[2024-01-25 18:55:35,488] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:35,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:35,489] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa57f745-d27f-4b08-8272-7d047194daa2/dqc_reference
[2024-01-25 18:55:36,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:36,647] [INFO] Task started: Prodigal
[2024-01-25 18:55:36,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d78dd5f-2409-4770-828b-8dc8483722df/GCF_020546685.1_ASM2054668v1_genomic.fna.gz | prodigal -d GCF_020546685.1_ASM2054668v1_genomic.fna/cds.fna -a GCF_020546685.1_ASM2054668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:45,288] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:45,288] [INFO] Task started: HMMsearch
[2024-01-25 18:55:45,288] [INFO] Running command: hmmsearch --tblout GCF_020546685.1_ASM2054668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa57f745-d27f-4b08-8272-7d047194daa2/dqc_reference/reference_markers.hmm GCF_020546685.1_ASM2054668v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:45,489] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:45,490] [INFO] Found 6/6 markers.
[2024-01-25 18:55:45,527] [INFO] Query marker FASTA was written to GCF_020546685.1_ASM2054668v1_genomic.fna/markers.fasta
[2024-01-25 18:55:45,527] [INFO] Task started: Blastn
[2024-01-25 18:55:45,527] [INFO] Running command: blastn -query GCF_020546685.1_ASM2054668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa57f745-d27f-4b08-8272-7d047194daa2/dqc_reference/reference_markers.fasta -out GCF_020546685.1_ASM2054668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:46,150] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:46,153] [INFO] Selected 7 target genomes.
[2024-01-25 18:55:46,153] [INFO] Target genome list was writen to GCF_020546685.1_ASM2054668v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:46,155] [INFO] Task started: fastANI
[2024-01-25 18:55:46,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d78dd5f-2409-4770-828b-8dc8483722df/GCF_020546685.1_ASM2054668v1_genomic.fna.gz --refList GCF_020546685.1_ASM2054668v1_genomic.fna/target_genomes.txt --output GCF_020546685.1_ASM2054668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:56,182] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:56,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa57f745-d27f-4b08-8272-7d047194daa2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:56,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa57f745-d27f-4b08-8272-7d047194daa2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:56,189] [INFO] Found 7 fastANI hits (7 hits with ANI > threshold)
[2024-01-25 18:55:56,189] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:56,190] [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	GCA_020546685.1	1299	1299	type	True	100.0	1092	1092	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. R1	GCA_020546805.1	1299	1299	type	True	99.9985	1064	1092	95	conclusive
Deinococcus radiodurans	strain=R1	GCA_001638825.1	1299	1299	type	True	99.9945	1091	1092	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. R2	GCA_020547025.1	1299	1299	type	True	99.9903	1063	1092	95	conclusive
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	99.9589	1039	1092	95	conclusive
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	99.9578	1085	1092	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939	GCA_000687895.1	1299	1299	type	True	99.9541	1052	1092	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 18:55:56,191] [INFO] DFAST Taxonomy check result was written to GCF_020546685.1_ASM2054668v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:56,191] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:56,191] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:56,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa57f745-d27f-4b08-8272-7d047194daa2/dqc_reference/checkm_data
[2024-01-25 18:55:56,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:56,227] [INFO] Task started: CheckM
[2024-01-25 18:55:56,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020546685.1_ASM2054668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020546685.1_ASM2054668v1_genomic.fna/checkm_input GCF_020546685.1_ASM2054668v1_genomic.fna/checkm_result
[2024-01-25 18:56:24,135] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:24,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:24,154] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:24,155] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:24,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020546685.1_ASM2054668v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:24,155] [INFO] Task started: Blastn
[2024-01-25 18:56:24,156] [INFO] Running command: blastn -query GCF_020546685.1_ASM2054668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa57f745-d27f-4b08-8272-7d047194daa2/dqc_reference/reference_markers_gtdb.fasta -out GCF_020546685.1_ASM2054668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:25,129] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:25,132] [INFO] Selected 13 target genomes.
[2024-01-25 18:56:25,132] [INFO] Target genome list was writen to GCF_020546685.1_ASM2054668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:25,133] [INFO] Task started: fastANI
[2024-01-25 18:56:25,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d78dd5f-2409-4770-828b-8dc8483722df/GCF_020546685.1_ASM2054668v1_genomic.fna.gz --refList GCF_020546685.1_ASM2054668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020546685.1_ASM2054668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:36,580] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:36,589] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:36,589] [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	99.9578	1085	1092	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	87.3972	862	1092	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	80.7322	647	1092	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	80.4117	618	1092	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	79.7105	491	1092	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	79.6373	570	1092	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	79.4855	550	1092	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	79.4689	533	1092	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	79.0936	490	1092	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	79.0506	509	1092	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	78.9198	508	1092	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	78.7618	472	1092	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	78.5879	501	1092	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:36,592] [INFO] GTDB search result was written to GCF_020546685.1_ASM2054668v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:36,592] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:36,595] [INFO] DFAST_QC result json was written to GCF_020546685.1_ASM2054668v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:36,595] [INFO] DFAST_QC completed!
[2024-01-25 18:56:36,595] [INFO] Total running time: 0h1m1s