[2024-01-25 19:49:35,534] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:35,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:35,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg524ea02d-9d5e-4a08-ad66-af7bc790eeda/dqc_reference
[2024-01-25 19:49:36,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:36,683] [INFO] Task started: Prodigal
[2024-01-25 19:49:36,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bb55d6f-b2b1-4b45-aef0-d4c2b250c065/GCF_014640515.1_ASM1464051v1_genomic.fna.gz | prodigal -d GCF_014640515.1_ASM1464051v1_genomic.fna/cds.fna -a GCF_014640515.1_ASM1464051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:58,496] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:58,496] [INFO] Task started: HMMsearch
[2024-01-25 19:49:58,496] [INFO] Running command: hmmsearch --tblout GCF_014640515.1_ASM1464051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg524ea02d-9d5e-4a08-ad66-af7bc790eeda/dqc_reference/reference_markers.hmm GCF_014640515.1_ASM1464051v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:58,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:58,826] [INFO] Found 6/6 markers.
[2024-01-25 19:49:58,887] [INFO] Query marker FASTA was written to GCF_014640515.1_ASM1464051v1_genomic.fna/markers.fasta
[2024-01-25 19:49:58,888] [INFO] Task started: Blastn
[2024-01-25 19:49:58,888] [INFO] Running command: blastn -query GCF_014640515.1_ASM1464051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg524ea02d-9d5e-4a08-ad66-af7bc790eeda/dqc_reference/reference_markers.fasta -out GCF_014640515.1_ASM1464051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:59,829] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:59,832] [INFO] Selected 21 target genomes.
[2024-01-25 19:49:59,832] [INFO] Target genome list was writen to GCF_014640515.1_ASM1464051v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:59,842] [INFO] Task started: fastANI
[2024-01-25 19:49:59,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb55d6f-b2b1-4b45-aef0-d4c2b250c065/GCF_014640515.1_ASM1464051v1_genomic.fna.gz --refList GCF_014640515.1_ASM1464051v1_genomic.fna/target_genomes.txt --output GCF_014640515.1_ASM1464051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:43,925] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:43,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg524ea02d-9d5e-4a08-ad66-af7bc790eeda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:43,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg524ea02d-9d5e-4a08-ad66-af7bc790eeda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:43,939] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:50:43,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:43,939] [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 guangdongense	strain=CGMCC 1.15034	GCA_014640515.1	1325090	1325090	type	True	100.0	2747	2750	95	conclusive
Bradyrhizobium guangdongense	strain=CCBAU 51649	GCA_004114975.1	1325090	1325090	type	True	99.9981	2748	2750	95	conclusive
Bradyrhizobium guangzhouense	strain=CCBAU 51670	GCA_004114955.1	1325095	1325095	type	True	90.1865	2136	2750	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	89.1658	2131	2750	95	below_threshold
Bradyrhizobium campsiandrae	strain=INPA 394B	GCA_014529705.1	1729892	1729892	type	True	88.8181	1904	2750	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	88.5802	1810	2750	95	below_threshold
Bradyrhizobium manausense	strain=BR 3351	GCA_001440035.1	989370	989370	suspected-type	True	88.2523	1826	2750	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	87.82	1863	2750	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	87.8113	1901	2750	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	87.7435	1885	2750	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	87.6682	1902	2750	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	87.5652	1864	2750	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	87.4729	1699	2750	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	87.4103	1784	2750	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	87.4024	1862	2750	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	87.3438	1777	2750	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	87.176	1868	2750	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	86.7984	1762	2750	95	below_threshold
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	82.5865	1406	2750	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.5198	1433	2750	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.4414	1337	2750	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:43,941] [INFO] DFAST Taxonomy check result was written to GCF_014640515.1_ASM1464051v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:43,941] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:43,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:43,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg524ea02d-9d5e-4a08-ad66-af7bc790eeda/dqc_reference/checkm_data
[2024-01-25 19:50:43,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:44,019] [INFO] Task started: CheckM
[2024-01-25 19:50:44,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640515.1_ASM1464051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640515.1_ASM1464051v1_genomic.fna/checkm_input GCF_014640515.1_ASM1464051v1_genomic.fna/checkm_result
[2024-01-25 19:51:46,625] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:46,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:46,644] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:46,644] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:46,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640515.1_ASM1464051v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:46,645] [INFO] Task started: Blastn
[2024-01-25 19:51:46,645] [INFO] Running command: blastn -query GCF_014640515.1_ASM1464051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg524ea02d-9d5e-4a08-ad66-af7bc790eeda/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640515.1_ASM1464051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:48,584] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:48,587] [INFO] Selected 17 target genomes.
[2024-01-25 19:51:48,587] [INFO] Target genome list was writen to GCF_014640515.1_ASM1464051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:48,654] [INFO] Task started: fastANI
[2024-01-25 19:51:48,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb55d6f-b2b1-4b45-aef0-d4c2b250c065/GCF_014640515.1_ASM1464051v1_genomic.fna.gz --refList GCF_014640515.1_ASM1464051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640515.1_ASM1464051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:24,968] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:24,979] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:24,979] [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_004114975.1	s__Bradyrhizobium guangdongense	99.9981	2748	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_900115265.1	s__Bradyrhizobium sp900115265	91.7205	1946	2750	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	91.3935	1947	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114955.1	s__Bradyrhizobium guangzhouense	90.197	2134	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	98.94	0.94	0.93	3	-
GCF_018130615.1	s__Bradyrhizobium manausense_A	89.2348	1898	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.96	98.89	0.93	0.91	3	-
GCF_004114915.1	s__Bradyrhizobium guangxiense	89.1611	2132	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008123515.1	s__Bradyrhizobium cytisi	88.5745	1811	2750	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	88.2596	1825	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113735.1	s__Bradyrhizobium sp900113735	87.9714	1757	2750	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	87.9032	1790	2750	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	87.8176	1863	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	-
GCF_007830635.1	s__Bradyrhizobium huanghuaihaiense	87.7536	1884	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.94	99.94	0.97	0.97	2	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	87.6548	1923	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCA_003963435.1	s__Bradyrhizobium sp003963435	87.6315	1424	2750	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	87.2866	1790	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114535.1	s__Bradyrhizobium nanningense	87.1871	1865	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.21	99.11	0.94	0.93	3	-
GCF_000261685.1	s__Bradyrhizobium sp000261685	87.1081	1649	2750	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:24,980] [INFO] GTDB search result was written to GCF_014640515.1_ASM1464051v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:24,981] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:24,985] [INFO] DFAST_QC result json was written to GCF_014640515.1_ASM1464051v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:24,985] [INFO] DFAST_QC completed!
[2024-01-25 19:52:24,985] [INFO] Total running time: 0h2m49s