[2024-01-25 20:02:05,835] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:05,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:05,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg187e2086-db92-4a0d-87bc-b5a9e9b4f334/dqc_reference
[2024-01-25 20:02:07,001] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:07,001] [INFO] Task started: Prodigal
[2024-01-25 20:02:07,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f49849c-5541-462b-a075-9475939c4eec/GCF_004114975.1_ASM411497v1_genomic.fna.gz | prodigal -d GCF_004114975.1_ASM411497v1_genomic.fna/cds.fna -a GCF_004114975.1_ASM411497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:29,814] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:29,814] [INFO] Task started: HMMsearch
[2024-01-25 20:02:29,815] [INFO] Running command: hmmsearch --tblout GCF_004114975.1_ASM411497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg187e2086-db92-4a0d-87bc-b5a9e9b4f334/dqc_reference/reference_markers.hmm GCF_004114975.1_ASM411497v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:30,134] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:30,135] [INFO] Found 6/6 markers.
[2024-01-25 20:02:30,196] [INFO] Query marker FASTA was written to GCF_004114975.1_ASM411497v1_genomic.fna/markers.fasta
[2024-01-25 20:02:30,196] [INFO] Task started: Blastn
[2024-01-25 20:02:30,196] [INFO] Running command: blastn -query GCF_004114975.1_ASM411497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg187e2086-db92-4a0d-87bc-b5a9e9b4f334/dqc_reference/reference_markers.fasta -out GCF_004114975.1_ASM411497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:31,182] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:31,185] [INFO] Selected 21 target genomes.
[2024-01-25 20:02:31,185] [INFO] Target genome list was writen to GCF_004114975.1_ASM411497v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:31,207] [INFO] Task started: fastANI
[2024-01-25 20:02:31,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f49849c-5541-462b-a075-9475939c4eec/GCF_004114975.1_ASM411497v1_genomic.fna.gz --refList GCF_004114975.1_ASM411497v1_genomic.fna/target_genomes.txt --output GCF_004114975.1_ASM411497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:17,710] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:17,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg187e2086-db92-4a0d-87bc-b5a9e9b4f334/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:17,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg187e2086-db92-4a0d-87bc-b5a9e9b4f334/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:17,724] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:03:17,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:17,724] [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=CCBAU 51649	GCA_004114975.1	1325090	1325090	type	True	100.0	2812	2812	95	conclusive
Bradyrhizobium guangdongense	strain=CGMCC 1.15034	GCA_014640515.1	1325090	1325090	type	True	99.9796	2744	2812	95	conclusive
Bradyrhizobium guangzhouense	strain=CCBAU 51670	GCA_004114955.1	1325095	1325095	type	True	90.2041	2171	2812	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	89.2456	2156	2812	95	below_threshold
Bradyrhizobium campsiandrae	strain=INPA 394B	GCA_014529705.1	1729892	1729892	type	True	88.7633	1920	2812	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	88.5175	1833	2812	95	below_threshold
Bradyrhizobium manausense	strain=BR 3351	GCA_001440035.1	989370	989370	suspected-type	True	88.1332	1876	2812	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	87.7881	1914	2812	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	87.7774	1876	2812	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	87.7534	1877	2812	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	87.6946	1922	2812	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	87.505	1852	2812	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	87.4848	1721	2812	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	87.3955	1879	2812	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	87.3844	1879	2812	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	87.3479	1777	2812	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	87.1817	1875	2812	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	87.0108	1771	2812	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	86.8302	1763	2812	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.6124	1451	2812	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.4302	1355	2812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:17,725] [INFO] DFAST Taxonomy check result was written to GCF_004114975.1_ASM411497v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:17,726] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:17,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:17,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg187e2086-db92-4a0d-87bc-b5a9e9b4f334/dqc_reference/checkm_data
[2024-01-25 20:03:17,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:17,804] [INFO] Task started: CheckM
[2024-01-25 20:03:17,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004114975.1_ASM411497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004114975.1_ASM411497v1_genomic.fna/checkm_input GCF_004114975.1_ASM411497v1_genomic.fna/checkm_result
[2024-01-25 20:04:28,083] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:28,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:28,105] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:28,106] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:28,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004114975.1_ASM411497v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:28,107] [INFO] Task started: Blastn
[2024-01-25 20:04:28,107] [INFO] Running command: blastn -query GCF_004114975.1_ASM411497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg187e2086-db92-4a0d-87bc-b5a9e9b4f334/dqc_reference/reference_markers_gtdb.fasta -out GCF_004114975.1_ASM411497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:30,205] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:30,208] [INFO] Selected 16 target genomes.
[2024-01-25 20:04:30,208] [INFO] Target genome list was writen to GCF_004114975.1_ASM411497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:30,223] [INFO] Task started: fastANI
[2024-01-25 20:04:30,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f49849c-5541-462b-a075-9475939c4eec/GCF_004114975.1_ASM411497v1_genomic.fna.gz --refList GCF_004114975.1_ASM411497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004114975.1_ASM411497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:06,010] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:06,020] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:06,020] [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	100.0	2812	2812	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	91.7425	1939	2812	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	91.3951	1955	2812	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	90.2102	2170	2812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	98.94	0.94	0.93	3	-
GCF_004114915.1	s__Bradyrhizobium guangxiense	89.2237	2160	2812	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	89.1957	1915	2812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.96	98.89	0.93	0.91	3	-
GCF_008123515.1	s__Bradyrhizobium cytisi	88.5025	1832	2812	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	88.1434	1874	2812	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	87.9709	1770	2812	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	87.7795	1876	2812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.54	96.50	0.90	0.85	3	-
GCF_018130765.1	s__Bradyrhizobium iriomotense_A	87.7575	1841	2812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830635.1	s__Bradyrhizobium huanghuaihaiense	87.7487	1877	2812	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	87.7134	1905	2812	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	87.6068	1432	2812	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	87.2823	1800	2812	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	87.166	1878	2812	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.21	99.11	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:06,022] [INFO] GTDB search result was written to GCF_004114975.1_ASM411497v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:06,022] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:06,026] [INFO] DFAST_QC result json was written to GCF_004114975.1_ASM411497v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:06,026] [INFO] DFAST_QC completed!
[2024-01-25 20:05:06,026] [INFO] Total running time: 0h3m0s