[2024-01-24 13:56:12,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:12,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:12,399] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f082a0c-d972-4be4-879f-6bc486aab9f4/dqc_reference
[2024-01-24 13:56:14,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,422] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,422] [INFO] Running command: gunzip -c /var/lib/cwl/stg11d2df5c-04fc-438d-94c6-6aedf92e938b/GCF_021044685.1_ASM2104468v1_genomic.fna.gz | prodigal -d GCF_021044685.1_ASM2104468v1_genomic.fna/cds.fna -a GCF_021044685.1_ASM2104468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:38,510] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:38,510] [INFO] Task started: HMMsearch
[2024-01-24 13:56:38,510] [INFO] Running command: hmmsearch --tblout GCF_021044685.1_ASM2104468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f082a0c-d972-4be4-879f-6bc486aab9f4/dqc_reference/reference_markers.hmm GCF_021044685.1_ASM2104468v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:38,873] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:38,875] [INFO] Found 6/6 markers.
[2024-01-24 13:56:38,931] [INFO] Query marker FASTA was written to GCF_021044685.1_ASM2104468v1_genomic.fna/markers.fasta
[2024-01-24 13:56:38,931] [INFO] Task started: Blastn
[2024-01-24 13:56:38,932] [INFO] Running command: blastn -query GCF_021044685.1_ASM2104468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f082a0c-d972-4be4-879f-6bc486aab9f4/dqc_reference/reference_markers.fasta -out GCF_021044685.1_ASM2104468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:40,054] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:40,058] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:40,059] [INFO] Target genome list was writen to GCF_021044685.1_ASM2104468v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:40,067] [INFO] Task started: fastANI
[2024-01-24 13:56:40,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d2df5c-04fc-438d-94c6-6aedf92e938b/GCF_021044685.1_ASM2104468v1_genomic.fna.gz --refList GCF_021044685.1_ASM2104468v1_genomic.fna/target_genomes.txt --output GCF_021044685.1_ASM2104468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:17,409] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:17,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f082a0c-d972-4be4-879f-6bc486aab9f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:17,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f082a0c-d972-4be4-879f-6bc486aab9f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:17,430] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:17,430] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:17,430] [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 daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	100.0	2666	2666	95	conclusive
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	99.9529	2574	2666	95	conclusive
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	89.9442	2099	2666	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	89.5422	2013	2666	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	88.9682	1983	2666	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.9223	1943	2666	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	88.7618	2028	2666	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	88.6987	1842	2666	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	88.6978	1894	2666	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	88.59	1883	2666	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	88.4969	1821	2666	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	88.385	2034	2666	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	88.3829	2023	2666	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.0634	1708	2666	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	82.69	1479	2666	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.4916	1397	2666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:17,432] [INFO] DFAST Taxonomy check result was written to GCF_021044685.1_ASM2104468v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:17,433] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:17,433] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:17,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f082a0c-d972-4be4-879f-6bc486aab9f4/dqc_reference/checkm_data
[2024-01-24 13:57:17,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:17,506] [INFO] Task started: CheckM
[2024-01-24 13:57:17,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021044685.1_ASM2104468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021044685.1_ASM2104468v1_genomic.fna/checkm_input GCF_021044685.1_ASM2104468v1_genomic.fna/checkm_result
[2024-01-24 13:58:27,883] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:27,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:27,908] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:27,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:27,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021044685.1_ASM2104468v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:27,909] [INFO] Task started: Blastn
[2024-01-24 13:58:27,910] [INFO] Running command: blastn -query GCF_021044685.1_ASM2104468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f082a0c-d972-4be4-879f-6bc486aab9f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_021044685.1_ASM2104468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:30,256] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:30,260] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:30,260] [INFO] Target genome list was writen to GCF_021044685.1_ASM2104468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:30,274] [INFO] Task started: fastANI
[2024-01-24 13:58:30,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d2df5c-04fc-438d-94c6-6aedf92e938b/GCF_021044685.1_ASM2104468v1_genomic.fna.gz --refList GCF_021044685.1_ASM2104468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021044685.1_ASM2104468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:07,222] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:07,242] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:07,243] [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_007830205.1	s__Bradyrhizobium daqingense	99.9529	2574	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000296215.2	s__Bradyrhizobium sp000296215	94.5636	2093	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.76	0.87	0.87	2	-
GCF_011602485.1	s__Bradyrhizobium sp011602485	91.1761	2028	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.68	97.67	0.91	0.90	3	-
GCF_004212635.1	s__Bradyrhizobium sp004212635	89.6505	1858	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.55	95.55	0.86	0.86	2	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	89.2238	1869	2666	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	88.9913	1887	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	88.9506	1890	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240495.1	s__Bradyrhizobium sp013240495	88.8465	1983	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.36	98.36	0.89	0.89	2	-
GCF_018130765.1	s__Bradyrhizobium iriomotense_A	88.7822	1878	2666	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	88.6413	1879	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571025.1	s__Bradyrhizobium niftali	88.6097	1984	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_015291725.1	s__Bradyrhizobium japonicum_D	88.5764	1999	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	95.51	95.51	0.86	0.86	2	-
GCF_004114915.1	s__Bradyrhizobium guangxiense	88.5723	1887	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002266435.2	s__Bradyrhizobium amphicarpaeae	88.5087	1819	2666	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	88.4404	1955	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291705.1	s__Bradyrhizobium arachidis	88.388	2035	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.47	0.91	0.88	5	-
GCF_018131015.1	s__Bradyrhizobium diazoefficiens_B	87.3764	1675	2666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.09	98.09	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:07,244] [INFO] GTDB search result was written to GCF_021044685.1_ASM2104468v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:07,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:07,251] [INFO] DFAST_QC result json was written to GCF_021044685.1_ASM2104468v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:07,251] [INFO] DFAST_QC completed!
[2024-01-24 13:59:07,251] [INFO] Total running time: 0h2m55s