[2024-01-24 14:12:01,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:01,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:01,940] [INFO] DQC Reference Directory: /var/lib/cwl/stge6c03b14-9ca0-4e5b-a22c-77e91fb36c54/dqc_reference
[2024-01-24 14:12:03,186] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:03,186] [INFO] Task started: Prodigal
[2024-01-24 14:12:03,187] [INFO] Running command: gunzip -c /var/lib/cwl/stg331bf106-5a21-42c3-85c2-60dabc3a47a7/GCF_000712255.1_Bneotomae2.0_genomic.fna.gz | prodigal -d GCF_000712255.1_Bneotomae2.0_genomic.fna/cds.fna -a GCF_000712255.1_Bneotomae2.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:13,285] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:13,286] [INFO] Task started: HMMsearch
[2024-01-24 14:12:13,286] [INFO] Running command: hmmsearch --tblout GCF_000712255.1_Bneotomae2.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6c03b14-9ca0-4e5b-a22c-77e91fb36c54/dqc_reference/reference_markers.hmm GCF_000712255.1_Bneotomae2.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:13,626] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:13,627] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg331bf106-5a21-42c3-85c2-60dabc3a47a7/GCF_000712255.1_Bneotomae2.0_genomic.fna.gz]
[2024-01-24 14:12:13,662] [INFO] Query marker FASTA was written to GCF_000712255.1_Bneotomae2.0_genomic.fna/markers.fasta
[2024-01-24 14:12:13,663] [INFO] Task started: Blastn
[2024-01-24 14:12:13,663] [INFO] Running command: blastn -query GCF_000712255.1_Bneotomae2.0_genomic.fna/markers.fasta -db /var/lib/cwl/stge6c03b14-9ca0-4e5b-a22c-77e91fb36c54/dqc_reference/reference_markers.fasta -out GCF_000712255.1_Bneotomae2.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:14,632] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:14,635] [INFO] Selected 13 target genomes.
[2024-01-24 14:12:14,635] [INFO] Target genome list was writen to GCF_000712255.1_Bneotomae2.0_genomic.fna/target_genomes.txt
[2024-01-24 14:12:14,643] [INFO] Task started: fastANI
[2024-01-24 14:12:14,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg331bf106-5a21-42c3-85c2-60dabc3a47a7/GCF_000712255.1_Bneotomae2.0_genomic.fna.gz --refList GCF_000712255.1_Bneotomae2.0_genomic.fna/target_genomes.txt --output GCF_000712255.1_Bneotomae2.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:25,021] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:25,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6c03b14-9ca0-4e5b-a22c-77e91fb36c54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:25,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6c03b14-9ca0-4e5b-a22c-77e91fb36c54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:25,032] [WARNING] The ANI hits belong to more than one indistinguishable-group. The ANI hits will be classified as 'inconclusive,indistinguishable'. {}, {29459: 'Brucella melitensis', 236: 'Brucella ovis', 29460: 'Brucella neotomae', 29461: 'Brucella suis', 36855: 'Brucella canis'}
[2024-01-24 14:12:25,033] [INFO] Found 13 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 14:12:25,033] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:12:25,033] [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 neotomae	strain=5K33	GCA_000712255.2	29460	29460	suspected-type	True	99.9999	1010	1014	95	inconclusive
Brucella neotomae	strain=NCTC10084	GCA_900446125.1	29460	29460	suspected-type	True	99.9788	1012	1014	95	inconclusive
Brucella neotomae	strain=5K33	GCA_000742255.1	29460	29460	suspected-type	True	99.9702	1014	1014	95	inconclusive
Brucella neotomae	strain=5K33	GCA_000158715.1	29460	29460	suspected-type	True	99.9694	1011	1014	95	inconclusive
Brucella suis	strain=1330	GCA_000007505.1	29461	29461	suspected-type	True	99.7184	1006	1014	95	inconclusive
Brucella ceti	strain=B1/94	GCA_000158775.1	120577	120577	suspected-type	True	99.7043	1002	1014	95	inconclusive
Brucella abortus	strain=544	GCA_000369945.1	235	235	type	True	99.6517	996	1014	95	inconclusive
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	99.637	997	1014	95	inconclusive
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.5364	247	1014	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.5363	247	1014	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.4293	235	1014	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.1051	207	1014	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	76.9506	225	1014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:25,034] [INFO] DFAST Taxonomy check result was written to GCF_000712255.1_Bneotomae2.0_genomic.fna/tc_result.tsv
[2024-01-24 14:12:25,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:25,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:25,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6c03b14-9ca0-4e5b-a22c-77e91fb36c54/dqc_reference/checkm_data
[2024-01-24 14:12:25,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:25,070] [INFO] Task started: CheckM
[2024-01-24 14:12:25,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000712255.1_Bneotomae2.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000712255.1_Bneotomae2.0_genomic.fna/checkm_input GCF_000712255.1_Bneotomae2.0_genomic.fna/checkm_result
[2024-01-24 14:12:57,700] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:57,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:57,721] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:57,721] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:57,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000712255.1_Bneotomae2.0_genomic.fna/markers.fasta)
[2024-01-24 14:12:57,722] [INFO] Task started: Blastn
[2024-01-24 14:12:57,722] [INFO] Running command: blastn -query GCF_000712255.1_Bneotomae2.0_genomic.fna/markers.fasta -db /var/lib/cwl/stge6c03b14-9ca0-4e5b-a22c-77e91fb36c54/dqc_reference/reference_markers_gtdb.fasta -out GCF_000712255.1_Bneotomae2.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:59,263] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:59,266] [INFO] Selected 16 target genomes.
[2024-01-24 14:12:59,266] [INFO] Target genome list was writen to GCF_000712255.1_Bneotomae2.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:59,284] [INFO] Task started: fastANI
[2024-01-24 14:12:59,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg331bf106-5a21-42c3-85c2-60dabc3a47a7/GCF_000712255.1_Bneotomae2.0_genomic.fna.gz --refList GCF_000712255.1_Bneotomae2.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000712255.1_Bneotomae2.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:14,291] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:14,310] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:14,310] [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_000007125.1	s__Brucella melitensis	99.6245	1000	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Brucella	95.0	99.71	97.51	0.99	0.88	877	conclusive
GCA_900473915.1	s__Ochrobactrum sp900473915	83.539	719	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000182645.1	s__Ochrobactrum intermedium	83.307	732	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	97.99	97.16	0.92	0.84	56	-
GCF_008932435.1	s__Ochrobactrum pseudintermedium	83.2991	712	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	98.90	97.85	0.90	0.89	7	-
GCF_003550135.1	s__Ochrobactrum_B haematophila_B	83.2161	741	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470195.1	s__Ochrobactrum sp900470195	83.1522	719	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.22	97.63	0.95	0.85	7	-
GCF_014199265.1	s__Ochrobactrum_C daejeonensis	83.0896	706	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_C	95.0	99.74	99.74	0.99	0.99	2	-
GCF_000017405.1	s__Ochrobactrum anthropi	82.9528	710	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.518	98.11	96.94	0.89	0.83	55	-
GCF_008932295.1	s__Ochrobactrum tritici	82.9208	710	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	98.18	96.73	0.91	0.84	6	-
GCF_902825325.1	s__Ochrobactrum sp003176975	82.8927	709	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	97.64	97.64	0.88	0.88	2	-
GCF_006376675.1	s__Ochrobactrum pecoris	82.7307	713	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.97	99.94	1.00	1.00	3	-
GCA_012103075.1	s__Ochrobactrum cytisi	82.6583	722	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.518	98.45	98.45	0.94	0.94	2	-
GCF_016427605.1	s__Ochrobactrum_B sp016427605	82.5158	693	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006376685.1	s__Ochrobactrum_B teleogrylli	82.2371	712	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	98.13	98.09	0.91	0.90	5	-
GCA_900465685.1	s__Ochrobactrum_B sp900465685	82.0744	695	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	99.22	99.21	0.91	0.91	3	-
GCF_014253075.1	s__JACLZJ01 sp014253075	81.3767	682	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__JACLZJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:14,312] [INFO] GTDB search result was written to GCF_000712255.1_Bneotomae2.0_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:14,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:14,316] [INFO] DFAST_QC result json was written to GCF_000712255.1_Bneotomae2.0_genomic.fna/dqc_result.json
[2024-01-24 14:13:14,316] [INFO] DFAST_QC completed!
[2024-01-24 14:13:14,316] [INFO] Total running time: 0h1m12s