[2024-01-24 13:35:27,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,625] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg25d96d9c-9e61-4cbb-9d29-9a7f1548baa6/dqc_reference
[2024-01-24 13:35:28,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,895] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b3576a0-a945-4058-895f-08d88b4ea38d/GCF_001641335.1_ASM164133v1_genomic.fna.gz | prodigal -d GCF_001641335.1_ASM164133v1_genomic.fna/cds.fna -a GCF_001641335.1_ASM164133v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:58,932] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:58,932] [INFO] Task started: HMMsearch
[2024-01-24 13:35:58,932] [INFO] Running command: hmmsearch --tblout GCF_001641335.1_ASM164133v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25d96d9c-9e61-4cbb-9d29-9a7f1548baa6/dqc_reference/reference_markers.hmm GCF_001641335.1_ASM164133v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:59,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:59,311] [INFO] Found 6/6 markers.
[2024-01-24 13:35:59,381] [INFO] Query marker FASTA was written to GCF_001641335.1_ASM164133v1_genomic.fna/markers.fasta
[2024-01-24 13:35:59,382] [INFO] Task started: Blastn
[2024-01-24 13:35:59,382] [INFO] Running command: blastn -query GCF_001641335.1_ASM164133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25d96d9c-9e61-4cbb-9d29-9a7f1548baa6/dqc_reference/reference_markers.fasta -out GCF_001641335.1_ASM164133v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:00,464] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:00,467] [INFO] Selected 21 target genomes.
[2024-01-24 13:36:00,468] [INFO] Target genome list was writen to GCF_001641335.1_ASM164133v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:00,483] [INFO] Task started: fastANI
[2024-01-24 13:36:00,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b3576a0-a945-4058-895f-08d88b4ea38d/GCF_001641335.1_ASM164133v1_genomic.fna.gz --refList GCF_001641335.1_ASM164133v1_genomic.fna/target_genomes.txt --output GCF_001641335.1_ASM164133v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:47,782] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:47,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25d96d9c-9e61-4cbb-9d29-9a7f1548baa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:47,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25d96d9c-9e61-4cbb-9d29-9a7f1548baa6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:47,801] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:47,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:47,802] [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 stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	100.0	2923	2925	95	conclusive
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	90.8567	2240	2925	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	90.2087	2137	2925	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.7869	2157	2925	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.7663	2159	2925	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	89.7622	2160	2925	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	89.7443	2194	2925	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	89.2775	1945	2925	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	89.1302	2060	2925	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	89.0841	2041	2925	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	89.024	1847	2925	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.9072	1989	2925	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	88.9022	1941	2925	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	88.828	1909	2925	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	88.783	1926	2925	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	88.742	1954	2925	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.4863	1943	2925	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	88.1623	1833	2925	95	below_threshold
Bradyrhizobium rifense	strain=CTAW71	GCA_008123425.1	515499	515499	type	True	88.0726	1963	2925	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	83.1688	1600	2925	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	83.0451	1458	2925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:47,804] [INFO] DFAST Taxonomy check result was written to GCF_001641335.1_ASM164133v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:47,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:47,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:47,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25d96d9c-9e61-4cbb-9d29-9a7f1548baa6/dqc_reference/checkm_data
[2024-01-24 13:36:47,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:47,887] [INFO] Task started: CheckM
[2024-01-24 13:36:47,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001641335.1_ASM164133v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001641335.1_ASM164133v1_genomic.fna/checkm_input GCF_001641335.1_ASM164133v1_genomic.fna/checkm_result
[2024-01-24 13:38:16,182] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:16,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:16,211] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:16,212] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:16,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001641335.1_ASM164133v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:16,213] [INFO] Task started: Blastn
[2024-01-24 13:38:16,213] [INFO] Running command: blastn -query GCF_001641335.1_ASM164133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25d96d9c-9e61-4cbb-9d29-9a7f1548baa6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001641335.1_ASM164133v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:18,546] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:18,550] [INFO] Selected 23 target genomes.
[2024-01-24 13:38:18,550] [INFO] Target genome list was writen to GCF_001641335.1_ASM164133v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:18,571] [INFO] Task started: fastANI
[2024-01-24 13:38:18,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b3576a0-a945-4058-895f-08d88b4ea38d/GCF_001641335.1_ASM164133v1_genomic.fna.gz --refList GCF_001641335.1_ASM164133v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001641335.1_ASM164133v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:10,952] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:10,972] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:10,973] [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_001641335.1	s__Bradyrhizobium stylosanthis	100.0	2923	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	conclusive
GCF_018130825.1	s__Bradyrhizobium liaoningense_B	91.1143	2206	2925	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	90.7604	2224	2925	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	90.6148	2115	2925	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	90.5056	2088	2925	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	90.2179	2135	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	89.7723	2158	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_015291705.1	s__Bradyrhizobium arachidis	89.7376	2195	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.87	98.47	0.91	0.88	5	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	89.6901	1895	2925	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	89.6451	2063	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	89.3172	1926	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130785.1	s__Bradyrhizobium liaoningense_A	89.2672	2082	2925	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	89.2638	1946	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	89.1929	2037	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_002278135.2	s__Bradyrhizobium ottawaense	89.1225	2061	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.77	95.31	0.93	0.88	13	-
GCF_001590795.1	s__Bradyrhizobium sp001590795	89.0955	2022	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094605.1	s__Bradyrhizobium shewense	89.0628	2044	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_003020125.1	s__Bradyrhizobium sp003020125	88.7174	1941	2925	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	88.6588	1987	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	95.51	95.51	0.86	0.86	2	-
GCF_018131015.1	s__Bradyrhizobium diazoefficiens_B	88.0628	1801	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.09	98.09	0.94	0.94	2	-
GCF_015291665.1	s__Bradyrhizobium sp015291665	88.026	1886	2925	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	88.0009	1937	2925	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.96	98.89	0.93	0.91	3	-
GCF_015291645.1	s__Bradyrhizobium sp015291645	87.9408	1991	2925	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 13:39:10,974] [INFO] GTDB search result was written to GCF_001641335.1_ASM164133v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:10,975] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:10,979] [INFO] DFAST_QC result json was written to GCF_001641335.1_ASM164133v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:10,980] [INFO] DFAST_QC completed!
[2024-01-24 13:39:10,980] [INFO] Total running time: 0h3m43s