[2024-01-24 10:57:38,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,824] [INFO] DQC Reference Directory: /var/lib/cwl/stgc901446f-5a18-40d9-a5b8-005d337750f8/dqc_reference
[2024-01-24 10:57:40,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,152] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg33a24863-14ad-46da-8371-ade2e601b27f/GCF_015291705.1_ASM1529170v1_genomic.fna.gz | prodigal -d GCF_015291705.1_ASM1529170v1_genomic.fna/cds.fna -a GCF_015291705.1_ASM1529170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:13,683] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:13,684] [INFO] Task started: HMMsearch
[2024-01-24 10:58:13,684] [INFO] Running command: hmmsearch --tblout GCF_015291705.1_ASM1529170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc901446f-5a18-40d9-a5b8-005d337750f8/dqc_reference/reference_markers.hmm GCF_015291705.1_ASM1529170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:14,070] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:14,071] [INFO] Found 6/6 markers.
[2024-01-24 10:58:14,148] [INFO] Query marker FASTA was written to GCF_015291705.1_ASM1529170v1_genomic.fna/markers.fasta
[2024-01-24 10:58:14,149] [INFO] Task started: Blastn
[2024-01-24 10:58:14,149] [INFO] Running command: blastn -query GCF_015291705.1_ASM1529170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc901446f-5a18-40d9-a5b8-005d337750f8/dqc_reference/reference_markers.fasta -out GCF_015291705.1_ASM1529170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:15,287] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:15,291] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:15,292] [INFO] Target genome list was writen to GCF_015291705.1_ASM1529170v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:15,300] [INFO] Task started: fastANI
[2024-01-24 10:58:15,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg33a24863-14ad-46da-8371-ade2e601b27f/GCF_015291705.1_ASM1529170v1_genomic.fna.gz --refList GCF_015291705.1_ASM1529170v1_genomic.fna/target_genomes.txt --output GCF_015291705.1_ASM1529170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:58,327] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:58,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc901446f-5a18-40d9-a5b8-005d337750f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:58,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc901446f-5a18-40d9-a5b8-005d337750f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:58,342] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:58,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:58,343] [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 arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	100.0	3287	3288	95	conclusive
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	99.9747	3209	3288	95	conclusive
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	89.7094	2173	3288	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.2484	2183	3288	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.185	2187	3288	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	89.1691	2140	3288	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.1558	2072	3288	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	89.1441	2200	3288	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	89.0601	2173	3288	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.9891	1844	3288	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	88.6241	1968	3288	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	88.5205	1987	3288	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	88.4023	2008	3288	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.2803	2058	3288	95	below_threshold
Bradyrhizobium manausense	strain=BR 3351	GCA_001440035.1	989370	989370	suspected-type	True	87.6493	1911	3288	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	83.0332	1631	3288	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.9933	1534	3288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:58,344] [INFO] DFAST Taxonomy check result was written to GCF_015291705.1_ASM1529170v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:58,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:58,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:58,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc901446f-5a18-40d9-a5b8-005d337750f8/dqc_reference/checkm_data
[2024-01-24 10:58:58,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:58,435] [INFO] Task started: CheckM
[2024-01-24 10:58:58,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015291705.1_ASM1529170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015291705.1_ASM1529170v1_genomic.fna/checkm_input GCF_015291705.1_ASM1529170v1_genomic.fna/checkm_result
[2024-01-24 11:00:35,995] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:35,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:36,029] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:36,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:36,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015291705.1_ASM1529170v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:36,030] [INFO] Task started: Blastn
[2024-01-24 11:00:36,030] [INFO] Running command: blastn -query GCF_015291705.1_ASM1529170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc901446f-5a18-40d9-a5b8-005d337750f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_015291705.1_ASM1529170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:38,264] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:38,269] [INFO] Selected 23 target genomes.
[2024-01-24 11:00:38,269] [INFO] Target genome list was writen to GCF_015291705.1_ASM1529170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:38,303] [INFO] Task started: fastANI
[2024-01-24 11:00:38,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg33a24863-14ad-46da-8371-ade2e601b27f/GCF_015291705.1_ASM1529170v1_genomic.fna.gz --refList GCF_015291705.1_ASM1529170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015291705.1_ASM1529170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:01:31,392] [INFO] Task succeeded: fastANI
[2024-01-24 11:01:31,418] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:01:31,418] [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_015291705.1	s__Bradyrhizobium arachidis	100.0	3287	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.47	0.91	0.88	5	conclusive
GCF_018130825.1	s__Bradyrhizobium liaoningense_B	90.0594	2128	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016616235.1	s__Bradyrhizobium diazoefficiens_H	89.8695	1939	3288	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	89.8305	2187	3288	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	89.8156	2118	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641335.1	s__Bradyrhizobium stylosanthis	89.6947	2175	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	-
GCF_004216735.1	s__Bradyrhizobium sp004216735	89.6037	2069	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291725.1	s__Bradyrhizobium japonicum_D	89.4317	2140	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	95.51	95.51	0.86	0.86	2	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	89.1709	2189	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_009759665.1	s__Bradyrhizobium cajani	89.1545	2143	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.56	95.54	0.80	0.80	3	-
GCF_002795245.1	s__Bradyrhizobium forestalis	89.1496	2072	3288	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	89.1281	2201	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_900094605.1	s__Bradyrhizobium shewense	89.0712	2171	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_018129995.1	s__Bradyrhizobium japonicum_G	88.8982	1913	3288	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	88.8625	2002	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602485.1	s__Bradyrhizobium sp011602485	88.8025	2063	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.68	97.67	0.91	0.90	3	-
GCF_013240495.1	s__Bradyrhizobium sp013240495	88.6588	2021	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.36	98.36	0.89	0.89	2	-
GCF_001590795.1	s__Bradyrhizobium sp001590795	88.6274	2008	3288	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	88.5146	1465	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114915.1	s__Bradyrhizobium guangxiense	88.4033	2007	3288	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	88.1437	1954	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131015.1	s__Bradyrhizobium diazoefficiens_B	88.0675	1819	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.09	98.09	0.94	0.94	2	-
GCF_900113735.1	s__Bradyrhizobium sp900113735	87.4281	1880	3288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:01:31,420] [INFO] GTDB search result was written to GCF_015291705.1_ASM1529170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:01:31,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:01:31,425] [INFO] DFAST_QC result json was written to GCF_015291705.1_ASM1529170v1_genomic.fna/dqc_result.json
[2024-01-24 11:01:31,425] [INFO] DFAST_QC completed!
[2024-01-24 11:01:31,425] [INFO] Total running time: 0h3m53s