[2024-01-25 19:41:35,614] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:35,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:35,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgee31e393-3bfb-4006-87da-05934303a1fa/dqc_reference
[2024-01-25 19:41:36,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:36,766] [INFO] Task started: Prodigal
[2024-01-25 19:41:36,766] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8b634d7-6a93-438d-b331-63eb7dd3447e/GCF_002795245.1_ASM279524v1_genomic.fna.gz | prodigal -d GCF_002795245.1_ASM279524v1_genomic.fna/cds.fna -a GCF_002795245.1_ASM279524v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:58,371] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:58,372] [INFO] Task started: HMMsearch
[2024-01-25 19:41:58,372] [INFO] Running command: hmmsearch --tblout GCF_002795245.1_ASM279524v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee31e393-3bfb-4006-87da-05934303a1fa/dqc_reference/reference_markers.hmm GCF_002795245.1_ASM279524v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:58,700] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:58,701] [INFO] Found 6/6 markers.
[2024-01-25 19:41:58,760] [INFO] Query marker FASTA was written to GCF_002795245.1_ASM279524v1_genomic.fna/markers.fasta
[2024-01-25 19:41:58,760] [INFO] Task started: Blastn
[2024-01-25 19:41:58,760] [INFO] Running command: blastn -query GCF_002795245.1_ASM279524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee31e393-3bfb-4006-87da-05934303a1fa/dqc_reference/reference_markers.fasta -out GCF_002795245.1_ASM279524v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:59,801] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:59,804] [INFO] Selected 22 target genomes.
[2024-01-25 19:41:59,804] [INFO] Target genome list was writen to GCF_002795245.1_ASM279524v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:59,830] [INFO] Task started: fastANI
[2024-01-25 19:41:59,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b634d7-6a93-438d-b331-63eb7dd3447e/GCF_002795245.1_ASM279524v1_genomic.fna.gz --refList GCF_002795245.1_ASM279524v1_genomic.fna/target_genomes.txt --output GCF_002795245.1_ASM279524v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:50,633] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:50,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee31e393-3bfb-4006-87da-05934303a1fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:50,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee31e393-3bfb-4006-87da-05934303a1fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:50,648] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:50,648] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:50,648] [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 forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	100.0	2677	2680	95	conclusive
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	91.7761	1953	2680	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	90.9117	1944	2680	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	90.7126	1997	2680	95	below_threshold
Bradyrhizobium glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	90.4576	1963	2680	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	90.3981	1988	2680	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	90.3761	2055	2680	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	89.8697	2043	2680	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	89.8667	2065	2680	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.563	2055	2680	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	89.5591	1982	2680	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	89.4411	1978	2680	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	89.3628	2033	2680	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.3159	2063	2680	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.2721	2062	2680	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	89.2651	2054	2680	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	89.26	1834	2680	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.9191	1986	2680	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.6409	1727	2680	95	below_threshold
Bradyrhizobium guangzhouense	strain=CCBAU 51670	GCA_004114955.1	1325095	1325095	type	True	87.2076	1782	2680	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9903	1491	2680	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.7603	1401	2680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:50,649] [INFO] DFAST Taxonomy check result was written to GCF_002795245.1_ASM279524v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:50,650] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:50,650] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:50,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee31e393-3bfb-4006-87da-05934303a1fa/dqc_reference/checkm_data
[2024-01-25 19:42:50,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:50,730] [INFO] Task started: CheckM
[2024-01-25 19:42:50,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002795245.1_ASM279524v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002795245.1_ASM279524v1_genomic.fna/checkm_input GCF_002795245.1_ASM279524v1_genomic.fna/checkm_result
[2024-01-25 19:43:56,130] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:56,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:56,149] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:56,150] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:56,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002795245.1_ASM279524v1_genomic.fna/markers.fasta)
[2024-01-25 19:43:56,150] [INFO] Task started: Blastn
[2024-01-25 19:43:56,150] [INFO] Running command: blastn -query GCF_002795245.1_ASM279524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee31e393-3bfb-4006-87da-05934303a1fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_002795245.1_ASM279524v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:58,399] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:58,402] [INFO] Selected 18 target genomes.
[2024-01-25 19:43:58,402] [INFO] Target genome list was writen to GCF_002795245.1_ASM279524v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:58,436] [INFO] Task started: fastANI
[2024-01-25 19:43:58,437] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b634d7-6a93-438d-b331-63eb7dd3447e/GCF_002795245.1_ASM279524v1_genomic.fna.gz --refList GCF_002795245.1_ASM279524v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002795245.1_ASM279524v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:41,223] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:41,237] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:41,238] [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_002795245.1	s__Bradyrhizobium forestalis	100.0	2677	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018130245.1	s__Bradyrhizobium japonicum_F	93.9595	2014	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473065.1	s__Bradyrhizobium sp000473065	92.7612	2068	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114425.1	s__Bradyrhizobium vignae	91.7672	1954	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.81	0.88	0.86	3	-
GCF_016031635.1	s__Bradyrhizobium diversitatis	90.9118	1944	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	96.64	96.14	0.84	0.83	6	-
GCF_013240495.1	s__Bradyrhizobium sp013240495	90.7766	2005	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.36	98.36	0.89	0.89	2	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	90.6491	1953	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003837805.1	s__Bradyrhizobium sp003837805	90.5821	1981	2680	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	90.4025	2076	2680	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	90.2485	1964	2680	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	90.121	1935	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130765.1	s__Bradyrhizobium iriomotense_A	90.0291	1971	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570865.1	s__Bradyrhizobium frederickii	89.8172	2068	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.35	97.32	0.89	0.89	3	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	89.6949	2105	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_001590795.1	s__Bradyrhizobium sp001590795	89.5143	1971	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482425.1	s__Bradyrhizobium japonicum_B	89.4106	1825	2680	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	89.2776	1969	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.82	97.81	0.93	0.92	4	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	89.2694	2063	2680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:41,240] [INFO] GTDB search result was written to GCF_002795245.1_ASM279524v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:41,240] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:41,244] [INFO] DFAST_QC result json was written to GCF_002795245.1_ASM279524v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:41,244] [INFO] DFAST_QC completed!
[2024-01-25 19:44:41,244] [INFO] Total running time: 0h3m6s