[2024-01-24 14:22:17,273] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,275] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg761c5167-32cf-44e6-ad7e-52fa5fe367c3/dqc_reference
[2024-01-24 14:22:18,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,530] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg989996fb-d4dc-4394-9fe0-12d32aecec76/GCF_900696085.1_ERZ807199_genomic.fna.gz | prodigal -d GCF_900696085.1_ERZ807199_genomic.fna/cds.fna -a GCF_900696085.1_ERZ807199_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:46,373] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:46,373] [INFO] Task started: HMMsearch
[2024-01-24 14:22:46,374] [INFO] Running command: hmmsearch --tblout GCF_900696085.1_ERZ807199_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg761c5167-32cf-44e6-ad7e-52fa5fe367c3/dqc_reference/reference_markers.hmm GCF_900696085.1_ERZ807199_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:46,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:46,741] [INFO] Found 6/6 markers.
[2024-01-24 14:22:46,809] [INFO] Query marker FASTA was written to GCF_900696085.1_ERZ807199_genomic.fna/markers.fasta
[2024-01-24 14:22:46,810] [INFO] Task started: Blastn
[2024-01-24 14:22:46,810] [INFO] Running command: blastn -query GCF_900696085.1_ERZ807199_genomic.fna/markers.fasta -db /var/lib/cwl/stg761c5167-32cf-44e6-ad7e-52fa5fe367c3/dqc_reference/reference_markers.fasta -out GCF_900696085.1_ERZ807199_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:47,862] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:47,865] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:47,866] [INFO] Target genome list was writen to GCF_900696085.1_ERZ807199_genomic.fna/target_genomes.txt
[2024-01-24 14:22:47,872] [INFO] Task started: fastANI
[2024-01-24 14:22:47,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg989996fb-d4dc-4394-9fe0-12d32aecec76/GCF_900696085.1_ERZ807199_genomic.fna.gz --refList GCF_900696085.1_ERZ807199_genomic.fna/target_genomes.txt --output GCF_900696085.1_ERZ807199_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:32,309] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:32,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg761c5167-32cf-44e6-ad7e-52fa5fe367c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:32,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg761c5167-32cf-44e6-ad7e-52fa5fe367c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:32,323] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:32,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:32,323] [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 ivorense	strain=CI-1B	GCA_900696085.2	2511166	2511166	type	True	100.0	3108	3112	95	conclusive
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	88.6275	2161	3112	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	88.6004	2087	3112	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	88.5592	2165	3112	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	88.3045	2063	3112	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	88.2447	1959	3112	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	87.948	2096	3112	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	87.8655	2017	3112	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	87.8255	1913	3112	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	87.7561	1907	3112	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	87.7528	2082	3112	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	87.6721	2017	3112	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	87.6568	2046	3112	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	87.5511	1938	3112	95	below_threshold
Bradyrhizobium macuxiense	strain=BR 10303	GCA_001542415.1	1755647	1755647	type	True	86.9716	1925	3112	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:32,325] [INFO] DFAST Taxonomy check result was written to GCF_900696085.1_ERZ807199_genomic.fna/tc_result.tsv
[2024-01-24 14:23:32,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:32,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:32,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg761c5167-32cf-44e6-ad7e-52fa5fe367c3/dqc_reference/checkm_data
[2024-01-24 14:23:32,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:32,411] [INFO] Task started: CheckM
[2024-01-24 14:23:32,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900696085.1_ERZ807199_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900696085.1_ERZ807199_genomic.fna/checkm_input GCF_900696085.1_ERZ807199_genomic.fna/checkm_result
[2024-01-24 14:24:52,205] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:52,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:52,231] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:52,231] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:52,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900696085.1_ERZ807199_genomic.fna/markers.fasta)
[2024-01-24 14:24:52,232] [INFO] Task started: Blastn
[2024-01-24 14:24:52,233] [INFO] Running command: blastn -query GCF_900696085.1_ERZ807199_genomic.fna/markers.fasta -db /var/lib/cwl/stg761c5167-32cf-44e6-ad7e-52fa5fe367c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900696085.1_ERZ807199_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:54,550] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:54,555] [INFO] Selected 17 target genomes.
[2024-01-24 14:24:54,555] [INFO] Target genome list was writen to GCF_900696085.1_ERZ807199_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:54,590] [INFO] Task started: fastANI
[2024-01-24 14:24:54,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg989996fb-d4dc-4394-9fe0-12d32aecec76/GCF_900696085.1_ERZ807199_genomic.fna.gz --refList GCF_900696085.1_ERZ807199_genomic.fna/target_genomes_gtdb.txt --output GCF_900696085.1_ERZ807199_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:41,680] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:41,699] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:41,700] [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_900696085.1	s__Bradyrhizobium ivorense	100.0	3108	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.20	96.86	0.90	0.88	3	conclusive
GCF_018130505.1	s__Bradyrhizobium tropiciagri_B	89.3816	1950	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379145.1	s__Bradyrhizobium elkanii	88.5453	2168	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.89	95.57	0.89	0.83	18	-
GCF_015291625.1	s__Bradyrhizobium sp015291625	88.4254	2200	3112	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	88.4135	2085	3112	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	88.3582	1945	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189245.1	s__Bradyrhizobium pachyrhizi	88.2976	2064	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	-
GCF_001982635.1	s__Bradyrhizobium mercantei	88.2289	1961	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015624485.1	s__Bradyrhizobium sp015624485	88.2178	1891	3112	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	88.1346	1971	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	-
GCF_016839165.1	s__Bradyrhizobium sp003020075	88.0076	1857	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.93	99.86	0.97	0.95	16	-
GCF_013373795.1	s__Bradyrhizobium quebecense	87.909	2021	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
GCF_002831585.1	s__Bradyrhizobium sp002831585	87.8965	1879	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.70	98.62	0.95	0.93	5	-
GCF_001189235.2	s__Bradyrhizobium embrapense	87.6798	2016	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001238275.1	s__Bradyrhizobium viridifuturi	87.6734	2042	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
GCF_001542415.1	s__Bradyrhizobium macuxiense	86.9742	1922	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130215.1	s__Bradyrhizobium jicamae_A	86.7656	1817	3112	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.26	99.26	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:41,701] [INFO] GTDB search result was written to GCF_900696085.1_ERZ807199_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:41,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:41,709] [INFO] DFAST_QC result json was written to GCF_900696085.1_ERZ807199_genomic.fna/dqc_result.json
[2024-01-24 14:25:41,710] [INFO] DFAST_QC completed!
[2024-01-24 14:25:41,710] [INFO] Total running time: 0h3m24s