[2024-01-24 12:27:19,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:19,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:19,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg476a39f5-9a7c-45af-96cc-2aa79d23bade/dqc_reference
[2024-01-24 12:27:20,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:20,817] [INFO] Task started: Prodigal
[2024-01-24 12:27:20,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgfebbe2be-da21-4848-8c5b-e5945a632739/GCF_020547025.1_ASM2054702v1_genomic.fna.gz | prodigal -d GCF_020547025.1_ASM2054702v1_genomic.fna/cds.fna -a GCF_020547025.1_ASM2054702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:30,116] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:30,117] [INFO] Task started: HMMsearch
[2024-01-24 12:27:30,117] [INFO] Running command: hmmsearch --tblout GCF_020547025.1_ASM2054702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg476a39f5-9a7c-45af-96cc-2aa79d23bade/dqc_reference/reference_markers.hmm GCF_020547025.1_ASM2054702v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:30,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:30,350] [INFO] Found 6/6 markers.
[2024-01-24 12:27:30,385] [INFO] Query marker FASTA was written to GCF_020547025.1_ASM2054702v1_genomic.fna/markers.fasta
[2024-01-24 12:27:30,385] [INFO] Task started: Blastn
[2024-01-24 12:27:30,386] [INFO] Running command: blastn -query GCF_020547025.1_ASM2054702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg476a39f5-9a7c-45af-96cc-2aa79d23bade/dqc_reference/reference_markers.fasta -out GCF_020547025.1_ASM2054702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:31,060] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:31,065] [INFO] Selected 8 target genomes.
[2024-01-24 12:27:31,066] [INFO] Target genome list was writen to GCF_020547025.1_ASM2054702v1_genomic.fna/target_genomes.txt
[2024-01-24 12:27:31,093] [INFO] Task started: fastANI
[2024-01-24 12:27:31,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgfebbe2be-da21-4848-8c5b-e5945a632739/GCF_020547025.1_ASM2054702v1_genomic.fna.gz --refList GCF_020547025.1_ASM2054702v1_genomic.fna/target_genomes.txt --output GCF_020547025.1_ASM2054702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:27:42,102] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:42,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg476a39f5-9a7c-45af-96cc-2aa79d23bade/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:27:42,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg476a39f5-9a7c-45af-96cc-2aa79d23bade/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:27:42,112] [INFO] Found 8 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 12:27:42,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:27:42,113] [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. R2	GCA_020547025.1	1299	1299	type	True	100.0	1064	1064	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939	GCA_020546685.1	1299	1299	type	True	99.9964	1062	1064	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. R1	GCA_020546805.1	1299	1299	type	True	99.9948	1063	1064	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. S2	GCA_020546785.1	1299	1299	type	True	99.993	1063	1064	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. R6	GCA_020547085.1	1299	1299	type	True	99.992	1060	1064	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. S1	GCA_020546705.1	1299	1299	type	True	99.992	1064	1064	95	conclusive
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	99.9532	1054	1064	95	conclusive
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	99.95	1017	1064	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:27:42,114] [INFO] DFAST Taxonomy check result was written to GCF_020547025.1_ASM2054702v1_genomic.fna/tc_result.tsv
[2024-01-24 12:27:42,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:27:42,115] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:27:42,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg476a39f5-9a7c-45af-96cc-2aa79d23bade/dqc_reference/checkm_data
[2024-01-24 12:27:42,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:27:42,149] [INFO] Task started: CheckM
[2024-01-24 12:27:42,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020547025.1_ASM2054702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020547025.1_ASM2054702v1_genomic.fna/checkm_input GCF_020547025.1_ASM2054702v1_genomic.fna/checkm_result
[2024-01-24 12:28:13,041] [INFO] Task succeeded: CheckM
[2024-01-24 12:28:13,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:28:13,067] [INFO] ===== Completeness check finished =====
[2024-01-24 12:28:13,067] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:28:13,068] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020547025.1_ASM2054702v1_genomic.fna/markers.fasta)
[2024-01-24 12:28:13,068] [INFO] Task started: Blastn
[2024-01-24 12:28:13,068] [INFO] Running command: blastn -query GCF_020547025.1_ASM2054702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg476a39f5-9a7c-45af-96cc-2aa79d23bade/dqc_reference/reference_markers_gtdb.fasta -out GCF_020547025.1_ASM2054702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:14,025] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:14,049] [INFO] Selected 13 target genomes.
[2024-01-24 12:28:14,049] [INFO] Target genome list was writen to GCF_020547025.1_ASM2054702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:28:14,102] [INFO] Task started: fastANI
[2024-01-24 12:28:14,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgfebbe2be-da21-4848-8c5b-e5945a632739/GCF_020547025.1_ASM2054702v1_genomic.fna.gz --refList GCF_020547025.1_ASM2054702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020547025.1_ASM2054702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:28:25,342] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:25,360] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:28:25,360] [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	99.9532	1054	1064	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	87.4013	841	1064	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	80.791	627	1064	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	80.4547	601	1064	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	79.8333	548	1064	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	79.6258	499	1064	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	79.5681	543	1064	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	79.4447	522	1064	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	79.0374	504	1064	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	79.0218	489	1064	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	78.9699	498	1064	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	78.7704	467	1064	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	78.5687	500	1064	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 12:28:25,362] [INFO] GTDB search result was written to GCF_020547025.1_ASM2054702v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:28:25,363] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:28:25,366] [INFO] DFAST_QC result json was written to GCF_020547025.1_ASM2054702v1_genomic.fna/dqc_result.json
[2024-01-24 12:28:25,366] [INFO] DFAST_QC completed!
[2024-01-24 12:28:25,366] [INFO] Total running time: 0h1m6s