[2024-01-25 20:20:20,836] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:20,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:20,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b30a948-2aeb-4048-aa9f-c1f4e371c831/dqc_reference
[2024-01-25 20:20:21,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:21,951] [INFO] Task started: Prodigal
[2024-01-25 20:20:21,951] [INFO] Running command: gunzip -c /var/lib/cwl/stgee9cb9fe-bb92-470a-b398-2239cfd58ee5/GCF_020889705.1_ASM2088970v1_genomic.fna.gz | prodigal -d GCF_020889705.1_ASM2088970v1_genomic.fna/cds.fna -a GCF_020889705.1_ASM2088970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:45,525] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:45,525] [INFO] Task started: HMMsearch
[2024-01-25 20:20:45,526] [INFO] Running command: hmmsearch --tblout GCF_020889705.1_ASM2088970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b30a948-2aeb-4048-aa9f-c1f4e371c831/dqc_reference/reference_markers.hmm GCF_020889705.1_ASM2088970v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:45,927] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:45,928] [INFO] Found 6/6 markers.
[2024-01-25 20:20:46,000] [INFO] Query marker FASTA was written to GCF_020889705.1_ASM2088970v1_genomic.fna/markers.fasta
[2024-01-25 20:20:46,000] [INFO] Task started: Blastn
[2024-01-25 20:20:46,000] [INFO] Running command: blastn -query GCF_020889705.1_ASM2088970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b30a948-2aeb-4048-aa9f-c1f4e371c831/dqc_reference/reference_markers.fasta -out GCF_020889705.1_ASM2088970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:46,928] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:46,934] [INFO] Selected 17 target genomes.
[2024-01-25 20:20:46,934] [INFO] Target genome list was writen to GCF_020889705.1_ASM2088970v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:46,943] [INFO] Task started: fastANI
[2024-01-25 20:20:46,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgee9cb9fe-bb92-470a-b398-2239cfd58ee5/GCF_020889705.1_ASM2088970v1_genomic.fna.gz --refList GCF_020889705.1_ASM2088970v1_genomic.fna/target_genomes.txt --output GCF_020889705.1_ASM2088970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:20,101] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:20,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b30a948-2aeb-4048-aa9f-c1f4e371c831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:20,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b30a948-2aeb-4048-aa9f-c1f4e371c831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:20,112] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:21:20,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:20,112] [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 altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	100.0	2938	2966	95	conclusive
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	94.3199	2133	2966	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	92.641	2229	2966	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	91.9222	2114	2966	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	90.964	1981	2966	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	90.828	2073	2966	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	90.7655	2150	2966	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	90.6566	2024	2966	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	90.5746	2020	2966	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	90.5375	2076	2966	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	90.5356	2082	2966	95	below_threshold
Bradyrhizobium campsiandrae	strain=INPA 394B	GCA_014529705.1	1729892	1729892	type	True	82.6378	1373	2966	95	below_threshold
Afipia carboxidovorans	strain=OM5	GCA_000218565.1	40137	40137	type	True	79.5045	553	2966	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	77.0618	384	2966	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	76.7963	317	2966	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	76.7504	344	2966	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.3779	229	2966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:20,114] [INFO] DFAST Taxonomy check result was written to GCF_020889705.1_ASM2088970v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:20,114] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:20,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:20,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b30a948-2aeb-4048-aa9f-c1f4e371c831/dqc_reference/checkm_data
[2024-01-25 20:21:20,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:20,206] [INFO] Task started: CheckM
[2024-01-25 20:21:20,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020889705.1_ASM2088970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020889705.1_ASM2088970v1_genomic.fna/checkm_input GCF_020889705.1_ASM2088970v1_genomic.fna/checkm_result
[2024-01-25 20:22:26,997] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:26,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:27,045] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:27,045] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:27,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020889705.1_ASM2088970v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:27,047] [INFO] Task started: Blastn
[2024-01-25 20:22:27,047] [INFO] Running command: blastn -query GCF_020889705.1_ASM2088970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b30a948-2aeb-4048-aa9f-c1f4e371c831/dqc_reference/reference_markers_gtdb.fasta -out GCF_020889705.1_ASM2088970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:28,838] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:28,841] [INFO] Selected 19 target genomes.
[2024-01-25 20:22:28,841] [INFO] Target genome list was writen to GCF_020889705.1_ASM2088970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:28,861] [INFO] Task started: fastANI
[2024-01-25 20:22:28,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgee9cb9fe-bb92-470a-b398-2239cfd58ee5/GCF_020889705.1_ASM2088970v1_genomic.fna.gz --refList GCF_020889705.1_ASM2088970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020889705.1_ASM2088970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:01,718] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:01,729] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:01,730] [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_900105845.1	s__Bradyrhizobium erythrophlei_E	95.3321	2217	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	conclusive
GCF_013373795.1	s__Bradyrhizobium quebecense	94.3183	2150	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
GCF_002532045.1	s__Bradyrhizobium sp002532045	93.1505	2111	2966	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	92.0161	2224	2966	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	91.9219	2114	2966	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	91.154	2095	2966	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	91.1179	1994	2966	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	90.9961	1983	2966	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	90.7645	2151	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529705.1	s__Bradyrhizobium campsiandrae	82.6238	1374	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000218565.1	s__Afipia carboxidovorans	79.5362	549	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.99	99.99	1.00	1.00	3	-
GCF_016756535.1	s__Mesorhizobium sp016756535	77.4836	469	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824825.2	s__Mesorhizobium sp000824825	77.3613	411	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020545.1	s__Mesorhizobium sp004020545	77.1241	443	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCA_905339215.1	s__DUSC01 sp008933895	77.0867	357	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCA_012842935.1	s__DUSC01 sp012842935	76.9203	273	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829385.1	s__Hoeflea sp018829385	76.7413	188	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642895.1	s__Roseitalea sp017642895	76.543	208	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	99.99	99.99	1.00	1.00	3	-
GCA_900469955.1	s__Neorhizobium sp900469955	76.54	204	2966	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:01,731] [INFO] GTDB search result was written to GCF_020889705.1_ASM2088970v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:01,733] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:01,736] [INFO] DFAST_QC result json was written to GCF_020889705.1_ASM2088970v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:01,737] [INFO] DFAST_QC completed!
[2024-01-25 20:23:01,737] [INFO] Total running time: 0h2m41s