[2024-01-24 13:49:44,834] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:44,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:44,839] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb41d58a-c221-4e4c-a0e0-bc26da59ea94/dqc_reference
[2024-01-24 13:49:46,244] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,245] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,245] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d673416-ffd8-4473-b50e-ed31a7da3cab/GCF_021378295.1_ASM2137829v1_genomic.fna.gz | prodigal -d GCF_021378295.1_ASM2137829v1_genomic.fna/cds.fna -a GCF_021378295.1_ASM2137829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:56,597] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:56,598] [INFO] Task started: HMMsearch
[2024-01-24 13:49:56,598] [INFO] Running command: hmmsearch --tblout GCF_021378295.1_ASM2137829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb41d58a-c221-4e4c-a0e0-bc26da59ea94/dqc_reference/reference_markers.hmm GCF_021378295.1_ASM2137829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:56,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:56,852] [INFO] Found 6/6 markers.
[2024-01-24 13:49:56,889] [INFO] Query marker FASTA was written to GCF_021378295.1_ASM2137829v1_genomic.fna/markers.fasta
[2024-01-24 13:49:56,890] [INFO] Task started: Blastn
[2024-01-24 13:49:56,890] [INFO] Running command: blastn -query GCF_021378295.1_ASM2137829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb41d58a-c221-4e4c-a0e0-bc26da59ea94/dqc_reference/reference_markers.fasta -out GCF_021378295.1_ASM2137829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:57,643] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:57,647] [INFO] Selected 7 target genomes.
[2024-01-24 13:49:57,647] [INFO] Target genome list was writen to GCF_021378295.1_ASM2137829v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:57,651] [INFO] Task started: fastANI
[2024-01-24 13:49:57,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d673416-ffd8-4473-b50e-ed31a7da3cab/GCF_021378295.1_ASM2137829v1_genomic.fna.gz --refList GCF_021378295.1_ASM2137829v1_genomic.fna/target_genomes.txt --output GCF_021378295.1_ASM2137829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:08,184] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:08,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb41d58a-c221-4e4c-a0e0-bc26da59ea94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:08,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb41d58a-c221-4e4c-a0e0-bc26da59ea94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:08,197] [INFO] Found 7 fastANI hits (7 hits with ANI > threshold)
[2024-01-24 13:50:08,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:08,198] [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	99.99	1092	1092	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. R1	GCA_020546805.1	1299	1299	type	True	99.9881	1064	1092	95	conclusive
Deinococcus radiodurans	strain=R1	GCA_001638825.1	1299	1299	type	True	99.9855	1091	1092	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939 substr. R2	GCA_020547025.1	1299	1299	type	True	99.9811	1062	1092	95	conclusive
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	99.9522	1085	1092	95	conclusive
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	99.9456	1042	1092	95	conclusive
Deinococcus radiodurans	strain=ATCC 13939	GCA_000687895.1	1299	1299	type	True	99.9406	1051	1092	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,199] [INFO] DFAST Taxonomy check result was written to GCF_021378295.1_ASM2137829v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:08,200] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:08,200] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:08,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb41d58a-c221-4e4c-a0e0-bc26da59ea94/dqc_reference/checkm_data
[2024-01-24 13:50:08,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:08,234] [INFO] Task started: CheckM
[2024-01-24 13:50:08,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021378295.1_ASM2137829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021378295.1_ASM2137829v1_genomic.fna/checkm_input GCF_021378295.1_ASM2137829v1_genomic.fna/checkm_result
[2024-01-24 13:50:40,235] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:40,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:40,258] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:40,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:40,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021378295.1_ASM2137829v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:40,260] [INFO] Task started: Blastn
[2024-01-24 13:50:40,260] [INFO] Running command: blastn -query GCF_021378295.1_ASM2137829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb41d58a-c221-4e4c-a0e0-bc26da59ea94/dqc_reference/reference_markers_gtdb.fasta -out GCF_021378295.1_ASM2137829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:41,251] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:41,254] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:41,254] [INFO] Target genome list was writen to GCF_021378295.1_ASM2137829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:41,272] [INFO] Task started: fastANI
[2024-01-24 13:50:41,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d673416-ffd8-4473-b50e-ed31a7da3cab/GCF_021378295.1_ASM2137829v1_genomic.fna.gz --refList GCF_021378295.1_ASM2137829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021378295.1_ASM2137829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:52,625] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:52,643] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:52,643] [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	99.9522	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	87.4618	855	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	80.7628	653	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	80.3923	613	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	79.7036	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	79.6601	565	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	79.4984	560	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	79.485	532	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	79.0339	495	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	79.0155	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_003028415.1	s__Deinococcus sp003028415	78.8678	515	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	78.8363	468	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	78.5656	507	1092	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:52,644] [INFO] GTDB search result was written to GCF_021378295.1_ASM2137829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:52,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:52,649] [INFO] DFAST_QC result json was written to GCF_021378295.1_ASM2137829v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:52,649] [INFO] DFAST_QC completed!
[2024-01-24 13:50:52,649] [INFO] Total running time: 0h1m8s