[2024-01-24 12:14:10,544] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ea91e33-7d29-4501-8f57-754886ec10ac/dqc_reference
[2024-01-24 12:14:11,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,897] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg31a2c9af-6fa4-4aa0-b466-da8609018170/GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna.gz | prodigal -d GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/cds.fna -a GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:27,926] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:27,926] [INFO] Task started: HMMsearch
[2024-01-24 12:14:27,926] [INFO] Running command: hmmsearch --tblout GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ea91e33-7d29-4501-8f57-754886ec10ac/dqc_reference/reference_markers.hmm GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:28,299] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:28,300] [INFO] Found 6/6 markers.
[2024-01-24 12:14:28,354] [INFO] Query marker FASTA was written to GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/markers.fasta
[2024-01-24 12:14:28,355] [INFO] Task started: Blastn
[2024-01-24 12:14:28,355] [INFO] Running command: blastn -query GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ea91e33-7d29-4501-8f57-754886ec10ac/dqc_reference/reference_markers.fasta -out GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:29,411] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:29,414] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:29,414] [INFO] Target genome list was writen to GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:29,422] [INFO] Task started: fastANI
[2024-01-24 12:14:29,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg31a2c9af-6fa4-4aa0-b466-da8609018170/GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna.gz --refList GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/target_genomes.txt --output GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:50,397] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:50,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ea91e33-7d29-4501-8f57-754886ec10ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:50,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ea91e33-7d29-4501-8f57-754886ec10ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:50,410] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:50,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:50,411] [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
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	100.0	1748	1753	95	conclusive
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	85.9642	1203	1753	95	below_threshold
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	85.8995	1227	1753	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	84.9263	1133	1753	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	80.1938	770	1753	95	below_threshold
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	80.0186	590	1753	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	80.0078	759	1753	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	79.958	815	1753	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	79.9099	765	1753	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	79.8791	852	1753	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	79.8544	765	1753	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	79.7569	777	1753	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	79.5745	758	1753	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	79.4965	744	1753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:50,412] [INFO] DFAST Taxonomy check result was written to GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:50,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:50,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:50,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ea91e33-7d29-4501-8f57-754886ec10ac/dqc_reference/checkm_data
[2024-01-24 12:14:50,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:50,468] [INFO] Task started: CheckM
[2024-01-24 12:14:50,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/checkm_input GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/checkm_result
[2024-01-24 12:15:38,531] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:38,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:38,556] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:38,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:38,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/markers.fasta)
[2024-01-24 12:15:38,558] [INFO] Task started: Blastn
[2024-01-24 12:15:38,558] [INFO] Running command: blastn -query GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ea91e33-7d29-4501-8f57-754886ec10ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:40,514] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:40,518] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:40,518] [INFO] Target genome list was writen to GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:40,534] [INFO] Task started: fastANI
[2024-01-24 12:15:40,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg31a2c9af-6fa4-4aa0-b466-da8609018170/GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna.gz --refList GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:50,620] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:50,632] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:50,632] [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_000314675.2	s__Afipia broomeae	100.0	1747	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.99	97.77	0.89	0.84	9	conclusive
GCF_000497575.1	s__Afipia sp000497575	90.8133	1327	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.26	97.37	0.94	0.78	8	-
GCA_017474385.1	s__Afipia sp017474385	89.5457	1030	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006325.2	s__Afipia massiliensis_A	86.0394	1157	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203115.1	s__Afipia massiliensis	85.9518	1205	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308295.2	s__Afipia birgiae	85.894	1228	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.96	98.31	0.86	0.83	3	-
GCF_000336555.1	s__Afipia clevelandensis	84.9277	1132	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.84	97.84	0.91	0.91	2	-
GCA_017308595.1	s__Afipia sp017308595	84.6422	1158	1753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:50,635] [INFO] GTDB search result was written to GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:50,635] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:50,638] [INFO] DFAST_QC result json was written to GCF_000314675.2_Afip_broo_ATCC_49717_V1_genomic.fna/dqc_result.json
[2024-01-24 12:15:50,639] [INFO] DFAST_QC completed!
[2024-01-24 12:15:50,639] [INFO] Total running time: 0h1m40s