[2024-01-24 12:30:05,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,393] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,394] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e69feaa-7224-4238-84d1-da7708e56a5b/dqc_reference
[2024-01-24 12:30:07,250] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,251] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg4231cb0d-d69a-4d85-9b67-f90b3bbe72fa/GCF_004114535.1_ASM411453v1_genomic.fna.gz | prodigal -d GCF_004114535.1_ASM411453v1_genomic.fna/cds.fna -a GCF_004114535.1_ASM411453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:29,279] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:29,280] [INFO] Task started: HMMsearch
[2024-01-24 12:30:29,280] [INFO] Running command: hmmsearch --tblout GCF_004114535.1_ASM411453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e69feaa-7224-4238-84d1-da7708e56a5b/dqc_reference/reference_markers.hmm GCF_004114535.1_ASM411453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:29,623] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:29,624] [INFO] Found 6/6 markers.
[2024-01-24 12:30:29,682] [INFO] Query marker FASTA was written to GCF_004114535.1_ASM411453v1_genomic.fna/markers.fasta
[2024-01-24 12:30:29,682] [INFO] Task started: Blastn
[2024-01-24 12:30:29,682] [INFO] Running command: blastn -query GCF_004114535.1_ASM411453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e69feaa-7224-4238-84d1-da7708e56a5b/dqc_reference/reference_markers.fasta -out GCF_004114535.1_ASM411453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:30,686] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:30,689] [INFO] Selected 20 target genomes.
[2024-01-24 12:30:30,689] [INFO] Target genome list was writen to GCF_004114535.1_ASM411453v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:30,694] [INFO] Task started: fastANI
[2024-01-24 12:30:30,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg4231cb0d-d69a-4d85-9b67-f90b3bbe72fa/GCF_004114535.1_ASM411453v1_genomic.fna.gz --refList GCF_004114535.1_ASM411453v1_genomic.fna/target_genomes.txt --output GCF_004114535.1_ASM411453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:17,884] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:17,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e69feaa-7224-4238-84d1-da7708e56a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:17,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e69feaa-7224-4238-84d1-da7708e56a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:17,897] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:17,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:17,898] [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 nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	100.0	2725	2731	95	conclusive
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	91.9662	2051	2731	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	90.7648	1929	2731	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	90.0919	2098	2731	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.3477	2041	2731	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	89.0695	1848	2731	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	88.9299	2099	2731	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	88.8022	1886	2731	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	88.8006	1952	2731	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	88.7634	2014	2731	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.7061	1923	2731	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	88.6158	1964	2731	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	88.5968	1992	2731	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	88.5697	1880	2731	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.562	1912	2731	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.4602	1726	2731	95	below_threshold
Bradyrhizobium guangdongense	strain=CCBAU 51649	GCA_004114975.1	1325090	1325090	type	True	87.2566	1873	2731	95	below_threshold
Bradyrhizobium guangzhouense	strain=CCBAU 51670	GCA_004114955.1	1325095	1325095	type	True	87.0254	1763	2731	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.6654	1384	2731	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.5927	1390	2731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:17,899] [INFO] DFAST Taxonomy check result was written to GCF_004114535.1_ASM411453v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:17,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:17,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:17,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e69feaa-7224-4238-84d1-da7708e56a5b/dqc_reference/checkm_data
[2024-01-24 12:31:17,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:17,981] [INFO] Task started: CheckM
[2024-01-24 12:31:17,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004114535.1_ASM411453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004114535.1_ASM411453v1_genomic.fna/checkm_input GCF_004114535.1_ASM411453v1_genomic.fna/checkm_result
[2024-01-24 12:32:19,323] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:19,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:19,345] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:19,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:19,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004114535.1_ASM411453v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:19,347] [INFO] Task started: Blastn
[2024-01-24 12:32:19,347] [INFO] Running command: blastn -query GCF_004114535.1_ASM411453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e69feaa-7224-4238-84d1-da7708e56a5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004114535.1_ASM411453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:21,428] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:21,431] [INFO] Selected 17 target genomes.
[2024-01-24 12:32:21,431] [INFO] Target genome list was writen to GCF_004114535.1_ASM411453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:21,439] [INFO] Task started: fastANI
[2024-01-24 12:32:21,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg4231cb0d-d69a-4d85-9b67-f90b3bbe72fa/GCF_004114535.1_ASM411453v1_genomic.fna.gz --refList GCF_004114535.1_ASM411453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004114535.1_ASM411453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:57,840] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:57,850] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:57,850] [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_004114535.1	s__Bradyrhizobium nanningense	100.0	2725	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.21	99.11	0.94	0.93	3	conclusive
GCF_004570865.1	s__Bradyrhizobium frederickii	91.9918	2047	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.35	97.32	0.89	0.89	3	-
GCF_015291745.1	s__Bradyrhizobium sp015291745	91.663	2014	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.82	97.81	0.93	0.92	4	-
GCF_000482425.1	s__Bradyrhizobium japonicum_B	91.5622	1835	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	90.7608	1929	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	90.7509	1920	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590795.1	s__Bradyrhizobium sp001590795	90.7409	1929	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131185.1	s__Bradyrhizobium diazoefficiens_G	90.1099	1821	2731	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	89.1442	1848	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004212635.1	s__Bradyrhizobium sp004212635	88.9712	1905	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.55	95.55	0.86	0.86	2	-
GCF_004114935.1	s__Bradyrhizobium zhanjiangense	88.9341	2099	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.50	97.97	0.92	0.89	4	-
GCF_001641335.1	s__Bradyrhizobium stylosanthis	88.8022	1886	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	-
GCF_009759665.1	s__Bradyrhizobium cajani	88.7005	1924	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.56	95.54	0.80	0.80	3	-
GCF_015291705.1	s__Bradyrhizobium arachidis	88.6108	1990	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.47	0.91	0.88	5	-
GCF_015624505.1	s__Bradyrhizobium sp015624505	87.7264	1720	2731	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	87.4884	1786	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.96	98.89	0.93	0.91	3	-
GCF_004114955.1	s__Bradyrhizobium guangzhouense	87.0231	1763	2731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	98.94	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:57,852] [INFO] GTDB search result was written to GCF_004114535.1_ASM411453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:57,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:57,856] [INFO] DFAST_QC result json was written to GCF_004114535.1_ASM411453v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:57,856] [INFO] DFAST_QC completed!
[2024-01-24 12:32:57,856] [INFO] Total running time: 0h2m52s