[2024-01-24 13:52:12,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,556] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb558829-56f3-4615-a6b0-7868c6f85184/dqc_reference
[2024-01-24 13:52:13,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:13,787] [INFO] Task started: Prodigal
[2024-01-24 13:52:13,788] [INFO] Running command: gunzip -c /var/lib/cwl/stgb48bb440-3cf3-4485-a0dd-2f3e5f653e77/GCF_007830635.1_ASM783063v1_genomic.fna.gz | prodigal -d GCF_007830635.1_ASM783063v1_genomic.fna/cds.fna -a GCF_007830635.1_ASM783063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:41,170] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:41,170] [INFO] Task started: HMMsearch
[2024-01-24 13:52:41,170] [INFO] Running command: hmmsearch --tblout GCF_007830635.1_ASM783063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb558829-56f3-4615-a6b0-7868c6f85184/dqc_reference/reference_markers.hmm GCF_007830635.1_ASM783063v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:41,546] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:41,548] [INFO] Found 6/6 markers.
[2024-01-24 13:52:41,624] [INFO] Query marker FASTA was written to GCF_007830635.1_ASM783063v1_genomic.fna/markers.fasta
[2024-01-24 13:52:41,624] [INFO] Task started: Blastn
[2024-01-24 13:52:41,624] [INFO] Running command: blastn -query GCF_007830635.1_ASM783063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb558829-56f3-4615-a6b0-7868c6f85184/dqc_reference/reference_markers.fasta -out GCF_007830635.1_ASM783063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:42,671] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:42,676] [INFO] Selected 20 target genomes.
[2024-01-24 13:52:42,676] [INFO] Target genome list was writen to GCF_007830635.1_ASM783063v1_genomic.fna/target_genomes.txt
[2024-01-24 13:52:42,700] [INFO] Task started: fastANI
[2024-01-24 13:52:42,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48bb440-3cf3-4485-a0dd-2f3e5f653e77/GCF_007830635.1_ASM783063v1_genomic.fna.gz --refList GCF_007830635.1_ASM783063v1_genomic.fna/target_genomes.txt --output GCF_007830635.1_ASM783063v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:53:32,293] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:32,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb558829-56f3-4615-a6b0-7868c6f85184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:53:32,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb558829-56f3-4615-a6b0-7868c6f85184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:53:32,313] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:53:32,313] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:53:32,314] [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 huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	100.0	3019	3024	95	conclusive
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	91.8658	2277	3024	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	91.2908	2403	3024	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	91.2612	2400	3024	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	90.8697	2245	3024	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.856	2220	3024	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	89.8017	2283	3024	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	89.7781	2288	3024	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.768	2054	3024	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	89.7169	2152	3024	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	89.7068	2102	3024	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	89.284	1990	3024	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	89.1854	1920	3024	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	89.1469	2112	3024	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	89.1032	1964	3024	95	below_threshold
Bradyrhizobium glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	88.9823	1954	3024	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.9546	1826	3024	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	88.8779	1962	3024	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	83.0047	1591	3024	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.9058	1492	3024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:53:32,315] [INFO] DFAST Taxonomy check result was written to GCF_007830635.1_ASM783063v1_genomic.fna/tc_result.tsv
[2024-01-24 13:53:32,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:53:32,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:53:32,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb558829-56f3-4615-a6b0-7868c6f85184/dqc_reference/checkm_data
[2024-01-24 13:53:32,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:53:32,411] [INFO] Task started: CheckM
[2024-01-24 13:53:32,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830635.1_ASM783063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830635.1_ASM783063v1_genomic.fna/checkm_input GCF_007830635.1_ASM783063v1_genomic.fna/checkm_result
[2024-01-24 13:54:48,181] [INFO] Task succeeded: CheckM
[2024-01-24 13:54:48,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:54:48,209] [INFO] ===== Completeness check finished =====
[2024-01-24 13:54:48,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:54:48,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830635.1_ASM783063v1_genomic.fna/markers.fasta)
[2024-01-24 13:54:48,210] [INFO] Task started: Blastn
[2024-01-24 13:54:48,210] [INFO] Running command: blastn -query GCF_007830635.1_ASM783063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb558829-56f3-4615-a6b0-7868c6f85184/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830635.1_ASM783063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:50,351] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:50,355] [INFO] Selected 13 target genomes.
[2024-01-24 13:54:50,355] [INFO] Target genome list was writen to GCF_007830635.1_ASM783063v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:54:50,377] [INFO] Task started: fastANI
[2024-01-24 13:54:50,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48bb440-3cf3-4485-a0dd-2f3e5f653e77/GCF_007830635.1_ASM783063v1_genomic.fna.gz --refList GCF_007830635.1_ASM783063v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830635.1_ASM783063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:26,048] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:26,062] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:26,062] [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_007830635.1	s__Bradyrhizobium huanghuaihaiense	100.0	3019	3024	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.94	99.94	0.97	0.97	2	conclusive
GCF_018130825.1	s__Bradyrhizobium liaoningense_B	93.6249	2331	3024	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	93.2941	2234	3024	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	93.2932	2258	3024	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	92.5092	2155	3024	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	92.4572	2245	3024	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002068095.1	s__Bradyrhizobium sacchari	91.8843	2275	3024	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001641335.1	s__Bradyrhizobium stylosanthis	90.8715	2245	3024	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	-
GCF_004571025.1	s__Bradyrhizobium niftali	89.8652	2217	3024	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	89.7897	2286	3024	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.47	0.91	0.88	5	-
GCF_002795245.1	s__Bradyrhizobium forestalis	89.7559	2057	3024	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	89.2002	1919	3024	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.81	0.88	0.86	3	-
GCF_004114935.1	s__Bradyrhizobium zhanjiangense	88.9421	2133	3024	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.50	97.97	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:26,064] [INFO] GTDB search result was written to GCF_007830635.1_ASM783063v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:26,064] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:26,068] [INFO] DFAST_QC result json was written to GCF_007830635.1_ASM783063v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:26,068] [INFO] DFAST_QC completed!
[2024-01-24 13:55:26,068] [INFO] Total running time: 0h3m14s