[2024-01-24 14:46:57,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg38a4111a-d994-4624-9839-17a6cf6d20a3/dqc_reference
[2024-01-24 14:46:59,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:59,204] [INFO] Task started: Prodigal
[2024-01-24 14:46:59,204] [INFO] Running command: gunzip -c /var/lib/cwl/stg4aa0ac0b-8608-49af-82b9-4a8b321939fb/GCF_004571025.1_ASM457102v1_genomic.fna.gz | prodigal -d GCF_004571025.1_ASM457102v1_genomic.fna/cds.fna -a GCF_004571025.1_ASM457102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:28,545] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:28,545] [INFO] Task started: HMMsearch
[2024-01-24 14:47:28,545] [INFO] Running command: hmmsearch --tblout GCF_004571025.1_ASM457102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38a4111a-d994-4624-9839-17a6cf6d20a3/dqc_reference/reference_markers.hmm GCF_004571025.1_ASM457102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:28,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:28,975] [INFO] Found 6/6 markers.
[2024-01-24 14:47:29,060] [INFO] Query marker FASTA was written to GCF_004571025.1_ASM457102v1_genomic.fna/markers.fasta
[2024-01-24 14:47:29,060] [INFO] Task started: Blastn
[2024-01-24 14:47:29,060] [INFO] Running command: blastn -query GCF_004571025.1_ASM457102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38a4111a-d994-4624-9839-17a6cf6d20a3/dqc_reference/reference_markers.fasta -out GCF_004571025.1_ASM457102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:30,215] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:30,218] [INFO] Selected 16 target genomes.
[2024-01-24 14:47:30,218] [INFO] Target genome list was writen to GCF_004571025.1_ASM457102v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:30,232] [INFO] Task started: fastANI
[2024-01-24 14:47:30,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa0ac0b-8608-49af-82b9-4a8b321939fb/GCF_004571025.1_ASM457102v1_genomic.fna.gz --refList GCF_004571025.1_ASM457102v1_genomic.fna/target_genomes.txt --output GCF_004571025.1_ASM457102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:13,429] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:13,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38a4111a-d994-4624-9839-17a6cf6d20a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:13,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38a4111a-d994-4624-9839-17a6cf6d20a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:13,442] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:13,443] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:13,443] [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 niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	100.0	3190	3193	95	conclusive
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	93.3991	2328	3193	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	93.3683	2340	3193	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	89.8217	2229	3193	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	89.689	2110	3193	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	89.687	2125	3193	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	89.614	2054	3193	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.5279	2053	3193	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	89.4107	1801	3193	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	89.3618	2188	3193	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	89.1158	1887	3193	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	88.7424	2023	3193	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	88.709	1953	3193	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.5152	1990	3193	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	83.071	1587	3193	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	83.0143	1505	3193	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:13,444] [INFO] DFAST Taxonomy check result was written to GCF_004571025.1_ASM457102v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:13,445] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:13,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:13,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38a4111a-d994-4624-9839-17a6cf6d20a3/dqc_reference/checkm_data
[2024-01-24 14:48:13,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:13,535] [INFO] Task started: CheckM
[2024-01-24 14:48:13,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004571025.1_ASM457102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004571025.1_ASM457102v1_genomic.fna/checkm_input GCF_004571025.1_ASM457102v1_genomic.fna/checkm_result
[2024-01-24 14:49:34,320] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:34,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:34,343] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:34,343] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:34,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004571025.1_ASM457102v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:34,344] [INFO] Task started: Blastn
[2024-01-24 14:49:34,344] [INFO] Running command: blastn -query GCF_004571025.1_ASM457102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38a4111a-d994-4624-9839-17a6cf6d20a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004571025.1_ASM457102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:36,919] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:36,923] [INFO] Selected 17 target genomes.
[2024-01-24 14:49:36,923] [INFO] Target genome list was writen to GCF_004571025.1_ASM457102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:36,939] [INFO] Task started: fastANI
[2024-01-24 14:49:36,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa0ac0b-8608-49af-82b9-4a8b321939fb/GCF_004571025.1_ASM457102v1_genomic.fna.gz --refList GCF_004571025.1_ASM457102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004571025.1_ASM457102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:20,220] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:20,234] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:20,234] [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_004571025.1	s__Bradyrhizobium niftali	100.0	3190	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	conclusive
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	93.349	2343	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_018130825.1	s__Bradyrhizobium liaoningense_B	90.3156	2067	3193	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	90.2372	2181	3193	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	90.1297	2093	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	90.0946	1859	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216735.1	s__Bradyrhizobium sp004216735	90.0743	2064	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830635.1	s__Bradyrhizobium huanghuaihaiense	89.8144	2230	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_011516635.3	s__Bradyrhizobium sp011516635	89.7098	2148	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	-
GCF_001641335.1	s__Bradyrhizobium stylosanthis	89.5895	2058	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	-
GCF_018130465.1	s__Bradyrhizobium canariense_C	89.5492	2020	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795245.1	s__Bradyrhizobium forestalis	89.5365	2053	3193	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	89.37	2187	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_007290395.1	s__Bradyrhizobium cosmicum	89.1209	1886	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.90	97.90	0.97	0.97	2	-
GCF_018131185.1	s__Bradyrhizobium diazoefficiens_G	88.7943	1865	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963435.1	s__Bradyrhizobium sp003963435	88.5289	1459	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130615.1	s__Bradyrhizobium manausense_A	88.2351	1902	3193	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.96	98.89	0.93	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:20,236] [INFO] GTDB search result was written to GCF_004571025.1_ASM457102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:20,237] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:20,241] [INFO] DFAST_QC result json was written to GCF_004571025.1_ASM457102v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:20,242] [INFO] DFAST_QC completed!
[2024-01-24 14:50:20,242] [INFO] Total running time: 0h3m22s