[2024-01-25 20:02:05,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:05,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:05,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg28120431-01d2-4096-8f54-c3f54c84238e/dqc_reference
[2024-01-25 20:02:06,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:06,900] [INFO] Task started: Prodigal
[2024-01-25 20:02:06,900] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5741c91-44aa-42ce-aec0-b95a08ff8ad8/GCF_030160715.1_ASM3016071v1_genomic.fna.gz | prodigal -d GCF_030160715.1_ASM3016071v1_genomic.fna/cds.fna -a GCF_030160715.1_ASM3016071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:32,412] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:32,413] [INFO] Task started: HMMsearch
[2024-01-25 20:02:32,413] [INFO] Running command: hmmsearch --tblout GCF_030160715.1_ASM3016071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28120431-01d2-4096-8f54-c3f54c84238e/dqc_reference/reference_markers.hmm GCF_030160715.1_ASM3016071v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:32,734] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:32,735] [INFO] Found 6/6 markers.
[2024-01-25 20:02:32,809] [INFO] Query marker FASTA was written to GCF_030160715.1_ASM3016071v1_genomic.fna/markers.fasta
[2024-01-25 20:02:32,809] [INFO] Task started: Blastn
[2024-01-25 20:02:32,809] [INFO] Running command: blastn -query GCF_030160715.1_ASM3016071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28120431-01d2-4096-8f54-c3f54c84238e/dqc_reference/reference_markers.fasta -out GCF_030160715.1_ASM3016071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:33,821] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:33,824] [INFO] Selected 25 target genomes.
[2024-01-25 20:02:33,824] [INFO] Target genome list was writen to GCF_030160715.1_ASM3016071v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:33,844] [INFO] Task started: fastANI
[2024-01-25 20:02:33,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5741c91-44aa-42ce-aec0-b95a08ff8ad8/GCF_030160715.1_ASM3016071v1_genomic.fna.gz --refList GCF_030160715.1_ASM3016071v1_genomic.fna/target_genomes.txt --output GCF_030160715.1_ASM3016071v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:26,208] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:26,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28120431-01d2-4096-8f54-c3f54c84238e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:26,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28120431-01d2-4096-8f54-c3f54c84238e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:26,223] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:03:26,223] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:03:26,223] [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 niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	86.5166	1903	3189	95	below_threshold
Bradyrhizobium centrolobii	strain=BR 10245	GCA_001641635.1	1505087	1505087	type	True	86.5077	1895	3189	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	86.4956	1909	3189	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	86.4861	1912	3189	95	below_threshold
Bradyrhizobium neotropicale	strain=BR 10247	GCA_001641695.1	1497615	1497615	type	True	86.2759	1875	3189	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	86.247	1834	3189	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	86.2117	1803	3189	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	86.1904	1853	3189	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	86.1292	1824	3189	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	86.0773	1858	3189	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000284375.1	375	375	type	True	86.0608	1858	3189	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	86.0418	1705	3189	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	85.9982	1622	3189	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	85.9676	1726	3189	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	85.8944	1791	3189	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	85.8903	1626	3189	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	85.8091	1653	3189	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	85.7957	1660	3189	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	85.7517	1707	3189	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	85.7428	1722	3189	95	below_threshold
Bradyrhizobium hipponense	strain=aSej3	GCA_008123965.1	2605638	2605638	type	True	85.732	1700	3189	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	85.6899	1698	3189	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	85.6198	1698	3189	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.7708	1525	3189	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	82.7266	1438	3189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:26,224] [INFO] DFAST Taxonomy check result was written to GCF_030160715.1_ASM3016071v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:26,225] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:26,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:26,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28120431-01d2-4096-8f54-c3f54c84238e/dqc_reference/checkm_data
[2024-01-25 20:03:26,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:26,313] [INFO] Task started: CheckM
[2024-01-25 20:03:26,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160715.1_ASM3016071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160715.1_ASM3016071v1_genomic.fna/checkm_input GCF_030160715.1_ASM3016071v1_genomic.fna/checkm_result
[2024-01-25 20:04:37,385] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:37,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:37,468] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:37,468] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:37,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160715.1_ASM3016071v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:37,469] [INFO] Task started: Blastn
[2024-01-25 20:04:37,469] [INFO] Running command: blastn -query GCF_030160715.1_ASM3016071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28120431-01d2-4096-8f54-c3f54c84238e/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160715.1_ASM3016071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:39,624] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:39,627] [INFO] Selected 25 target genomes.
[2024-01-25 20:04:39,627] [INFO] Target genome list was writen to GCF_030160715.1_ASM3016071v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:39,652] [INFO] Task started: fastANI
[2024-01-25 20:04:39,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5741c91-44aa-42ce-aec0-b95a08ff8ad8/GCF_030160715.1_ASM3016071v1_genomic.fna.gz --refList GCF_030160715.1_ASM3016071v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160715.1_ASM3016071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:39,691] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:39,706] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:05:39,706] [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_000472925.1	s__Bradyrhizobium sp000472925	90.6258	2233	3189	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	86.5452	1896	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_001641635.1	s__Bradyrhizobium centrolobii	86.5058	1895	3189	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	86.4789	1915	3189	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	86.399	1836	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129405.1	s__Bradyrhizobium iriomotense_B	86.3439	1870	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130945.1	s__Bradyrhizobium manausense_C	86.323	1870	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641695.1	s__Bradyrhizobium neotropicale	86.2872	1873	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.90	97.90	0.88	0.88	2	-
GCF_009759665.1	s__Bradyrhizobium cajani	86.2305	1799	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.56	95.54	0.80	0.80	3	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	86.2113	1821	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	86.0676	1623	3189	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	86.0594	1859	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.38	95.55	0.91	0.80	22	-
GCF_002795245.1	s__Bradyrhizobium forestalis	86.0353	1707	3189	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	86.0063	1701	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.55	95.55	0.86	0.86	2	-
GCF_018130785.1	s__Bradyrhizobium liaoningense_A	85.9999	1785	3189	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	85.9427	1708	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.68	97.67	0.91	0.90	3	-
GCF_013240495.1	s__Bradyrhizobium sp013240495	85.931	1750	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.36	98.36	0.89	0.89	2	-
GCF_001908185.1	s__Bradyrhizobium sp001908185	85.9027	1683	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473065.1	s__Bradyrhizobium sp000473065	85.8537	1682	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908205.1	s__Bradyrhizobium sp001908205	85.8058	1672	3189	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	85.7656	1700	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	95.51	95.51	0.86	0.86	2	-
GCF_008123965.1	s__Bradyrhizobium hipponense	85.7141	1704	3189	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	85.7051	1639	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830205.1	s__Bradyrhizobium daqingense	85.6171	1700	3189	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016616425.1	s__Bradyrhizobium diazoefficiens_E	85.6001	1551	3189	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 20:05:39,708] [INFO] GTDB search result was written to GCF_030160715.1_ASM3016071v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:39,708] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:39,712] [INFO] DFAST_QC result json was written to GCF_030160715.1_ASM3016071v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:39,712] [INFO] DFAST_QC completed!
[2024-01-25 20:05:39,712] [INFO] Total running time: 0h3m34s