[2024-01-24 13:32:39,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:39,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:39,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg677a2f62-ff3e-4f0a-bb7b-9754b12f7694/dqc_reference
[2024-01-24 13:32:40,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:40,987] [INFO] Task started: Prodigal
[2024-01-24 13:32:40,987] [INFO] Running command: gunzip -c /var/lib/cwl/stg40e16a70-16c6-4b4c-a235-60fb98695057/GCF_020547085.1_ASM2054708v1_genomic.fna.gz | prodigal -d GCF_020547085.1_ASM2054708v1_genomic.fna/cds.fna -a GCF_020547085.1_ASM2054708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:49,384] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:49,384] [INFO] Task started: HMMsearch
[2024-01-24 13:32:49,384] [INFO] Running command: hmmsearch --tblout GCF_020547085.1_ASM2054708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg677a2f62-ff3e-4f0a-bb7b-9754b12f7694/dqc_reference/reference_markers.hmm GCF_020547085.1_ASM2054708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:49,570] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:49,571] [INFO] Found 6/6 markers.
[2024-01-24 13:32:49,596] [INFO] Query marker FASTA was written to GCF_020547085.1_ASM2054708v1_genomic.fna/markers.fasta
[2024-01-24 13:32:49,596] [INFO] Task started: Blastn
[2024-01-24 13:32:49,596] [INFO] Running command: blastn -query GCF_020547085.1_ASM2054708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg677a2f62-ff3e-4f0a-bb7b-9754b12f7694/dqc_reference/reference_markers.fasta -out GCF_020547085.1_ASM2054708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:50,200] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:50,203] [INFO] Selected 8 target genomes.
[2024-01-24 13:32:50,203] [INFO] Target genome list was writen to GCF_020547085.1_ASM2054708v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:50,269] [INFO] Task started: fastANI
[2024-01-24 13:32:50,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e16a70-16c6-4b4c-a235-60fb98695057/GCF_020547085.1_ASM2054708v1_genomic.fna.gz --refList GCF_020547085.1_ASM2054708v1_genomic.fna/target_genomes.txt --output GCF_020547085.1_ASM2054708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:01,557] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:01,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg677a2f62-ff3e-4f0a-bb7b-9754b12f7694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:01,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg677a2f62-ff3e-4f0a-bb7b-9754b12f7694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:01,591] [INFO] Found 8 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 13:33:01,591] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:01,591] [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
Deinococcus radiodurans	strain=ATCC 13939 substr. R6	GCA_020547085.1	1299	1299	type	True	100.0	1081	1082	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. R2	GCA_020547025.1	1299	1299	type	True	99.9989	1059	1082	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. S1	GCA_020546705.1	1299	1299	type	True	99.9984	1067	1082	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. R1	GCA_020546805.1	1299	1299	type	True	99.9977	1061	1082	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. S2	GCA_020546785.1	1299	1299	type	True	99.9946	1070	1082	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939	GCA_020546685.1	1299	1299	type	True	99.9926	1076	1082	95	conclusive
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	99.95	1070	1082	95	conclusive
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	99.9479	1024	1082	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:33:01,594] [INFO] DFAST Taxonomy check result was written to GCF_020547085.1_ASM2054708v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:01,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:01,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:01,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg677a2f62-ff3e-4f0a-bb7b-9754b12f7694/dqc_reference/checkm_data
[2024-01-24 13:33:01,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:01,640] [INFO] Task started: CheckM
[2024-01-24 13:33:01,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020547085.1_ASM2054708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020547085.1_ASM2054708v1_genomic.fna/checkm_input GCF_020547085.1_ASM2054708v1_genomic.fna/checkm_result
[2024-01-24 13:33:31,367] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:31,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:31,381] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:31,381] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:31,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020547085.1_ASM2054708v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:31,382] [INFO] Task started: Blastn
[2024-01-24 13:33:31,382] [INFO] Running command: blastn -query GCF_020547085.1_ASM2054708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg677a2f62-ff3e-4f0a-bb7b-9754b12f7694/dqc_reference/reference_markers_gtdb.fasta -out GCF_020547085.1_ASM2054708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:32,325] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:32,327] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:32,327] [INFO] Target genome list was writen to GCF_020547085.1_ASM2054708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:32,341] [INFO] Task started: fastANI
[2024-01-24 13:33:32,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e16a70-16c6-4b4c-a235-60fb98695057/GCF_020547085.1_ASM2054708v1_genomic.fna.gz --refList GCF_020547085.1_ASM2054708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020547085.1_ASM2054708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:43,657] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:43,677] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:43,678] [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_000008565.1	s__Deinococcus radiodurans	99.95	1070	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	conclusive
GCF_011067105.1	s__Deinococcus wulumuqiensis	87.4176	855	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.82	97.50	0.97	0.83	19	-
GCF_900109185.1	s__Deinococcus reticulitermitis	80.743	636	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	80.4637	606	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424185.1	s__Deinococcus sp001424185	79.6533	566	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377345.1	s__Deinococcus sp009377345	79.6445	490	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201885.1	s__Deinococcus budaensis	79.5298	546	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599865.1	s__Deinococcus phoenicis	79.4579	536	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647075.1	s__Deinococcus aerophilus	79.1102	487	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897375.1	s__Deinococcus aerius	79.0345	502	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003028415.1	s__Deinococcus sp003028415	78.9087	504	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003444775.1	s__Deinococcus ficus	78.8234	460	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	-
GCF_001485435.1	s__Deinococcus grandis	78.5079	497	1082	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:43,679] [INFO] GTDB search result was written to GCF_020547085.1_ASM2054708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:43,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:43,682] [INFO] DFAST_QC result json was written to GCF_020547085.1_ASM2054708v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:43,682] [INFO] DFAST_QC completed!
[2024-01-24 13:33:43,682] [INFO] Total running time: 0h1m4s