[2024-01-25 19:35:05,543] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:05,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:05,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f6dc0b0-25d0-43db-9911-e097dd6929b9/dqc_reference
[2024-01-25 19:35:06,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:06,659] [INFO] Task started: Prodigal
[2024-01-25 19:35:06,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cdc0a04-34a1-475c-afe1-f39acc80b877/GCF_009759665.1_ASM975966v1_genomic.fna.gz | prodigal -d GCF_009759665.1_ASM975966v1_genomic.fna/cds.fna -a GCF_009759665.1_ASM975966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:28,335] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:28,336] [INFO] Task started: HMMsearch
[2024-01-25 19:35:28,336] [INFO] Running command: hmmsearch --tblout GCF_009759665.1_ASM975966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f6dc0b0-25d0-43db-9911-e097dd6929b9/dqc_reference/reference_markers.hmm GCF_009759665.1_ASM975966v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:28,620] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:28,622] [INFO] Found 6/6 markers.
[2024-01-25 19:35:28,684] [INFO] Query marker FASTA was written to GCF_009759665.1_ASM975966v1_genomic.fna/markers.fasta
[2024-01-25 19:35:28,684] [INFO] Task started: Blastn
[2024-01-25 19:35:28,685] [INFO] Running command: blastn -query GCF_009759665.1_ASM975966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f6dc0b0-25d0-43db-9911-e097dd6929b9/dqc_reference/reference_markers.fasta -out GCF_009759665.1_ASM975966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:29,708] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:29,712] [INFO] Selected 22 target genomes.
[2024-01-25 19:35:29,712] [INFO] Target genome list was writen to GCF_009759665.1_ASM975966v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:29,718] [INFO] Task started: fastANI
[2024-01-25 19:35:29,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cdc0a04-34a1-475c-afe1-f39acc80b877/GCF_009759665.1_ASM975966v1_genomic.fna.gz --refList GCF_009759665.1_ASM975966v1_genomic.fna/target_genomes.txt --output GCF_009759665.1_ASM975966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:21,225] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:21,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f6dc0b0-25d0-43db-9911-e097dd6929b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:21,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f6dc0b0-25d0-43db-9911-e097dd6929b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:21,240] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:21,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:21,240] [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 cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	100.0	2738	2746	95	conclusive
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	90.3073	2078	2746	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.7789	2102	2746	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	89.7458	2056	2746	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	89.4826	2134	2746	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.4012	2080	2746	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	89.3371	2112	2746	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	89.3152	2119	2746	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.3111	2095	2746	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	89.0887	2039	2746	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	89.0474	2067	2746	95	below_threshold
Bradyrhizobium stylosanthis	strain=BR 446	GCA_001641335.1	1803665	1803665	type	True	89.047	1970	2746	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	89.0065	2042	2746	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	88.97	1925	2746	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000284375.1	375	375	type	True	88.952	2114	2746	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.8662	1753	2746	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	88.8543	1979	2746	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	88.8299	1877	2746	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	88.6966	2039	2746	95	below_threshold
Bradyrhizobium nanningense	strain=CCBAU 53390	GCA_004114535.1	1325118	1325118	type	True	88.654	1959	2746	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	83.0745	1531	2746	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.9791	1416	2746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:21,245] [INFO] DFAST Taxonomy check result was written to GCF_009759665.1_ASM975966v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:21,245] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:21,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:21,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f6dc0b0-25d0-43db-9911-e097dd6929b9/dqc_reference/checkm_data
[2024-01-25 19:36:21,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:21,324] [INFO] Task started: CheckM
[2024-01-25 19:36:21,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009759665.1_ASM975966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009759665.1_ASM975966v1_genomic.fna/checkm_input GCF_009759665.1_ASM975966v1_genomic.fna/checkm_result
[2024-01-25 19:37:24,709] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:24,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:24,733] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:24,733] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:24,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009759665.1_ASM975966v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:24,734] [INFO] Task started: Blastn
[2024-01-25 19:37:24,734] [INFO] Running command: blastn -query GCF_009759665.1_ASM975966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f6dc0b0-25d0-43db-9911-e097dd6929b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009759665.1_ASM975966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:26,953] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:26,960] [INFO] Selected 19 target genomes.
[2024-01-25 19:37:26,961] [INFO] Target genome list was writen to GCF_009759665.1_ASM975966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:26,971] [INFO] Task started: fastANI
[2024-01-25 19:37:26,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cdc0a04-34a1-475c-afe1-f39acc80b877/GCF_009759665.1_ASM975966v1_genomic.fna.gz --refList GCF_009759665.1_ASM975966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009759665.1_ASM975966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:12,583] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:12,595] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:12,595] [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_009759665.1	s__Bradyrhizobium cajani	100.0	2738	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.56	95.54	0.80	0.80	3	conclusive
GCF_002795245.1	s__Bradyrhizobium forestalis	90.3121	2077	2746	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	89.981	1912	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.55	95.55	0.86	0.86	2	-
GCF_004571025.1	s__Bradyrhizobium niftali	89.8014	2098	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	89.7749	2049	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114935.1	s__Bradyrhizobium zhanjiangense	89.7657	2053	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.50	97.97	0.92	0.89	4	-
GCF_018130825.1	s__Bradyrhizobium liaoningense_B	89.4862	1995	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602485.1	s__Bradyrhizobium sp011602485	89.434	1897	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.68	97.67	0.91	0.90	3	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	89.4286	1861	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011365.1	s__Bradyrhizobium diazoefficiens	89.3161	2094	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_018130765.1	s__Bradyrhizobium iriomotense_A	89.289	1977	2746	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	89.203	2057	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_018130785.1	s__Bradyrhizobium liaoningense_A	89.1882	1978	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129995.1	s__Bradyrhizobium japonicum_G	89.1015	1848	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284375.1	s__Bradyrhizobium japonicum	88.9401	2116	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.38	95.55	0.91	0.80	22	-
GCF_011516635.3	s__Bradyrhizobium sp011516635	88.907	2045	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	-
GCF_001556045.1	s__Bradyrhizobium sp001556045	88.7631	1756	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016616235.1	s__Bradyrhizobium diazoefficiens_H	88.5903	1767	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291665.1	s__Bradyrhizobium sp015291665	87.6768	1745	2746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:12,597] [INFO] GTDB search result was written to GCF_009759665.1_ASM975966v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:12,597] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:12,601] [INFO] DFAST_QC result json was written to GCF_009759665.1_ASM975966v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:12,601] [INFO] DFAST_QC completed!
[2024-01-25 19:38:12,601] [INFO] Total running time: 0h3m7s