF_002252445.1	s__Ochrobactrum_A thiophenivorans	82.3665	758	1230	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_002252505.1	s__Ochrobactrum_A grignonensis	82.1473	737	1230	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	99.78	99.78	1.00	1.00	2	-
GCF_002252475.1	s__Ochrobactrum_A rhizosphaerae	81.8708	733	1230	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:55,807] [INFO] GTDB search result was written to GCF_006476605.1_ASM647660v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:55,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:55,811] [INFO] DFAST_QC result json was written to GCF_006476605.1_ASM647660v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:55,811] [INFO] DFAST_QC completed!
[2024-01-24 11:35:55,811] [INFO] Total running time: 0h1m15s