[2024-01-24 13:55:58,195] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:58,197] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:58,197] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4289ca9-ec47-4c3d-bca1-ba825750b3bd/dqc_reference
[2024-01-24 13:55:59,408] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,409] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg1893cade-5e91-43e1-b656-1ef1222b7f0a/GCF_022012485.1_ASM2201248v1_genomic.fna.gz | prodigal -d GCF_022012485.1_ASM2201248v1_genomic.fna/cds.fna -a GCF_022012485.1_ASM2201248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:26,697] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:26,698] [INFO] Task started: HMMsearch
[2024-01-24 13:56:26,698] [INFO] Running command: hmmsearch --tblout GCF_022012485.1_ASM2201248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4289ca9-ec47-4c3d-bca1-ba825750b3bd/dqc_reference/reference_markers.hmm GCF_022012485.1_ASM2201248v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:27,064] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:27,066] [INFO] Found 6/6 markers.
[2024-01-24 13:56:27,144] [INFO] Query marker FASTA was written to GCF_022012485.1_ASM2201248v1_genomic.fna/markers.fasta
[2024-01-24 13:56:27,145] [INFO] Task started: Blastn
[2024-01-24 13:56:27,145] [INFO] Running command: blastn -query GCF_022012485.1_ASM2201248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4289ca9-ec47-4c3d-bca1-ba825750b3bd/dqc_reference/reference_markers.fasta -out GCF_022012485.1_ASM2201248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:28,187] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:28,190] [INFO] Selected 23 target genomes.
[2024-01-24 13:56:28,191] [INFO] Target genome list was writen to GCF_022012485.1_ASM2201248v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:28,206] [INFO] Task started: fastANI
[2024-01-24 13:56:28,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg1893cade-5e91-43e1-b656-1ef1222b7f0a/GCF_022012485.1_ASM2201248v1_genomic.fna.gz --refList GCF_022012485.1_ASM2201248v1_genomic.fna/target_genomes.txt --output GCF_022012485.1_ASM2201248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:15,607] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:15,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4289ca9-ec47-4c3d-bca1-ba825750b3bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:15,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4289ca9-ec47-4c3d-bca1-ba825750b3bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:15,631] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:15,631] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:15,631] [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 guangzhouense	strain=CCBAU 51670	GCA_004114955.1	1325095	1325095	type	True	93.1126	2358	2935	95	below_threshold
Bradyrhizobium manausense	strain=BR 3351	GCA_001440035.1	989370	989370	suspected-type	True	91.144	2033	2935	95	below_threshold
Bradyrhizobium guangdongense	strain=CCBAU 51649	GCA_004114975.1	1325090	1325090	type	True	89.9644	2226	2935	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	89.0676	2104	2935	95	below_threshold
Bradyrhizobium rifense	strain=CTAW71	GCA_008123425.1	515499	515499	type	True	89.0359	1984	2935	95	below_threshold
Bradyrhizobium campsiandrae	strain=INPA 394B	GCA_014529705.1	1729892	1729892	type	True	88.8972	1934	2935	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	88.8614	1877	2935	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	87.7567	1931	2935	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	87.7171	1909	2935	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	87.6618	1947	2935	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	87.6434	1972	2935	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	87.5722	1951	2935	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	87.5427	1936	2935	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	87.5287	1749	2935	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000284375.1	375	375	type	True	87.5087	1972	2935	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	87.3784	1844	2935	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	87.2806	1843	2935	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	87.2082	1893	2935	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	87.0203	1820	2935	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	86.9896	1791	2935	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	86.7851	1766	2935	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.5889	1454	2935	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.3941	1394	2935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:15,633] [INFO] DFAST Taxonomy check result was written to GCF_022012485.1_ASM2201248v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:15,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:15,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:15,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4289ca9-ec47-4c3d-bca1-ba825750b3bd/dqc_reference/checkm_data
[2024-01-24 13:57:15,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:15,719] [INFO] Task started: CheckM
[2024-01-24 13:57:15,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022012485.1_ASM2201248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022012485.1_ASM2201248v1_genomic.fna/checkm_input GCF_022012485.1_ASM2201248v1_genomic.fna/checkm_result
[2024-01-24 13:58:34,806] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:34,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:34,828] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:34,829] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:34,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022012485.1_ASM2201248v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:34,830] [INFO] Task started: Blastn
[2024-01-24 13:58:34,830] [INFO] Running command: blastn -query GCF_022012485.1_ASM2201248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4289ca9-ec47-4c3d-bca1-ba825750b3bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_022012485.1_ASM2201248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:36,976] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:36,980] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:36,980] [INFO] Target genome list was writen to GCF_022012485.1_ASM2201248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:37,010] [INFO] Task started: fastANI
[2024-01-24 13:58:37,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg1893cade-5e91-43e1-b656-1ef1222b7f0a/GCF_022012485.1_ASM2201248v1_genomic.fna.gz --refList GCF_022012485.1_ASM2201248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022012485.1_ASM2201248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:27,359] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:27,382] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:27,382] [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_004114955.1	s__Bradyrhizobium guangzhouense	93.1186	2357	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	98.94	0.94	0.93	3	-
GCF_015291665.1	s__Bradyrhizobium sp015291665	91.1419	2213	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440035.1	s__Bradyrhizobium manausense	91.1412	2033	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291645.1	s__Bradyrhizobium sp015291645	91.0915	2242	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131105.1	s__Bradyrhizobium manausense_B	89.1171	1872	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291745.1	s__Bradyrhizobium sp015291745	89.0606	2129	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.82	97.81	0.93	0.92	4	-
GCF_018130615.1	s__Bradyrhizobium manausense_A	89.0255	1962	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.96	98.89	0.93	0.91	3	-
GCF_014529705.1	s__Bradyrhizobium campsiandrae	88.8999	1934	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_008123515.1	s__Bradyrhizobium cytisi	88.8525	1879	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473045.1	s__Bradyrhizobium sp000473045	88.7686	1919	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872875.1	s__Bradyrhizobium sp017872875	88.7421	1878	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115265.1	s__Bradyrhizobium sp900115265	88.1549	1887	2935	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	87.7244	1908	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_015291705.1	s__Bradyrhizobium arachidis	87.6677	1968	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.47	0.91	0.88	5	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	87.5859	1872	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284375.1	s__Bradyrhizobium japonicum	87.4944	1974	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.38	95.55	0.91	0.80	22	-
GCF_011516635.3	s__Bradyrhizobium sp011516635	87.475	1961	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	87.4685	1841	2935	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	87.3833	1844	2935	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	87.2068	1856	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_900094605.1	s__Bradyrhizobium shewense	87.1982	1893	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_011602485.1	s__Bradyrhizobium sp011602485	87.0769	1799	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.68	97.67	0.91	0.90	3	-
GCF_004570865.1	s__Bradyrhizobium frederickii	86.9745	1793	2935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.35	97.32	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:27,384] [INFO] GTDB search result was written to GCF_022012485.1_ASM2201248v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:27,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:27,906] [INFO] DFAST_QC result json was written to GCF_022012485.1_ASM2201248v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:27,907] [INFO] DFAST_QC completed!
[2024-01-24 13:59:27,907] [INFO] Total running time: 0h3m30s