[2024-01-25 18:11:50,799] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:50,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:50,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg288e8576-8241-4d5d-8a5a-c98db93d7b11/dqc_reference
[2024-01-25 18:11:51,985] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:51,985] [INFO] Task started: Prodigal
[2024-01-25 18:11:51,986] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb839302-a62e-4350-9257-caa959688001/GCF_020889785.1_ASM2088978v1_genomic.fna.gz | prodigal -d GCF_020889785.1_ASM2088978v1_genomic.fna/cds.fna -a GCF_020889785.1_ASM2088978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:13,314] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:13,315] [INFO] Task started: HMMsearch
[2024-01-25 18:12:13,315] [INFO] Running command: hmmsearch --tblout GCF_020889785.1_ASM2088978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg288e8576-8241-4d5d-8a5a-c98db93d7b11/dqc_reference/reference_markers.hmm GCF_020889785.1_ASM2088978v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:13,618] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:13,619] [INFO] Found 6/6 markers.
[2024-01-25 18:12:13,682] [INFO] Query marker FASTA was written to GCF_020889785.1_ASM2088978v1_genomic.fna/markers.fasta
[2024-01-25 18:12:13,683] [INFO] Task started: Blastn
[2024-01-25 18:12:13,683] [INFO] Running command: blastn -query GCF_020889785.1_ASM2088978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg288e8576-8241-4d5d-8a5a-c98db93d7b11/dqc_reference/reference_markers.fasta -out GCF_020889785.1_ASM2088978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:14,683] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:14,686] [INFO] Selected 11 target genomes.
[2024-01-25 18:12:14,686] [INFO] Target genome list was writen to GCF_020889785.1_ASM2088978v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:14,695] [INFO] Task started: fastANI
[2024-01-25 18:12:14,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb839302-a62e-4350-9257-caa959688001/GCF_020889785.1_ASM2088978v1_genomic.fna.gz --refList GCF_020889785.1_ASM2088978v1_genomic.fna/target_genomes.txt --output GCF_020889785.1_ASM2088978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:41,151] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:41,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg288e8576-8241-4d5d-8a5a-c98db93d7b11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:41,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg288e8576-8241-4d5d-8a5a-c98db93d7b11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:41,160] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:12:41,160] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:12:41,160] [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 acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	100.0	2635	2653	95	inconclusive
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	95.7406	2136	2653	95	inconclusive
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	95.1257	2043	2653	95	inconclusive
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	90.9713	2077	2653	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	90.961	2080	2653	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	90.9357	2141	2653	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	90.862	1966	2653	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	90.567	2062	2653	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	90.4814	2082	2653	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	90.321	2020	2653	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	90.0463	1997	2653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:41,162] [INFO] DFAST Taxonomy check result was written to GCF_020889785.1_ASM2088978v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:41,162] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:41,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:41,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg288e8576-8241-4d5d-8a5a-c98db93d7b11/dqc_reference/checkm_data
[2024-01-25 18:12:41,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:41,241] [INFO] Task started: CheckM
[2024-01-25 18:12:41,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020889785.1_ASM2088978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020889785.1_ASM2088978v1_genomic.fna/checkm_input GCF_020889785.1_ASM2088978v1_genomic.fna/checkm_result
[2024-01-25 18:13:44,297] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:44,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:44,317] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:44,317] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:44,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020889785.1_ASM2088978v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:44,318] [INFO] Task started: Blastn
[2024-01-25 18:13:44,318] [INFO] Running command: blastn -query GCF_020889785.1_ASM2088978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg288e8576-8241-4d5d-8a5a-c98db93d7b11/dqc_reference/reference_markers_gtdb.fasta -out GCF_020889785.1_ASM2088978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:46,479] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:46,482] [INFO] Selected 16 target genomes.
[2024-01-25 18:13:46,482] [INFO] Target genome list was writen to GCF_020889785.1_ASM2088978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:46,502] [INFO] Task started: fastANI
[2024-01-25 18:13:46,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb839302-a62e-4350-9257-caa959688001/GCF_020889785.1_ASM2088978v1_genomic.fna.gz --refList GCF_020889785.1_ASM2088978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020889785.1_ASM2088978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:23,691] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:23,702] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:14:23,703] [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_018130545.1	s__Bradyrhizobium tropiciagri_A	91.5916	2005	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105845.1	s__Bradyrhizobium erythrophlei_E	91.2513	2032	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	-
GCF_001982635.1	s__Bradyrhizobium mercantei	91.2154	1949	2653	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	91.1752	2177	2653	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	91.0669	2063	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001755.1	s__Bradyrhizobium sp003001755	91.0174	1947	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013373795.1	s__Bradyrhizobium quebecense	90.9785	2073	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
GCA_001238275.1	s__Bradyrhizobium viridifuturi	90.965	2077	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
GCF_001189235.2	s__Bradyrhizobium embrapense	90.9558	2138	2653	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	90.8367	2011	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002532045.1	s__Bradyrhizobium sp002532045	90.7984	2086	2653	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	90.7473	1928	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.93	99.86	0.97	0.95	16	-
GCF_000379145.1	s__Bradyrhizobium elkanii	90.5506	2064	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.89	95.57	0.89	0.83	18	-
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	90.3339	2018	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
GCF_002831585.1	s__Bradyrhizobium sp002831585	90.0049	1887	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.70	98.62	0.95	0.93	5	-
GCF_011516645.2	s__Bradyrhizobium septentrionale	89.9838	2002	2653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.80	95.80	0.83	0.78	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:23,705] [INFO] GTDB search result was written to GCF_020889785.1_ASM2088978v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:23,706] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:23,709] [INFO] DFAST_QC result json was written to GCF_020889785.1_ASM2088978v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:23,709] [INFO] DFAST_QC completed!
[2024-01-25 18:14:23,710] [INFO] Total running time: 0h2m33s