[2023-06-16 19:05:46,690] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:05:46,694] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:05:46,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c2e86ef-8415-462d-b865-93207576f562/dqc_reference
[2023-06-16 19:05:47,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:05:47,890] [INFO] Task started: Prodigal
[2023-06-16 19:05:47,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcaead2a-9ed9-43fc-b84d-4a664d1e897c/GCA_003528245.1_ASM352824v1_genomic.fna.gz | prodigal -d GCA_003528245.1_ASM352824v1_genomic.fna/cds.fna -a GCA_003528245.1_ASM352824v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:05:57,200] [INFO] Task succeeded: Prodigal
[2023-06-16 19:05:57,200] [INFO] Task started: HMMsearch
[2023-06-16 19:05:57,200] [INFO] Running command: hmmsearch --tblout GCA_003528245.1_ASM352824v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c2e86ef-8415-462d-b865-93207576f562/dqc_reference/reference_markers.hmm GCA_003528245.1_ASM352824v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:05:57,401] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:05:57,402] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfcaead2a-9ed9-43fc-b84d-4a664d1e897c/GCA_003528245.1_ASM352824v1_genomic.fna.gz]
[2023-06-16 19:05:57,436] [INFO] Query marker FASTA was written to GCA_003528245.1_ASM352824v1_genomic.fna/markers.fasta
[2023-06-16 19:05:57,437] [INFO] Task started: Blastn
[2023-06-16 19:05:57,437] [INFO] Running command: blastn -query GCA_003528245.1_ASM352824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c2e86ef-8415-462d-b865-93207576f562/dqc_reference/reference_markers.fasta -out GCA_003528245.1_ASM352824v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:05:58,134] [INFO] Task succeeded: Blastn
[2023-06-16 19:05:58,141] [INFO] Selected 12 target genomes.
[2023-06-16 19:05:58,142] [INFO] Target genome list was writen to GCA_003528245.1_ASM352824v1_genomic.fna/target_genomes.txt
[2023-06-16 19:05:58,148] [INFO] Task started: fastANI
[2023-06-16 19:05:58,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcaead2a-9ed9-43fc-b84d-4a664d1e897c/GCA_003528245.1_ASM352824v1_genomic.fna.gz --refList GCA_003528245.1_ASM352824v1_genomic.fna/target_genomes.txt --output GCA_003528245.1_ASM352824v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:06:08,392] [INFO] Task succeeded: fastANI
[2023-06-16 19:06:08,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c2e86ef-8415-462d-b865-93207576f562/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:06:08,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c2e86ef-8415-462d-b865-93207576f562/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:06:08,403] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-06-16 19:06:08,403] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-16 19:06:08,404] [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 anthropi	strain=NCTC12168	GCA_900454235.1	529	529	type	True	99.2405	912	986	95	conclusive
Brucella anthropi	strain=ATCC 49188	GCA_000017405.1	529	529	type	True	99.2189	918	986	95	conclusive
Brucella tritici	strain=LMG 18957	GCA_008932295.1	94626	94626	type	True	91.251	830	986	95	below_threshold
Brucella pecoris	strain=08RB2639	GCA_006376675.1	867683	867683	type	True	88.7759	833	986	95	below_threshold
Brucella pecoris	strain=DSM 23868	GCA_014197065.1	867683	867683	type	True	88.7297	841	986	95	below_threshold
Brucella intermedia	strain=LMG 3301	GCA_000182645.1	94625	94625	suspected-type	True	87.7206	794	986	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	87.706	801	986	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	77.4509	170	986	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.2734	176	986	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.2734	176	986	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	76.8876	162	986	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	76.536	127	986	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:06:08,406] [INFO] DFAST Taxonomy check result was written to GCA_003528245.1_ASM352824v1_genomic.fna/tc_result.tsv
[2023-06-16 19:06:08,406] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:06:08,406] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:06:08,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c2e86ef-8415-462d-b865-93207576f562/dqc_reference/checkm_data
[2023-06-16 19:06:08,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:06:08,446] [INFO] Task started: CheckM
[2023-06-16 19:06:08,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003528245.1_ASM352824v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003528245.1_ASM352824v1_genomic.fna/checkm_input GCA_003528245.1_ASM352824v1_genomic.fna/checkm_result
[2023-06-16 19:06:40,003] [INFO] Task succeeded: CheckM
[2023-06-16 19:06:40,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:06:40,023] [INFO] ===== Completeness check finished =====
[2023-06-16 19:06:40,024] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:06:40,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003528245.1_ASM352824v1_genomic.fna/markers.fasta)
[2023-06-16 19:06:40,025] [INFO] Task started: Blastn
[2023-06-16 19:06:40,025] [INFO] Running command: blastn -query GCA_003528245.1_ASM352824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c2e86ef-8415-462d-b865-93207576f562/dqc_reference/reference_markers_gtdb.fasta -out GCA_003528245.1_ASM352824v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:06:41,214] [INFO] Task succeeded: Blastn
[2023-06-16 19:06:41,218] [INFO] Selected 10 target genomes.
[2023-06-16 19:06:41,218] [INFO] Target genome list was writen to GCA_003528245.1_ASM352824v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:06:41,234] [INFO] Task started: fastANI
[2023-06-16 19:06:41,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcaead2a-9ed9-43fc-b84d-4a664d1e897c/GCA_003528245.1_ASM352824v1_genomic.fna.gz --refList GCA_003528245.1_ASM352824v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003528245.1_ASM352824v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:06:51,627] [INFO] Task succeeded: fastANI
[2023-06-16 19:06:51,636] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:06:51,637] [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_000017405.1	s__Ochrobactrum anthropi	99.2189	918	986	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	conclusive
GCA_012103075.1	s__Ochrobactrum cytisi	95.3256	867	986	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_008932295.1	s__Ochrobactrum tritici	91.251	830	986	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	90.4414	834	986	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_012103035.1	s__Ochrobactrum oryzae	89.0979	780	986	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.03	98.38	0.88	0.83	3	-
GCF_006376675.1	s__Ochrobactrum pecoris	88.7759	833	986	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	-
GCF_000182645.1	s__Ochrobactrum intermedium	87.7108	795	986	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	-
GCA_900470195.1	s__Ochrobactrum sp900470195	87.4353	806	986	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_006345815.1	s__Ochrobactrum sp006345815	87.3584	783	986	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_900473915.1	s__Ochrobactrum sp900473915	87.2459	771	986	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	-
--------------------------------------------------------------------------------
[2023-06-16 19:06:51,639] [INFO] GTDB search result was written to GCA_003528245.1_ASM352824v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:06:51,639] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:06:51,643] [INFO] DFAST_QC result json was written to GCA_003528245.1_ASM352824v1_genomic.fna/dqc_result.json
[2023-06-16 19:06:51,644] [INFO] DFAST_QC completed!
[2023-06-16 19:06:51,644] [INFO] Total running time: 0h1m5s