[2024-01-25 18:42:20,631] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:20,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:20,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg82ba78ef-9368-47a3-a863-ed462a8c75ce/dqc_reference
[2024-01-25 18:42:21,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:21,797] [INFO] Task started: Prodigal
[2024-01-25 18:42:21,797] [INFO] Running command: gunzip -c /var/lib/cwl/stgb40e0a99-cc22-48d3-9283-6046ed538322/GCF_013373795.3_ASM1337379v3_genomic.fna.gz | prodigal -d GCF_013373795.3_ASM1337379v3_genomic.fna/cds.fna -a GCF_013373795.3_ASM1337379v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:46,247] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:46,248] [INFO] Task started: HMMsearch
[2024-01-25 18:42:46,248] [INFO] Running command: hmmsearch --tblout GCF_013373795.3_ASM1337379v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82ba78ef-9368-47a3-a863-ed462a8c75ce/dqc_reference/reference_markers.hmm GCF_013373795.3_ASM1337379v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:46,563] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:46,564] [INFO] Found 6/6 markers.
[2024-01-25 18:42:46,628] [INFO] Query marker FASTA was written to GCF_013373795.3_ASM1337379v3_genomic.fna/markers.fasta
[2024-01-25 18:42:46,629] [INFO] Task started: Blastn
[2024-01-25 18:42:46,629] [INFO] Running command: blastn -query GCF_013373795.3_ASM1337379v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg82ba78ef-9368-47a3-a863-ed462a8c75ce/dqc_reference/reference_markers.fasta -out GCF_013373795.3_ASM1337379v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:47,640] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:47,644] [INFO] Selected 10 target genomes.
[2024-01-25 18:42:47,644] [INFO] Target genome list was writen to GCF_013373795.3_ASM1337379v3_genomic.fna/target_genomes.txt
[2024-01-25 18:42:47,648] [INFO] Task started: fastANI
[2024-01-25 18:42:47,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgb40e0a99-cc22-48d3-9283-6046ed538322/GCF_013373795.3_ASM1337379v3_genomic.fna.gz --refList GCF_013373795.3_ASM1337379v3_genomic.fna/target_genomes.txt --output GCF_013373795.3_ASM1337379v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:17,192] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:17,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82ba78ef-9368-47a3-a863-ed462a8c75ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:17,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82ba78ef-9368-47a3-a863-ed462a8c75ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:17,200] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:17,200] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:17,200] [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
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	100.0	3052	3056	95	conclusive
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	94.3044	2126	3056	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	92.025	2186	3056	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	91.2128	2318	3056	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	91.1669	2061	3056	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	91.1587	2185	3056	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	90.9214	2064	3056	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	90.9042	2052	3056	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	90.885	2216	3056	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	90.868	2200	3056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:17,202] [INFO] DFAST Taxonomy check result was written to GCF_013373795.3_ASM1337379v3_genomic.fna/tc_result.tsv
[2024-01-25 18:43:17,202] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:17,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:17,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82ba78ef-9368-47a3-a863-ed462a8c75ce/dqc_reference/checkm_data
[2024-01-25 18:43:17,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:17,287] [INFO] Task started: CheckM
[2024-01-25 18:43:17,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013373795.3_ASM1337379v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013373795.3_ASM1337379v3_genomic.fna/checkm_input GCF_013373795.3_ASM1337379v3_genomic.fna/checkm_result
[2024-01-25 18:44:31,629] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:31,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:31,655] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:31,655] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:31,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013373795.3_ASM1337379v3_genomic.fna/markers.fasta)
[2024-01-25 18:44:31,657] [INFO] Task started: Blastn
[2024-01-25 18:44:31,657] [INFO] Running command: blastn -query GCF_013373795.3_ASM1337379v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg82ba78ef-9368-47a3-a863-ed462a8c75ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_013373795.3_ASM1337379v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:33,850] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:33,853] [INFO] Selected 10 target genomes.
[2024-01-25 18:44:33,853] [INFO] Target genome list was writen to GCF_013373795.3_ASM1337379v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:33,860] [INFO] Task started: fastANI
[2024-01-25 18:44:33,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgb40e0a99-cc22-48d3-9283-6046ed538322/GCF_013373795.3_ASM1337379v3_genomic.fna.gz --refList GCF_013373795.3_ASM1337379v3_genomic.fna/target_genomes_gtdb.txt --output GCF_013373795.3_ASM1337379v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:01,029] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:01,036] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:01,036] [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_013373795.1	s__Bradyrhizobium quebecense	99.9933	2997	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	conclusive
GCF_900105845.1	s__Bradyrhizobium erythrophlei_E	95.1508	2285	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	-
GCF_002532045.1	s__Bradyrhizobium sp002532045	93.0883	2293	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291625.1	s__Bradyrhizobium sp015291625	92.2925	2318	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189235.2	s__Bradyrhizobium embrapense	92.0183	2187	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993935.1	s__Bradyrhizobium macuxiense_A	91.3928	2213	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908235.1	s__Bradyrhizobium sp001908235	91.2657	2098	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189845.1	s__Bradyrhizobium tropiciagri	91.1538	2185	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839165.1	s__Bradyrhizobium sp003020075	91.0762	2066	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.93	99.86	0.97	0.95	16	-
GCF_018130545.1	s__Bradyrhizobium tropiciagri_A	91.0227	2108	3056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:01,038] [INFO] GTDB search result was written to GCF_013373795.3_ASM1337379v3_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:01,038] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:01,042] [INFO] DFAST_QC result json was written to GCF_013373795.3_ASM1337379v3_genomic.fna/dqc_result.json
[2024-01-25 18:45:01,042] [INFO] DFAST_QC completed!
[2024-01-25 18:45:01,042] [INFO] Total running time: 0h2m40s