[2024-01-24 14:39:02,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:02,896] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:02,896] [INFO] DQC Reference Directory: /var/lib/cwl/stgba1d9aae-60a9-4766-80a4-51de0f69d65e/dqc_reference
[2024-01-24 14:39:04,308] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,311] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,311] [INFO] Running command: gunzip -c /var/lib/cwl/stga54d5515-5227-49ba-90a9-c4dbc8fa7a79/GCF_001440415.1_ASM144041v1_genomic.fna.gz | prodigal -d GCF_001440415.1_ASM144041v1_genomic.fna/cds.fna -a GCF_001440415.1_ASM144041v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:30,688] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:30,689] [INFO] Task started: HMMsearch
[2024-01-24 14:39:30,689] [INFO] Running command: hmmsearch --tblout GCF_001440415.1_ASM144041v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba1d9aae-60a9-4766-80a4-51de0f69d65e/dqc_reference/reference_markers.hmm GCF_001440415.1_ASM144041v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:31,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:31,050] [INFO] Found 6/6 markers.
[2024-01-24 14:39:31,114] [INFO] Query marker FASTA was written to GCF_001440415.1_ASM144041v1_genomic.fna/markers.fasta
[2024-01-24 14:39:31,114] [INFO] Task started: Blastn
[2024-01-24 14:39:31,115] [INFO] Running command: blastn -query GCF_001440415.1_ASM144041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba1d9aae-60a9-4766-80a4-51de0f69d65e/dqc_reference/reference_markers.fasta -out GCF_001440415.1_ASM144041v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:32,169] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:32,173] [INFO] Selected 13 target genomes.
[2024-01-24 14:39:32,173] [INFO] Target genome list was writen to GCF_001440415.1_ASM144041v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:32,179] [INFO] Task started: fastANI
[2024-01-24 14:39:32,179] [INFO] Running command: fastANI --query /var/lib/cwl/stga54d5515-5227-49ba-90a9-c4dbc8fa7a79/GCF_001440415.1_ASM144041v1_genomic.fna.gz --refList GCF_001440415.1_ASM144041v1_genomic.fna/target_genomes.txt --output GCF_001440415.1_ASM144041v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:00,247] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:00,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba1d9aae-60a9-4766-80a4-51de0f69d65e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:00,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba1d9aae-60a9-4766-80a4-51de0f69d65e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:00,261] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:00,262] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:00,262] [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 retamae	strain=Ro19	GCA_001440415.1	1300035	1300035	type	True	100.0	2687	2708	95	conclusive
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	93.564	2026	2708	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	91.4806	2017	2708	95	below_threshold
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	90.1276	1880	2708	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	89.1132	1952	2708	95	below_threshold
Bradyrhizobium archetypum	strain=WSM 1744	GCA_013114835.1	2721160	2721160	type	True	88.0698	1850	2708	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	87.8645	1860	2708	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	87.4994	1774	2708	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	83.0029	1215	2708	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	82.5048	1445	2708	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.432	1391	2708	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.4317	1330	2708	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.357	1316	2708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:00,264] [INFO] DFAST Taxonomy check result was written to GCF_001440415.1_ASM144041v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:00,264] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:00,264] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:00,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba1d9aae-60a9-4766-80a4-51de0f69d65e/dqc_reference/checkm_data
[2024-01-24 14:40:00,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:00,346] [INFO] Task started: CheckM
[2024-01-24 14:40:00,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001440415.1_ASM144041v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001440415.1_ASM144041v1_genomic.fna/checkm_input GCF_001440415.1_ASM144041v1_genomic.fna/checkm_result
[2024-01-24 14:41:08,115] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:08,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:08,137] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:08,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:08,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001440415.1_ASM144041v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:08,138] [INFO] Task started: Blastn
[2024-01-24 14:41:08,138] [INFO] Running command: blastn -query GCF_001440415.1_ASM144041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba1d9aae-60a9-4766-80a4-51de0f69d65e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001440415.1_ASM144041v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:10,087] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:10,090] [INFO] Selected 9 target genomes.
[2024-01-24 14:41:10,091] [INFO] Target genome list was writen to GCF_001440415.1_ASM144041v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:10,106] [INFO] Task started: fastANI
[2024-01-24 14:41:10,106] [INFO] Running command: fastANI --query /var/lib/cwl/stga54d5515-5227-49ba-90a9-c4dbc8fa7a79/GCF_001440415.1_ASM144041v1_genomic.fna.gz --refList GCF_001440415.1_ASM144041v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001440415.1_ASM144041v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:29,608] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:29,618] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:29,618] [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_001440415.1	s__Bradyrhizobium retamae	100.0	2689	2708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018398875.1	s__Bradyrhizobium sp018398875	94.313	2115	2708	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	94.2046	2026	2708	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	93.5667	2025	2708	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	92.1754	2071	2708	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	91.4866	2017	2708	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	90.1276	1880	2708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013114835.1	s__Bradyrhizobium archetypum	88.0883	1847	2708	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	87.8824	1857	2708	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 14:41:29,620] [INFO] GTDB search result was written to GCF_001440415.1_ASM144041v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:29,620] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:29,624] [INFO] DFAST_QC result json was written to GCF_001440415.1_ASM144041v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:29,624] [INFO] DFAST_QC completed!
[2024-01-24 14:41:29,624] [INFO] Total running time: 0h2m27s