[2024-01-24 11:12:58,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,014] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg67cf2bce-2088-4fb5-a797-3b9317776576/dqc_reference
[2024-01-24 11:12:59,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,410] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,411] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e55f774-8251-44ff-aab6-c4769d57e3ee/GCF_017565685.3_ASM1756568v3_genomic.fna.gz | prodigal -d GCF_017565685.3_ASM1756568v3_genomic.fna/cds.fna -a GCF_017565685.3_ASM1756568v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:35,109] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:35,109] [INFO] Task started: HMMsearch
[2024-01-24 11:13:35,109] [INFO] Running command: hmmsearch --tblout GCF_017565685.3_ASM1756568v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67cf2bce-2088-4fb5-a797-3b9317776576/dqc_reference/reference_markers.hmm GCF_017565685.3_ASM1756568v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:35,563] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:35,564] [INFO] Found 6/6 markers.
[2024-01-24 11:13:35,650] [INFO] Query marker FASTA was written to GCF_017565685.3_ASM1756568v3_genomic.fna/markers.fasta
[2024-01-24 11:13:35,650] [INFO] Task started: Blastn
[2024-01-24 11:13:35,650] [INFO] Running command: blastn -query GCF_017565685.3_ASM1756568v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg67cf2bce-2088-4fb5-a797-3b9317776576/dqc_reference/reference_markers.fasta -out GCF_017565685.3_ASM1756568v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:36,807] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:36,811] [INFO] Selected 16 target genomes.
[2024-01-24 11:13:36,812] [INFO] Target genome list was writen to GCF_017565685.3_ASM1756568v3_genomic.fna/target_genomes.txt
[2024-01-24 11:13:36,821] [INFO] Task started: fastANI
[2024-01-24 11:13:36,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e55f774-8251-44ff-aab6-c4769d57e3ee/GCF_017565685.3_ASM1756568v3_genomic.fna.gz --refList GCF_017565685.3_ASM1756568v3_genomic.fna/target_genomes.txt --output GCF_017565685.3_ASM1756568v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:17,069] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:17,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67cf2bce-2088-4fb5-a797-3b9317776576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:17,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67cf2bce-2088-4fb5-a797-3b9317776576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:17,086] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:14:17,087] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:14:17,087] [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 japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	94.9876	2399	3508	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	94.9381	2437	3508	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000284375.1	375	375	type	True	94.866	2469	3508	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	89.5604	2175	3508	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.5392	2139	3508	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	89.5029	2193	3508	95	below_threshold
Bradyrhizobium betae	strain=PL7HG1	GCA_008932115.1	244734	244734	type	True	89.4793	1896	3508	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	89.4336	1892	3508	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	89.1886	1961	3508	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	89.0145	2114	3508	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.7966	2063	3508	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	88.6829	2067	3508	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	88.6732	2070	3508	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	87.9317	1993	3508	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9594	1632	3508	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.8242	1523	3508	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:17,088] [INFO] DFAST Taxonomy check result was written to GCF_017565685.3_ASM1756568v3_genomic.fna/tc_result.tsv
[2024-01-24 11:14:17,089] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:17,089] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:17,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67cf2bce-2088-4fb5-a797-3b9317776576/dqc_reference/checkm_data
[2024-01-24 11:14:17,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:17,185] [INFO] Task started: CheckM
[2024-01-24 11:14:17,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017565685.3_ASM1756568v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017565685.3_ASM1756568v3_genomic.fna/checkm_input GCF_017565685.3_ASM1756568v3_genomic.fna/checkm_result
[2024-01-24 11:15:54,710] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:54,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:54,736] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:54,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:54,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017565685.3_ASM1756568v3_genomic.fna/markers.fasta)
[2024-01-24 11:15:54,737] [INFO] Task started: Blastn
[2024-01-24 11:15:54,737] [INFO] Running command: blastn -query GCF_017565685.3_ASM1756568v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg67cf2bce-2088-4fb5-a797-3b9317776576/dqc_reference/reference_markers_gtdb.fasta -out GCF_017565685.3_ASM1756568v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:56,888] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:56,892] [INFO] Selected 17 target genomes.
[2024-01-24 11:15:56,892] [INFO] Target genome list was writen to GCF_017565685.3_ASM1756568v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:56,921] [INFO] Task started: fastANI
[2024-01-24 11:15:56,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e55f774-8251-44ff-aab6-c4769d57e3ee/GCF_017565685.3_ASM1756568v3_genomic.fna.gz --refList GCF_017565685.3_ASM1756568v3_genomic.fna/target_genomes_gtdb.txt --output GCF_017565685.3_ASM1756568v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:16:49,312] [INFO] Task succeeded: fastANI
[2024-01-24 11:16:49,333] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:16:49,333] [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_011516635.3	s__Bradyrhizobium sp011516635	99.3143	2922	3508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	conclusive
GCF_000284375.1	s__Bradyrhizobium japonicum	94.9027	2462	3508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.38	95.55	0.91	0.80	22	-
GCF_018130785.1	s__Bradyrhizobium liaoningense_A	92.9327	2208	3508	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	89.6451	1879	3508	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	89.5331	2178	3508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_004571025.1	s__Bradyrhizobium niftali	89.5248	2140	3508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_008932115.1	s__Bradyrhizobium betae	89.4671	1900	3508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123905.1	s__Bradyrhizobium betae_A	89.3738	2096	3508	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	89.2157	2003	3508	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	89.1413	2009	3508	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	88.8482	2017	3508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908185.1	s__Bradyrhizobium sp001908185	88.7026	1872	3508	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	88.6804	2029	3508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_900094605.1	s__Bradyrhizobium shewense	88.6761	2067	3508	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	88.4941	1886	3508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008123425.1	s__Bradyrhizobium rifense	88.3435	2059	3508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016616885.1	s__Bradyrhizobium diazoefficiens_F	88.1797	1940	3508	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 11:16:49,334] [INFO] GTDB search result was written to GCF_017565685.3_ASM1756568v3_genomic.fna/result_gtdb.tsv
[2024-01-24 11:16:49,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:16:49,338] [INFO] DFAST_QC result json was written to GCF_017565685.3_ASM1756568v3_genomic.fna/dqc_result.json
[2024-01-24 11:16:49,338] [INFO] DFAST_QC completed!
[2024-01-24 11:16:49,338] [INFO] Total running time: 0h3m51s