[2024-01-24 11:12:36,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b1b852f-96aa-4fc5-a73c-e2ee2172a789/dqc_reference
[2024-01-24 11:12:38,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,666] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,666] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7bc41df-e1b7-4ca4-b291-c777be34ce1a/GCF_001440405.1_ASM144040v1_genomic.fna.gz | prodigal -d GCF_001440405.1_ASM144040v1_genomic.fna/cds.fna -a GCF_001440405.1_ASM144040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:04,684] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:04,684] [INFO] Task started: HMMsearch
[2024-01-24 11:13:04,684] [INFO] Running command: hmmsearch --tblout GCF_001440405.1_ASM144040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b1b852f-96aa-4fc5-a73c-e2ee2172a789/dqc_reference/reference_markers.hmm GCF_001440405.1_ASM144040v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:04,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:04,982] [INFO] Found 6/6 markers.
[2024-01-24 11:13:05,042] [INFO] Query marker FASTA was written to GCF_001440405.1_ASM144040v1_genomic.fna/markers.fasta
[2024-01-24 11:13:05,043] [INFO] Task started: Blastn
[2024-01-24 11:13:05,043] [INFO] Running command: blastn -query GCF_001440405.1_ASM144040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b1b852f-96aa-4fc5-a73c-e2ee2172a789/dqc_reference/reference_markers.fasta -out GCF_001440405.1_ASM144040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:06,043] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:06,046] [INFO] Selected 13 target genomes.
[2024-01-24 11:13:06,046] [INFO] Target genome list was writen to GCF_001440405.1_ASM144040v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:06,052] [INFO] Task started: fastANI
[2024-01-24 11:13:06,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7bc41df-e1b7-4ca4-b291-c777be34ce1a/GCF_001440405.1_ASM144040v1_genomic.fna.gz --refList GCF_001440405.1_ASM144040v1_genomic.fna/target_genomes.txt --output GCF_001440405.1_ASM144040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:33,544] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:33,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b1b852f-96aa-4fc5-a73c-e2ee2172a789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:33,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b1b852f-96aa-4fc5-a73c-e2ee2172a789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:33,555] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:33,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:33,555] [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 valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	100.0	2812	2826	95	conclusive
Bradyrhizobium retamae	strain=Ro19	GCA_001440415.1	1300035	1300035	type	True	89.0878	1953	2826	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	88.5529	1940	2826	95	below_threshold
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	88.4788	1948	2826	95	below_threshold
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	88.0434	1823	2826	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	87.849	1925	2826	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	87.811	1917	2826	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	87.4549	1862	2826	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	83.2526	1238	2826	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	82.7712	1467	2826	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.681	1356	2826	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.6635	1396	2826	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.6474	1328	2826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:33,557] [INFO] DFAST Taxonomy check result was written to GCF_001440405.1_ASM144040v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:33,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:33,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:33,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b1b852f-96aa-4fc5-a73c-e2ee2172a789/dqc_reference/checkm_data
[2024-01-24 11:13:33,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:33,638] [INFO] Task started: CheckM
[2024-01-24 11:13:33,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001440405.1_ASM144040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001440405.1_ASM144040v1_genomic.fna/checkm_input GCF_001440405.1_ASM144040v1_genomic.fna/checkm_result
[2024-01-24 11:14:42,416] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:42,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:42,445] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:42,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:42,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001440405.1_ASM144040v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:42,445] [INFO] Task started: Blastn
[2024-01-24 11:14:42,445] [INFO] Running command: blastn -query GCF_001440405.1_ASM144040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b1b852f-96aa-4fc5-a73c-e2ee2172a789/dqc_reference/reference_markers_gtdb.fasta -out GCF_001440405.1_ASM144040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:44,507] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:44,511] [INFO] Selected 14 target genomes.
[2024-01-24 11:14:44,511] [INFO] Target genome list was writen to GCF_001440405.1_ASM144040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:44,520] [INFO] Task started: fastANI
[2024-01-24 11:14:44,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7bc41df-e1b7-4ca4-b291-c777be34ce1a/GCF_001440405.1_ASM144040v1_genomic.fna.gz --refList GCF_001440405.1_ASM144040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001440405.1_ASM144040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:16,245] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:16,257] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:16,257] [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_001440405.1	s__Bradyrhizobium valentinum	100.0	2812	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	99.35	0.91	0.91	2	conclusive
GCF_003062295.1	s__Bradyrhizobium algeriense	90.2201	2083	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018596315.1	s__Bradyrhizobium sp018596315	89.9005	2071	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130385.1	s__Bradyrhizobium sp018130385	89.2679	1804	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398895.1	s__Bradyrhizobium sp018398895	89.1943	2084	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693485.1	s__Bradyrhizobium sp001693485	88.6224	1947	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693385.1	s__Bradyrhizobium icense	88.5404	1941	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472965.1	s__Bradyrhizobium murdochi	88.4776	1949	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009930815.1	s__Bradyrhizobium sp009930815	88.1441	2025	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013114825.1	s__Bradyrhizobium australiense	88.0315	1825	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693515.2	s__Bradyrhizobium paxllaeri	87.8472	1926	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440475.1	s__Bradyrhizobium lablabi	87.7909	1920	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440395.1	s__Bradyrhizobium jicamae	87.4434	1864	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099825.1	s__Bradyrhizobium ottawaense_A	84.7875	1498	2826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.73	99.45	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:16,258] [INFO] GTDB search result was written to GCF_001440405.1_ASM144040v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:16,259] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:16,262] [INFO] DFAST_QC result json was written to GCF_001440405.1_ASM144040v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:16,263] [INFO] DFAST_QC completed!
[2024-01-24 11:15:16,263] [INFO] Total running time: 0h2m40s