[2024-01-24 12:39:40,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:40,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:40,322] [INFO] DQC Reference Directory: /var/lib/cwl/stgea15a3ae-c609-4eac-96d3-df672c9383b4/dqc_reference
[2024-01-24 12:39:41,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:41,661] [INFO] Task started: Prodigal
[2024-01-24 12:39:41,662] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc9fc9fc-183e-4472-91bb-d1e16884255a/GCF_001969825.1_ASM196982v1_genomic.fna.gz | prodigal -d GCF_001969825.1_ASM196982v1_genomic.fna/cds.fna -a GCF_001969825.1_ASM196982v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:08,116] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:08,117] [INFO] Task started: HMMsearch
[2024-01-24 12:40:08,117] [INFO] Running command: hmmsearch --tblout GCF_001969825.1_ASM196982v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea15a3ae-c609-4eac-96d3-df672c9383b4/dqc_reference/reference_markers.hmm GCF_001969825.1_ASM196982v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:08,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:08,533] [INFO] Found 6/6 markers.
[2024-01-24 12:40:08,601] [INFO] Query marker FASTA was written to GCF_001969825.1_ASM196982v1_genomic.fna/markers.fasta
[2024-01-24 12:40:08,602] [INFO] Task started: Blastn
[2024-01-24 12:40:08,602] [INFO] Running command: blastn -query GCF_001969825.1_ASM196982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea15a3ae-c609-4eac-96d3-df672c9383b4/dqc_reference/reference_markers.fasta -out GCF_001969825.1_ASM196982v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:09,692] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:09,699] [INFO] Selected 12 target genomes.
[2024-01-24 12:40:09,700] [INFO] Target genome list was writen to GCF_001969825.1_ASM196982v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:09,705] [INFO] Task started: fastANI
[2024-01-24 12:40:09,705] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc9fc9fc-183e-4472-91bb-d1e16884255a/GCF_001969825.1_ASM196982v1_genomic.fna.gz --refList GCF_001969825.1_ASM196982v1_genomic.fna/target_genomes.txt --output GCF_001969825.1_ASM196982v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:41,587] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:41,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea15a3ae-c609-4eac-96d3-df672c9383b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:41,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea15a3ae-c609-4eac-96d3-df672c9383b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:41,604] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:41,605] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:41,605] [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 pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	95.3269	2345	2820	95	conclusive
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	94.7218	2398	2820	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	94.7212	2327	2820	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	94.6942	2398	2820	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	91.0163	2054	2820	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	90.9489	2205	2820	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	90.8942	2056	2820	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	90.8648	2120	2820	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	90.8015	2114	2820	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	90.6451	2125	2820	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	90.5797	1990	2820	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	90.5475	2022	2820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,607] [INFO] DFAST Taxonomy check result was written to GCF_001969825.1_ASM196982v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:41,607] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:41,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:41,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea15a3ae-c609-4eac-96d3-df672c9383b4/dqc_reference/checkm_data
[2024-01-24 12:40:41,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:41,691] [INFO] Task started: CheckM
[2024-01-24 12:40:41,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001969825.1_ASM196982v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001969825.1_ASM196982v1_genomic.fna/checkm_input GCF_001969825.1_ASM196982v1_genomic.fna/checkm_result
[2024-01-24 12:41:52,040] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:52,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:52,068] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:52,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:52,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001969825.1_ASM196982v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:52,069] [INFO] Task started: Blastn
[2024-01-24 12:41:52,070] [INFO] Running command: blastn -query GCF_001969825.1_ASM196982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea15a3ae-c609-4eac-96d3-df672c9383b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_001969825.1_ASM196982v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:54,241] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:54,246] [INFO] Selected 15 target genomes.
[2024-01-24 12:41:54,246] [INFO] Target genome list was writen to GCF_001969825.1_ASM196982v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:54,276] [INFO] Task started: fastANI
[2024-01-24 12:41:54,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc9fc9fc-183e-4472-91bb-d1e16884255a/GCF_001969825.1_ASM196982v1_genomic.fna.gz --refList GCF_001969825.1_ASM196982v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001969825.1_ASM196982v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:33,994] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:34,013] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:34,013] [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_001189245.1	s__Bradyrhizobium pachyrhizi	95.3284	2344	2820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.66	95.38	0.85	0.82	8	conclusive
GCF_000379145.1	s__Bradyrhizobium elkanii	94.7071	2396	2820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.89	95.57	0.89	0.83	18	-
GCF_001982635.1	s__Bradyrhizobium mercantei	91.1583	2073	2820	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	91.1432	2087	2820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	-
GCF_001189845.1	s__Bradyrhizobium tropiciagri	90.9397	2206	2820	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	90.8605	2121	2820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
GCF_007993935.1	s__Bradyrhizobium macuxiense_A	90.8429	2083	2820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130545.1	s__Bradyrhizobium tropiciagri_A	90.8394	2033	2820	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	90.8016	2114	2820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
GCF_015291625.1	s__Bradyrhizobium sp015291625	90.7969	2214	2820	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	90.6891	2004	2820	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	90.6454	2125	2820	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	90.5412	2111	2820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516645.2	s__Bradyrhizobium septentrionale	90.3363	2190	2820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.80	95.80	0.83	0.78	5	-
GCF_018130505.1	s__Bradyrhizobium tropiciagri_B	88.3595	1852	2820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:34,016] [INFO] GTDB search result was written to GCF_001969825.1_ASM196982v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:34,017] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:34,022] [INFO] DFAST_QC result json was written to GCF_001969825.1_ASM196982v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:34,022] [INFO] DFAST_QC completed!
[2024-01-24 12:42:34,022] [INFO] Total running time: 0h2m54s