[2024-01-24 14:55:26,859] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:26,861] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:26,861] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb49b4be-b318-439a-bcd8-5a01c6b481c0/dqc_reference
[2024-01-24 14:55:28,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:28,275] [INFO] Task started: Prodigal
[2024-01-24 14:55:28,275] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb4f555a-7423-47b8-ba3b-e4b3748338c9/GCF_018863415.1_ASM1886341v1_genomic.fna.gz | prodigal -d GCF_018863415.1_ASM1886341v1_genomic.fna/cds.fna -a GCF_018863415.1_ASM1886341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:57,285] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:57,286] [INFO] Task started: HMMsearch
[2024-01-24 14:55:57,286] [INFO] Running command: hmmsearch --tblout GCF_018863415.1_ASM1886341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb49b4be-b318-439a-bcd8-5a01c6b481c0/dqc_reference/reference_markers.hmm GCF_018863415.1_ASM1886341v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:57,515] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:57,516] [INFO] Found 6/6 markers.
[2024-01-24 14:55:57,563] [INFO] Query marker FASTA was written to GCF_018863415.1_ASM1886341v1_genomic.fna/markers.fasta
[2024-01-24 14:55:57,563] [INFO] Task started: Blastn
[2024-01-24 14:55:57,563] [INFO] Running command: blastn -query GCF_018863415.1_ASM1886341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb49b4be-b318-439a-bcd8-5a01c6b481c0/dqc_reference/reference_markers.fasta -out GCF_018863415.1_ASM1886341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:58,279] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:58,282] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:58,283] [INFO] Target genome list was writen to GCF_018863415.1_ASM1886341v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:58,287] [INFO] Task started: fastANI
[2024-01-24 14:55:58,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb4f555a-7423-47b8-ba3b-e4b3748338c9/GCF_018863415.1_ASM1886341v1_genomic.fna.gz --refList GCF_018863415.1_ASM1886341v1_genomic.fna/target_genomes.txt --output GCF_018863415.1_ASM1886341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:08,922] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:08,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb49b4be-b318-439a-bcd8-5a01c6b481c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:08,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb49b4be-b318-439a-bcd8-5a01c6b481c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:08,935] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:56:08,935] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:56:08,935] [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 planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	90.8769	1082	1661	95	below_threshold
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	84.05	944	1661	95	below_threshold
Deinococcus apachensis	strain=DSM 19763	GCA_000381345.1	309886	309886	type	True	82.9627	878	1661	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	82.6063	843	1661	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	82.5769	859	1661	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	82.5441	859	1661	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	82.3802	838	1661	95	below_threshold
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	81.9007	745	1661	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	81.8919	786	1661	95	below_threshold
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	78.7568	600	1661	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	78.7049	606	1661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:08,937] [INFO] DFAST Taxonomy check result was written to GCF_018863415.1_ASM1886341v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:08,938] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:08,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:08,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb49b4be-b318-439a-bcd8-5a01c6b481c0/dqc_reference/checkm_data
[2024-01-24 14:56:08,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:08,988] [INFO] Task started: CheckM
[2024-01-24 14:56:08,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018863415.1_ASM1886341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018863415.1_ASM1886341v1_genomic.fna/checkm_input GCF_018863415.1_ASM1886341v1_genomic.fna/checkm_result
[2024-01-24 14:57:25,375] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:25,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:25,393] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:25,393] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:25,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018863415.1_ASM1886341v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:25,394] [INFO] Task started: Blastn
[2024-01-24 14:57:25,394] [INFO] Running command: blastn -query GCF_018863415.1_ASM1886341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb49b4be-b318-439a-bcd8-5a01c6b481c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_018863415.1_ASM1886341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:26,457] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:26,459] [INFO] Selected 10 target genomes.
[2024-01-24 14:57:26,459] [INFO] Target genome list was writen to GCF_018863415.1_ASM1886341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:26,466] [INFO] Task started: fastANI
[2024-01-24 14:57:26,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb4f555a-7423-47b8-ba3b-e4b3748338c9/GCF_018863415.1_ASM1886341v1_genomic.fna.gz --refList GCF_018863415.1_ASM1886341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018863415.1_ASM1886341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:36,940] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:36,949] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:36,949] [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_018863415.1	s__Deinococcus sp018863415	100.0	1655	1661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002869765.1	s__Deinococcus planocerae	90.8858	1081	1661	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	84.0359	946	1661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381345.1	s__Deinococcus apachensis	82.9836	874	1661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004758605.1	s__Deinococcus metallilatus	82.5253	861	1661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_014201885.1	s__Deinococcus budaensis	82.397	838	1661	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	81.9088	785	1661	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	81.9017	745	1661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953415.1	s__Deinococcus sp002953415	81.8411	754	1661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335125.1	s__Deinococcus radiopugnans	78.7338	604	1661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:36,951] [INFO] GTDB search result was written to GCF_018863415.1_ASM1886341v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:36,952] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:36,955] [INFO] DFAST_QC result json was written to GCF_018863415.1_ASM1886341v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:36,955] [INFO] DFAST_QC completed!
[2024-01-24 14:57:36,955] [INFO] Total running time: 0h2m10s