[2024-01-24 13:55:18,082] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:18,084] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:18,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg42f098c8-6898-4b75-aaf8-52240e1d091f/dqc_reference
[2024-01-24 13:55:19,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:19,410] [INFO] Task started: Prodigal
[2024-01-24 13:55:19,410] [INFO] Running command: gunzip -c /var/lib/cwl/stg16810a77-a07a-4b8b-bbe8-8779436b80f5/GCF_000284375.1_ASM28437v1_genomic.fna.gz | prodigal -d GCF_000284375.1_ASM28437v1_genomic.fna/cds.fna -a GCF_000284375.1_ASM28437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:49,095] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:49,096] [INFO] Task started: HMMsearch
[2024-01-24 13:55:49,096] [INFO] Running command: hmmsearch --tblout GCF_000284375.1_ASM28437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42f098c8-6898-4b75-aaf8-52240e1d091f/dqc_reference/reference_markers.hmm GCF_000284375.1_ASM28437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:49,492] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:49,493] [INFO] Found 6/6 markers.
[2024-01-24 13:55:49,566] [INFO] Query marker FASTA was written to GCF_000284375.1_ASM28437v1_genomic.fna/markers.fasta
[2024-01-24 13:55:49,566] [INFO] Task started: Blastn
[2024-01-24 13:55:49,567] [INFO] Running command: blastn -query GCF_000284375.1_ASM28437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42f098c8-6898-4b75-aaf8-52240e1d091f/dqc_reference/reference_markers.fasta -out GCF_000284375.1_ASM28437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:50,799] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:50,802] [INFO] Selected 16 target genomes.
[2024-01-24 13:55:50,803] [INFO] Target genome list was writen to GCF_000284375.1_ASM28437v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:50,817] [INFO] Task started: fastANI
[2024-01-24 13:55:50,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg16810a77-a07a-4b8b-bbe8-8779436b80f5/GCF_000284375.1_ASM28437v1_genomic.fna.gz --refList GCF_000284375.1_ASM28437v1_genomic.fna/target_genomes.txt --output GCF_000284375.1_ASM28437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:29,184] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:29,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42f098c8-6898-4b75-aaf8-52240e1d091f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:29,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42f098c8-6898-4b75-aaf8-52240e1d091f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:29,201] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:56:29,201] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:29,202] [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=USDA 6	GCA_000284375.1	375	375	type	True	100.0	3068	3069	95	conclusive
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	99.9662	2985	3069	95	conclusive
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	99.9556	2938	3069	95	conclusive
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	90.9031	2351	3069	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	90.8498	2381	3069	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	90.3231	2323	3069	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	90.2099	2218	3069	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	89.6661	1857	3069	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.6336	2158	3069	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	89.4778	2091	3069	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	88.9621	2086	3069	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	88.7975	2117	3069	95	below_threshold
Bradyrhizobium forestalis	strain=INPA54B	GCA_002795245.1	1419263	1419263	type	True	88.669	1987	3069	95	below_threshold
Bradyrhizobium rifense	strain=CTAW71	GCA_008123425.1	515499	515499	type	True	88.4501	2043	3069	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9913	1588	3069	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.8437	1510	3069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:29,203] [INFO] DFAST Taxonomy check result was written to GCF_000284375.1_ASM28437v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:29,204] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:29,204] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:29,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42f098c8-6898-4b75-aaf8-52240e1d091f/dqc_reference/checkm_data
[2024-01-24 13:56:29,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:29,285] [INFO] Task started: CheckM
[2024-01-24 13:56:29,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000284375.1_ASM28437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000284375.1_ASM28437v1_genomic.fna/checkm_input GCF_000284375.1_ASM28437v1_genomic.fna/checkm_result
[2024-01-24 13:58:03,065] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:03,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:03,087] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:03,087] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:03,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000284375.1_ASM28437v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:03,088] [INFO] Task started: Blastn
[2024-01-24 13:58:03,088] [INFO] Running command: blastn -query GCF_000284375.1_ASM28437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42f098c8-6898-4b75-aaf8-52240e1d091f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000284375.1_ASM28437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:05,475] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:05,477] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:05,478] [INFO] Target genome list was writen to GCF_000284375.1_ASM28437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:05,487] [INFO] Task started: fastANI
[2024-01-24 13:58:05,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg16810a77-a07a-4b8b-bbe8-8779436b80f5/GCF_000284375.1_ASM28437v1_genomic.fna.gz --refList GCF_000284375.1_ASM28437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000284375.1_ASM28437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:42,414] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:42,427] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:42,427] [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_000284375.1	s__Bradyrhizobium japonicum	100.0	3068	3069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.38	95.55	0.91	0.80	22	conclusive
GCF_011516635.3	s__Bradyrhizobium sp011516635	94.8317	2495	3069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	-
GCF_018130785.1	s__Bradyrhizobium liaoningense_A	93.3527	2301	3069	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	90.8529	2380	3069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.15	98.13	0.93	0.84	23	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	89.6811	1876	3069	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	89.6254	2159	3069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.00	95.49	0.80	0.80	3	-
GCF_018130765.1	s__Bradyrhizobium iriomotense_A	89.4901	2030	3069	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	89.3396	2000	3069	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	89.0708	2061	3069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	88.8603	1862	3069	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	88.8275	2061	3069	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	88.825	2112	3069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_001908185.1	s__Bradyrhizobium sp001908185	88.8103	1875	3069	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	88.6844	1985	3069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003020125.1	s__Bradyrhizobium sp003020125	88.6646	1886	3069	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 13:58:42,429] [INFO] GTDB search result was written to GCF_000284375.1_ASM28437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:42,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:42,433] [INFO] DFAST_QC result json was written to GCF_000284375.1_ASM28437v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:42,433] [INFO] DFAST_QC completed!
[2024-01-24 13:58:42,433] [INFO] Total running time: 0h3m24s