[2024-01-24 13:49:45,118] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,125] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc8d7bad-c7c4-4055-93a2-460acacb1c9f/dqc_reference
[2024-01-24 13:49:46,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,513] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,513] [INFO] Running command: gunzip -c /var/lib/cwl/stg476d5449-00b5-455c-bcce-1143f7ecda3a/GCF_003049685.1_ASM304968v2_genomic.fna.gz | prodigal -d GCF_003049685.1_ASM304968v2_genomic.fna/cds.fna -a GCF_003049685.1_ASM304968v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:04,805] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:04,805] [INFO] Task started: HMMsearch
[2024-01-24 13:50:04,805] [INFO] Running command: hmmsearch --tblout GCF_003049685.1_ASM304968v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc8d7bad-c7c4-4055-93a2-460acacb1c9f/dqc_reference/reference_markers.hmm GCF_003049685.1_ASM304968v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:05,134] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:05,136] [INFO] Found 6/6 markers.
[2024-01-24 13:50:05,185] [INFO] Query marker FASTA was written to GCF_003049685.1_ASM304968v2_genomic.fna/markers.fasta
[2024-01-24 13:50:05,186] [INFO] Task started: Blastn
[2024-01-24 13:50:05,186] [INFO] Running command: blastn -query GCF_003049685.1_ASM304968v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc8d7bad-c7c4-4055-93a2-460acacb1c9f/dqc_reference/reference_markers.fasta -out GCF_003049685.1_ASM304968v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:05,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:05,911] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:05,911] [INFO] Target genome list was writen to GCF_003049685.1_ASM304968v2_genomic.fna/target_genomes.txt
[2024-01-24 13:50:05,917] [INFO] Task started: fastANI
[2024-01-24 13:50:05,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg476d5449-00b5-455c-bcce-1143f7ecda3a/GCF_003049685.1_ASM304968v2_genomic.fna.gz --refList GCF_003049685.1_ASM304968v2_genomic.fna/target_genomes.txt --output GCF_003049685.1_ASM304968v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:18,542] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:18,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc8d7bad-c7c4-4055-93a2-460acacb1c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:18,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc8d7bad-c7c4-4055-93a2-460acacb1c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:18,561] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:18,561] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:18,562] [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_003049685.2	571256	571256	type	True	100.0	1834	1835	95	conclusive
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	99.9744	1697	1835	95	conclusive
Brucella grignonensis	strain=OgA9a	GCA_002252505.1	94627	94627	type	True	92.9683	1237	1835	95	below_threshold
[Ochrobactrum] quorumnocens	strain=A44	GCA_002278035.1	271865	271865	type	True	88.899	1299	1835	95	below_threshold
Brucella rhizosphaerae	strain=PR17	GCA_002252475.1	571254	571254	type	True	87.3906	1267	1835	95	below_threshold
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	85.9906	1206	1835	95	below_threshold
Brucella gallinifaecis	strain=ISO 196	GCA_006476605.1	215590	215590	type	True	82.5557	774	1835	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	78.646	314	1835	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	78.6324	314	1835	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	77.2779	221	1835	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.3326	124	1835	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.3183	125	1835	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:18,563] [INFO] DFAST Taxonomy check result was written to GCF_003049685.1_ASM304968v2_genomic.fna/tc_result.tsv
[2024-01-24 13:50:18,564] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:18,564] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:18,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc8d7bad-c7c4-4055-93a2-460acacb1c9f/dqc_reference/checkm_data
[2024-01-24 13:50:18,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:18,617] [INFO] Task started: CheckM
[2024-01-24 13:50:18,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003049685.1_ASM304968v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003049685.1_ASM304968v2_genomic.fna/checkm_input GCF_003049685.1_ASM304968v2_genomic.fna/checkm_result
[2024-01-24 13:51:10,169] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:10,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:10,193] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:10,193] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:10,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003049685.1_ASM304968v2_genomic.fna/markers.fasta)
[2024-01-24 13:51:10,194] [INFO] Task started: Blastn
[2024-01-24 13:51:10,194] [INFO] Running command: blastn -query GCF_003049685.1_ASM304968v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc8d7bad-c7c4-4055-93a2-460acacb1c9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003049685.1_ASM304968v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:11,290] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:11,294] [INFO] Selected 9 target genomes.
[2024-01-24 13:51:11,294] [INFO] Target genome list was writen to GCF_003049685.1_ASM304968v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:11,318] [INFO] Task started: fastANI
[2024-01-24 13:51:11,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg476d5449-00b5-455c-bcce-1143f7ecda3a/GCF_003049685.1_ASM304968v2_genomic.fna.gz --refList GCF_003049685.1_ASM304968v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003049685.1_ASM304968v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:22,670] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:22,686] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:22,687] [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	100.0	1833	1835	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	92.9833	1236	1835	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	88.8946	1298	1835	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	87.3906	1267	1835	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	86.7376	1260	1835	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	85.9805	1208	1835	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	85.4291	1140	1835	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	83.6223	956	1835	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	82.5663	773	1835	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 13:51:22,689] [INFO] GTDB search result was written to GCF_003049685.1_ASM304968v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:22,690] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:22,698] [INFO] DFAST_QC result json was written to GCF_003049685.1_ASM304968v2_genomic.fna/dqc_result.json
[2024-01-24 13:51:22,698] [INFO] DFAST_QC completed!
[2024-01-24 13:51:22,699] [INFO] Total running time: 0h1m38s