[2024-01-24 13:18:46,081] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,086] [INFO] DQC Reference Directory: /var/lib/cwl/stgd95ecdbd-6cdb-42a8-9f7a-5631ab4770d1/dqc_reference
[2024-01-24 13:18:47,402] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,403] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,403] [INFO] Running command: gunzip -c /var/lib/cwl/stgba83c661-8f4a-4486-8911-75a5e949edf1/GCF_007830205.1_ASM783020v1_genomic.fna.gz | prodigal -d GCF_007830205.1_ASM783020v1_genomic.fna/cds.fna -a GCF_007830205.1_ASM783020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:10,319] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:10,320] [INFO] Task started: HMMsearch
[2024-01-24 13:19:10,320] [INFO] Running command: hmmsearch --tblout GCF_007830205.1_ASM783020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd95ecdbd-6cdb-42a8-9f7a-5631ab4770d1/dqc_reference/reference_markers.hmm GCF_007830205.1_ASM783020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:10,675] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:10,677] [INFO] Found 6/6 markers.
[2024-01-24 13:19:10,733] [INFO] Query marker FASTA was written to GCF_007830205.1_ASM783020v1_genomic.fna/markers.fasta
[2024-01-24 13:19:10,734] [INFO] Task started: Blastn
[2024-01-24 13:19:10,734] [INFO] Running command: blastn -query GCF_007830205.1_ASM783020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd95ecdbd-6cdb-42a8-9f7a-5631ab4770d1/dqc_reference/reference_markers.fasta -out GCF_007830205.1_ASM783020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:11,856] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:11,859] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:11,860] [INFO] Target genome list was writen to GCF_007830205.1_ASM783020v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:11,868] [INFO] Task started: fastANI
[2024-01-24 13:19:11,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgba83c661-8f4a-4486-8911-75a5e949edf1/GCF_007830205.1_ASM783020v1_genomic.fna.gz --refList GCF_007830205.1_ASM783020v1_genomic.fna/target_genomes.txt --output GCF_007830205.1_ASM783020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:46,453] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:46,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd95ecdbd-6cdb-42a8-9f7a-5631ab4770d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:46,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd95ecdbd-6cdb-42a8-9f7a-5631ab4770d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:46,467] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:46,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:46,468] [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=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	100.0	2570	2577	95	conclusive
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	99.9975	2576	2577	95	conclusive
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	89.9	2079	2577	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	89.5218	1987	2577	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	88.9953	1972	2577	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.9684	1922	2577	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	88.7832	2013	2577	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	88.6773	1838	2577	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	88.6623	1896	2577	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	88.5158	1882	2577	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	88.4583	1823	2577	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	88.4078	2000	2577	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	88.3572	2022	2577	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.1098	1696	2577	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	82.6193	1481	2577	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.5007	1392	2577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:46,473] [INFO] DFAST Taxonomy check result was written to GCF_007830205.1_ASM783020v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:46,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:46,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:46,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd95ecdbd-6cdb-42a8-9f7a-5631ab4770d1/dqc_reference/checkm_data
[2024-01-24 13:19:46,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:46,548] [INFO] Task started: CheckM
[2024-01-24 13:19:46,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830205.1_ASM783020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830205.1_ASM783020v1_genomic.fna/checkm_input GCF_007830205.1_ASM783020v1_genomic.fna/checkm_result
[2024-01-24 13:20:50,975] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:50,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:50,997] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:50,997] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:50,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830205.1_ASM783020v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:50,998] [INFO] Task started: Blastn
[2024-01-24 13:20:50,998] [INFO] Running command: blastn -query GCF_007830205.1_ASM783020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd95ecdbd-6cdb-42a8-9f7a-5631ab4770d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830205.1_ASM783020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:53,128] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:53,130] [INFO] Selected 17 target genomes.
[2024-01-24 13:20:53,131] [INFO] Target genome list was writen to GCF_007830205.1_ASM783020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:53,175] [INFO] Task started: fastANI
[2024-01-24 13:20:53,175] [INFO] Running command: fastANI --query /var/lib/cwl/stgba83c661-8f4a-4486-8911-75a5e949edf1/GCF_007830205.1_ASM783020v1_genomic.fna.gz --refList GCF_007830205.1_ASM783020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830205.1_ASM783020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:28,351] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:28,367] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:28,367] [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	100.0	2570	2577	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	94.5866	2084	2577	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	91.2054	2015	2577	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	89.6384	1841	2577	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	89.2873	1859	2577	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	89.0127	1880	2577	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	88.9689	1879	2577	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	88.8444	1959	2577	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	88.7752	1859	2577	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	88.6782	1944	2577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_004216735.1	s__Bradyrhizobium sp004216735	88.6497	1871	2577	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	88.5824	1989	2577	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	88.5159	1882	2577	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	88.4518	1824	2577	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	88.4097	1941	2577	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	88.3641	2021	2577	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	87.3763	1664	2577	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 13:21:28,371] [INFO] GTDB search result was written to GCF_007830205.1_ASM783020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:28,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:28,378] [INFO] DFAST_QC result json was written to GCF_007830205.1_ASM783020v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:28,379] [INFO] DFAST_QC completed!
[2024-01-24 13:21:28,379] [INFO] Total running time: 0h2m42s