[2024-01-24 13:49:41,328] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:41,330] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:41,330] [INFO] DQC Reference Directory: /var/lib/cwl/stg2051cd33-c2ab-4e66-9ae4-b04c97bdc2b6/dqc_reference
[2024-01-24 13:49:42,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,623] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,623] [INFO] Running command: gunzip -c /var/lib/cwl/stg49ce1492-e704-4910-8950-4f8559582166/GCF_014199265.1_ASM1419926v1_genomic.fna.gz | prodigal -d GCF_014199265.1_ASM1419926v1_genomic.fna/cds.fna -a GCF_014199265.1_ASM1419926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:56,746] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:56,747] [INFO] Task started: HMMsearch
[2024-01-24 13:49:56,747] [INFO] Running command: hmmsearch --tblout GCF_014199265.1_ASM1419926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2051cd33-c2ab-4e66-9ae4-b04c97bdc2b6/dqc_reference/reference_markers.hmm GCF_014199265.1_ASM1419926v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:57,063] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:57,064] [INFO] Found 6/6 markers.
[2024-01-24 13:49:57,104] [INFO] Query marker FASTA was written to GCF_014199265.1_ASM1419926v1_genomic.fna/markers.fasta
[2024-01-24 13:49:57,104] [INFO] Task started: Blastn
[2024-01-24 13:49:57,104] [INFO] Running command: blastn -query GCF_014199265.1_ASM1419926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2051cd33-c2ab-4e66-9ae4-b04c97bdc2b6/dqc_reference/reference_markers.fasta -out GCF_014199265.1_ASM1419926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:58,030] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:58,034] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:58,035] [INFO] Target genome list was writen to GCF_014199265.1_ASM1419926v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:58,045] [INFO] Task started: fastANI
[2024-01-24 13:49:58,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ce1492-e704-4910-8950-4f8559582166/GCF_014199265.1_ASM1419926v1_genomic.fna.gz --refList GCF_014199265.1_ASM1419926v1_genomic.fna/target_genomes.txt --output GCF_014199265.1_ASM1419926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:15,662] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:15,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2051cd33-c2ab-4e66-9ae4-b04c97bdc2b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:15,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2051cd33-c2ab-4e66-9ae4-b04c97bdc2b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:15,685] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:15,685] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:15,685] [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 daejeonensis	strain=DSM 26944	GCA_014199265.1	659015	659015	type	True	100.0	1517	1520	95	conclusive
Brucella intermedia	strain=LMG 3301	GCA_000182645.1	94625	94625	suspected-type	True	84.2291	978	1520	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	84.1583	1007	1520	95	below_threshold
Brucella tritici	strain=LMG 18957	GCA_008932295.1	94626	94626	type	True	84.1448	985	1520	95	below_threshold
Brucella anthropi	strain=NCTC12168	GCA_900454235.1	529	529	type	True	83.749	998	1520	95	below_threshold
Brucella anthropi	strain=ATCC 49188	GCA_000017405.1	529	529	type	True	83.7235	1008	1520	95	below_threshold
Brucella pecoris	strain=DSM 23868	GCA_014197065.1	867683	867683	type	True	83.4424	988	1520	95	below_threshold
Brucella neotomae	strain=5K33	GCA_000742255.1	29460	29460	suspected-type	True	82.9978	760	1520	95	below_threshold
Brucella haematophila	strain=CCUG 38531	GCA_005938105.1	419474	419474	type	True	82.5498	894	1520	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	80.4016	721	1520	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_003049685.2	571256	571256	type	True	80.3699	728	1520	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.682	303	1520	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.5868	268	1520	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.5867	268	1520	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.5204	363	1520	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.1795	257	1520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:15,687] [INFO] DFAST Taxonomy check result was written to GCF_014199265.1_ASM1419926v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:15,688] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:15,688] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:15,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2051cd33-c2ab-4e66-9ae4-b04c97bdc2b6/dqc_reference/checkm_data
[2024-01-24 13:50:15,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:15,734] [INFO] Task started: CheckM
[2024-01-24 13:50:15,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199265.1_ASM1419926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199265.1_ASM1419926v1_genomic.fna/checkm_input GCF_014199265.1_ASM1419926v1_genomic.fna/checkm_result
[2024-01-24 13:50:58,829] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:58,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:58,849] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:58,850] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:58,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199265.1_ASM1419926v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:58,851] [INFO] Task started: Blastn
[2024-01-24 13:50:58,851] [INFO] Running command: blastn -query GCF_014199265.1_ASM1419926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2051cd33-c2ab-4e66-9ae4-b04c97bdc2b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199265.1_ASM1419926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:00,329] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:00,333] [INFO] Selected 16 target genomes.
[2024-01-24 13:51:00,333] [INFO] Target genome list was writen to GCF_014199265.1_ASM1419926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:00,348] [INFO] Task started: fastANI
[2024-01-24 13:51:00,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ce1492-e704-4910-8950-4f8559582166/GCF_014199265.1_ASM1419926v1_genomic.fna.gz --refList GCF_014199265.1_ASM1419926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199265.1_ASM1419926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:16,873] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:16,896] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:16,897] [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_014199265.1	s__Ochrobactrum_C daejeonensis	100.0	1517	1520	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	conclusive
GCA_900473915.1	s__Ochrobactrum sp900473915	84.5634	999	1520	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	-
GCA_900470195.1	s__Ochrobactrum sp900470195	84.4929	972	1520	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_008932435.1	s__Ochrobactrum pseudintermedium	84.4359	1010	1520	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_000182645.1	s__Ochrobactrum intermedium	84.219	979	1520	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_008932295.1	s__Ochrobactrum tritici	84.1694	982	1520	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_003550135.1	s__Ochrobactrum_B haematophila_B	83.9957	914	1520	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_000017405.1	s__Ochrobactrum anthropi	83.7277	1008	1520	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_902825325.1	s__Ochrobactrum sp003176975	83.5098	954	1520	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	-
GCA_012103075.1	s__Ochrobactrum cytisi	83.409	989	1520	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_006376685.1	s__Ochrobactrum_B teleogrylli	82.7929	871	1520	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	-
GCF_005938105.1	s__Ochrobactrum_B haematophila	82.5501	894	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	98.61	97.38	0.92	0.84	3	-
GCA_900465685.1	s__Ochrobactrum_B sp900465685	82.5457	877	1520	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_014138095.1	s__Ochrobactrum_B sp014138095	82.3701	913	1520	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_017512425.1	s__Hyphomicrobium sp017512425	76.1477	68	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183985.1	s__Dongia sp016183985	75.9818	90	1520	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:16,899] [INFO] GTDB search result was written to GCF_014199265.1_ASM1419926v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:16,899] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:16,903] [INFO] DFAST_QC result json was written to GCF_014199265.1_ASM1419926v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:16,903] [INFO] DFAST_QC completed!
[2024-01-24 13:51:16,903] [INFO] Total running time: 0h1m36s