[2024-01-24 13:48:59,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,802] [INFO] DQC Reference Directory: /var/lib/cwl/stgd25c245a-e4e9-454a-8a64-625e6c3951c6/dqc_reference
[2024-01-24 13:49:01,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,214] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,214] [INFO] Running command: gunzip -c /var/lib/cwl/stgc77f24d2-b7f3-4b34-8fb3-3a13eaa9c1b8/GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/cds.fna -a GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:20,172] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:20,173] [INFO] Task started: HMMsearch
[2024-01-24 13:49:20,173] [INFO] Running command: hmmsearch --tblout GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd25c245a-e4e9-454a-8a64-625e6c3951c6/dqc_reference/reference_markers.hmm GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:20,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:20,505] [INFO] Found 6/6 markers.
[2024-01-24 13:49:20,560] [INFO] Query marker FASTA was written to GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:20,561] [INFO] Task started: Blastn
[2024-01-24 13:49:20,561] [INFO] Running command: blastn -query GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd25c245a-e4e9-454a-8a64-625e6c3951c6/dqc_reference/reference_markers.fasta -out GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:21,544] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:21,548] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:21,549] [INFO] Target genome list was writen to GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:21,552] [INFO] Task started: fastANI
[2024-01-24 13:49:21,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgc77f24d2-b7f3-4b34-8fb3-3a13eaa9c1b8/GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna.gz --refList GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:34,860] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:34,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd25c245a-e4e9-454a-8a64-625e6c3951c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:34,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd25c245a-e4e9-454a-8a64-625e6c3951c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:34,870] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:34,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:34,871] [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
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	100.0	2149	2152	95	conclusive
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	92.2988	1541	2152	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	83.9275	1208	2152	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	81.9508	927	2152	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	81.9182	1061	2152	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	81.7243	918	2152	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	81.6818	920	2152	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	81.6791	1039	2152	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	81.587	904	2152	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	81.1991	883	2152	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	81.1044	886	2152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:34,873] [INFO] DFAST Taxonomy check result was written to GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:49:34,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:34,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:34,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd25c245a-e4e9-454a-8a64-625e6c3951c6/dqc_reference/checkm_data
[2024-01-24 13:49:34,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:34,938] [INFO] Task started: CheckM
[2024-01-24 13:49:34,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/checkm_input GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:30,015] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:30,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:30,038] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:30,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:30,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:30,040] [INFO] Task started: Blastn
[2024-01-24 13:50:30,040] [INFO] Running command: blastn -query GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd25c245a-e4e9-454a-8a64-625e6c3951c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:31,912] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:31,915] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:31,915] [INFO] Target genome list was writen to GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:31,952] [INFO] Task started: fastANI
[2024-01-24 13:50:31,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgc77f24d2-b7f3-4b34-8fb3-3a13eaa9c1b8/GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna.gz --refList GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:44,757] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:44,766] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:44,767] [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_900220975.1	s__Mycoplana subbaraonis	100.0	2149	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013378445.1	s__Mycoplana rhizolycopersici	92.3049	1540	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469965.1	s__Mycoplana sp900469965	84.5776	1213	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	98.03	97.96	0.94	0.92	10	-
GCF_014196765.1	s__Mycoplana azooxidifex	83.9352	1207	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046475.1	s__Mycoplana dimorpha	82.5836	959	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851675.1	s__Mycoplana sp014851675	81.9333	969	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	81.727	918	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574625.1	s__Shinella zoogloeoides_A	81.5982	924	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004514435.1	s__Shinella sp004514435	81.2344	876	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.21	98.45	0.95	0.91	3	-
GCF_001262505.1	s__Shinella sp001262505	81.1629	1024	2152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:44,768] [INFO] GTDB search result was written to GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:44,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:44,772] [INFO] DFAST_QC result json was written to GCF_900220975.1_IMG-taxon_2740891857_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:50:44,773] [INFO] DFAST_QC completed!
[2024-01-24 13:50:44,773] [INFO] Total running time: 0h1m45s