[2024-01-24 14:47:19,722] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:19,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:19,725] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1372a3a-92d9-4a37-a840-3b78747c46db/dqc_reference
[2024-01-24 14:47:21,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:21,181] [INFO] Task started: Prodigal
[2024-01-24 14:47:21,182] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b0bf50c-f169-4c84-9543-32773b2a88a5/GCF_008801705.1_ASM880170v1_genomic.fna.gz | prodigal -d GCF_008801705.1_ASM880170v1_genomic.fna/cds.fna -a GCF_008801705.1_ASM880170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:37,580] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:37,580] [INFO] Task started: HMMsearch
[2024-01-24 14:47:37,580] [INFO] Running command: hmmsearch --tblout GCF_008801705.1_ASM880170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1372a3a-92d9-4a37-a840-3b78747c46db/dqc_reference/reference_markers.hmm GCF_008801705.1_ASM880170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:37,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:37,930] [INFO] Found 6/6 markers.
[2024-01-24 14:47:37,978] [INFO] Query marker FASTA was written to GCF_008801705.1_ASM880170v1_genomic.fna/markers.fasta
[2024-01-24 14:47:37,979] [INFO] Task started: Blastn
[2024-01-24 14:47:37,979] [INFO] Running command: blastn -query GCF_008801705.1_ASM880170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1372a3a-92d9-4a37-a840-3b78747c46db/dqc_reference/reference_markers.fasta -out GCF_008801705.1_ASM880170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:38,750] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:38,754] [INFO] Selected 12 target genomes.
[2024-01-24 14:47:38,754] [INFO] Target genome list was writen to GCF_008801705.1_ASM880170v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:38,760] [INFO] Task started: fastANI
[2024-01-24 14:47:38,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b0bf50c-f169-4c84-9543-32773b2a88a5/GCF_008801705.1_ASM880170v1_genomic.fna.gz --refList GCF_008801705.1_ASM880170v1_genomic.fna/target_genomes.txt --output GCF_008801705.1_ASM880170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:51,832] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:51,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1372a3a-92d9-4a37-a840-3b78747c46db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:51,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1372a3a-92d9-4a37-a840-3b78747c46db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:51,844] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:51,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:51,844] [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 pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	100.0	1703	1706	95	conclusive
Brucella pituitosa	strain=CCUG 50899	GCA_003049685.2	571256	571256	type	True	99.9881	1704	1706	95	conclusive
Brucella grignonensis	strain=OgA9a	GCA_002252505.1	94627	94627	type	True	92.932	1243	1706	95	below_threshold
[Ochrobactrum] quorumnocens	strain=A44	GCA_002278035.1	271865	271865	type	True	88.7795	1306	1706	95	below_threshold
Brucella rhizosphaerae	strain=PR17	GCA_002252475.1	571254	571254	type	True	87.2776	1276	1706	95	below_threshold
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	85.8681	1214	1706	95	below_threshold
Brucella gallinifaecis	strain=ISO 196	GCA_006476605.1	215590	215590	type	True	82.6867	757	1706	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	78.4198	299	1706	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	78.4064	300	1706	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	77.2002	220	1706	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.437	118	1706	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.437	118	1706	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:51,851] [INFO] DFAST Taxonomy check result was written to GCF_008801705.1_ASM880170v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:51,852] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:51,853] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:51,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1372a3a-92d9-4a37-a840-3b78747c46db/dqc_reference/checkm_data
[2024-01-24 14:47:51,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:51,919] [INFO] Task started: CheckM
[2024-01-24 14:47:51,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008801705.1_ASM880170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008801705.1_ASM880170v1_genomic.fna/checkm_input GCF_008801705.1_ASM880170v1_genomic.fna/checkm_result
[2024-01-24 14:48:40,894] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:40,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:40,919] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:40,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:40,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008801705.1_ASM880170v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:40,920] [INFO] Task started: Blastn
[2024-01-24 14:48:40,920] [INFO] Running command: blastn -query GCF_008801705.1_ASM880170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1372a3a-92d9-4a37-a840-3b78747c46db/dqc_reference/reference_markers_gtdb.fasta -out GCF_008801705.1_ASM880170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:41,909] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:41,912] [INFO] Selected 9 target genomes.
[2024-01-24 14:48:41,912] [INFO] Target genome list was writen to GCF_008801705.1_ASM880170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:41,919] [INFO] Task started: fastANI
[2024-01-24 14:48:41,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b0bf50c-f169-4c84-9543-32773b2a88a5/GCF_008801705.1_ASM880170v1_genomic.fna.gz --refList GCF_008801705.1_ASM880170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008801705.1_ASM880170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:54,887] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:54,895] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:54,896] [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_003049685.1	s__Ochrobactrum_A pituitosa	99.9881	1704	1706	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	conclusive
GCF_002252505.1	s__Ochrobactrum_A grignonensis	92.932	1243	1706	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_002278035.1	s__Ochrobactrum_A quorumnocens	88.7795	1306	1706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_A	95.0	97.19	96.78	0.85	0.82	5	-
GCF_002252475.1	s__Ochrobactrum_A rhizosphaerae	87.2776	1276	1706	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_004368705.1	s__Ochrobactrum_A sp004368705	86.6622	1266	1706	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_002252525.1	s__Ochrobactrum_A pseudogrignonensis	85.8647	1214	1706	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	85.3282	1154	1706	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_014397025.1	s__Ochrobactrum_A sp014397025	83.5274	951	1706	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_006476605.1	s__Ochrobactrum_A gallinifaecis	82.6867	757	1706	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 14:48:54,897] [INFO] GTDB search result was written to GCF_008801705.1_ASM880170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:54,898] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:54,901] [INFO] DFAST_QC result json was written to GCF_008801705.1_ASM880170v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:54,901] [INFO] DFAST_QC completed!
[2024-01-24 14:48:54,901] [INFO] Total running time: 0h1m35s