[2024-01-24 12:44:10,435] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:10,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:10,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg478c63fb-f900-47b3-b082-472c5baf0915/dqc_reference
[2024-01-24 12:44:11,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:11,758] [INFO] Task started: Prodigal
[2024-01-24 12:44:11,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg4caab3b2-1582-4480-82e1-f0b3aa5eedd9/GCF_017565645.3_ASM1756564v3_genomic.fna.gz | prodigal -d GCF_017565645.3_ASM1756564v3_genomic.fna/cds.fna -a GCF_017565645.3_ASM1756564v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:54,116] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:54,117] [INFO] Task started: HMMsearch
[2024-01-24 12:44:54,117] [INFO] Running command: hmmsearch --tblout GCF_017565645.3_ASM1756564v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg478c63fb-f900-47b3-b082-472c5baf0915/dqc_reference/reference_markers.hmm GCF_017565645.3_ASM1756564v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:54,655] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:54,657] [INFO] Found 6/6 markers.
[2024-01-24 12:44:54,743] [INFO] Query marker FASTA was written to GCF_017565645.3_ASM1756564v3_genomic.fna/markers.fasta
[2024-01-24 12:44:54,744] [INFO] Task started: Blastn
[2024-01-24 12:44:54,744] [INFO] Running command: blastn -query GCF_017565645.3_ASM1756564v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg478c63fb-f900-47b3-b082-472c5baf0915/dqc_reference/reference_markers.fasta -out GCF_017565645.3_ASM1756564v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:55,778] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:55,782] [INFO] Selected 18 target genomes.
[2024-01-24 12:44:55,783] [INFO] Target genome list was writen to GCF_017565645.3_ASM1756564v3_genomic.fna/target_genomes.txt
[2024-01-24 12:44:55,787] [INFO] Task started: fastANI
[2024-01-24 12:44:55,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg4caab3b2-1582-4480-82e1-f0b3aa5eedd9/GCF_017565645.3_ASM1756564v3_genomic.fna.gz --refList GCF_017565645.3_ASM1756564v3_genomic.fna/target_genomes.txt --output GCF_017565645.3_ASM1756564v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:41,709] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:41,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg478c63fb-f900-47b3-b082-472c5baf0915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:41,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg478c63fb-f900-47b3-b082-472c5baf0915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:41,728] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:45:41,728] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:41,729] [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 japonicum	strain=USDA 6	GCA_000284375.1	375	375	type	True	95.38	2581	3797	95	conclusive
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	95.2893	2551	3797	95	conclusive
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	95.2861	2511	3797	95	conclusive
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	90.4177	2282	3797	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	90.3598	2290	3797	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	89.8355	2233	3797	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	89.782	2159	3797	95	below_threshold
Bradyrhizobium betae	strain=PL7HG1	GCA_008932115.1	244734	244734	type	True	89.4833	1896	3797	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	89.4797	1894	3797	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	89.0145	2081	3797	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.8948	2094	3797	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	88.747	2115	3797	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	88.6682	1949	3797	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	88.466	1998	3797	95	below_threshold
Bradyrhizobium rifense	strain=CTAW71	GCA_008123425.1	515499	515499	type	True	88.2088	2109	3797	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9241	1631	3797	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.7872	1532	3797	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:41,730] [INFO] DFAST Taxonomy check result was written to GCF_017565645.3_ASM1756564v3_genomic.fna/tc_result.tsv
[2024-01-24 12:45:41,731] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:41,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:41,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg478c63fb-f900-47b3-b082-472c5baf0915/dqc_reference/checkm_data
[2024-01-24 12:45:41,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:41,830] [INFO] Task started: CheckM
[2024-01-24 12:45:41,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017565645.3_ASM1756564v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017565645.3_ASM1756564v3_genomic.fna/checkm_input GCF_017565645.3_ASM1756564v3_genomic.fna/checkm_result
[2024-01-24 12:47:38,119] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:38,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:38,154] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:38,155] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:38,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017565645.3_ASM1756564v3_genomic.fna/markers.fasta)
[2024-01-24 12:47:38,155] [INFO] Task started: Blastn
[2024-01-24 12:47:38,156] [INFO] Running command: blastn -query GCF_017565645.3_ASM1756564v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg478c63fb-f900-47b3-b082-472c5baf0915/dqc_reference/reference_markers_gtdb.fasta -out GCF_017565645.3_ASM1756564v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:39,868] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:39,874] [INFO] Selected 26 target genomes.
[2024-01-24 12:47:39,874] [INFO] Target genome list was writen to GCF_017565645.3_ASM1756564v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:39,900] [INFO] Task started: fastANI
[2024-01-24 12:47:39,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg4caab3b2-1582-4480-82e1-f0b3aa5eedd9/GCF_017565645.3_ASM1756564v3_genomic.fna.gz --refList GCF_017565645.3_ASM1756564v3_genomic.fna/target_genomes_gtdb.txt --output GCF_017565645.3_ASM1756564v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:34,873] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:34,894] [INFO] Found 26 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:48:34,894] [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_011516635.3	s__Bradyrhizobium sp011516635	96.1166	2675	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	inconclusive
GCF_000284375.1	s__Bradyrhizobium japonicum	95.3951	2580	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.38	95.55	0.91	0.80	22	inconclusive
GCF_018130785.1	s__Bradyrhizobium liaoningense_A	92.8815	2238	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	90.3556	2292	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	89.6277	1855	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571025.1	s__Bradyrhizobium niftali	89.4956	2211	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_008932115.1	s__Bradyrhizobium betae	89.4875	1897	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130825.1	s__Bradyrhizobium liaoningense_B	89.3646	2047	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129405.1	s__Bradyrhizobium iriomotense_B	89.1243	2009	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	88.8502	2095	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094605.1	s__Bradyrhizobium shewense	88.7581	2112	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_001908185.1	s__Bradyrhizobium sp001908185	88.7111	1868	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	88.6506	1953	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	88.6497	2074	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_003020125.1	s__Bradyrhizobium sp003020125	88.4575	1924	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908205.1	s__Bradyrhizobium sp001908205	88.3459	1902	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008123425.1	s__Bradyrhizobium rifense	88.2102	2109	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612535.1	s__Bradyrhizobium diazoefficiens_C	87.8819	1857	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295845.1	s__Rhodopseudomonas sp001295845	80.676	988	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304555.1	s__JAFKKS01 sp017304555	77.5022	378	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__JAFKKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651875.1	s__Sinorhizobium saheli	77.2377	364	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCF_013044135.1	s__Enterovirga sp013044135	77.1168	407	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000745135.1	s__Microvirga sp000745135	77.0476	322	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927285.1	s__Mongoliimonas terrestris	76.9943	398	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046675.1	s__AWTP1-13 sp011046675	76.5743	371	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464955.1	s__Ga0077555 sp001464955	76.3135	244	3797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:34,896] [INFO] GTDB search result was written to GCF_017565645.3_ASM1756564v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:34,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:34,901] [INFO] DFAST_QC result json was written to GCF_017565645.3_ASM1756564v3_genomic.fna/dqc_result.json
[2024-01-24 12:48:34,901] [INFO] DFAST_QC completed!
[2024-01-24 12:48:34,901] [INFO] Total running time: 0h4m24s