[2024-01-24 11:26:12,535] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d870b5d-fad5-43b9-979e-8d31102240b2/dqc_reference
[2024-01-24 11:26:13,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:13,947] [INFO] Task started: Prodigal
[2024-01-24 11:26:13,947] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaafb8b5-d117-411f-9773-d28e3b394e16/GCF_021462405.1_ASM2146240v1_genomic.fna.gz | prodigal -d GCF_021462405.1_ASM2146240v1_genomic.fna/cds.fna -a GCF_021462405.1_ASM2146240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:28,239] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:28,239] [INFO] Task started: HMMsearch
[2024-01-24 11:26:28,240] [INFO] Running command: hmmsearch --tblout GCF_021462405.1_ASM2146240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d870b5d-fad5-43b9-979e-8d31102240b2/dqc_reference/reference_markers.hmm GCF_021462405.1_ASM2146240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:28,494] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:28,496] [INFO] Found 6/6 markers.
[2024-01-24 11:26:28,522] [INFO] Query marker FASTA was written to GCF_021462405.1_ASM2146240v1_genomic.fna/markers.fasta
[2024-01-24 11:26:28,522] [INFO] Task started: Blastn
[2024-01-24 11:26:28,522] [INFO] Running command: blastn -query GCF_021462405.1_ASM2146240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d870b5d-fad5-43b9-979e-8d31102240b2/dqc_reference/reference_markers.fasta -out GCF_021462405.1_ASM2146240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:29,161] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:29,165] [INFO] Selected 9 target genomes.
[2024-01-24 11:26:29,165] [INFO] Target genome list was writen to GCF_021462405.1_ASM2146240v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:29,169] [INFO] Task started: fastANI
[2024-01-24 11:26:29,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaafb8b5-d117-411f-9773-d28e3b394e16/GCF_021462405.1_ASM2146240v1_genomic.fna.gz --refList GCF_021462405.1_ASM2146240v1_genomic.fna/target_genomes.txt --output GCF_021462405.1_ASM2146240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:34,805] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:34,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d870b5d-fad5-43b9-979e-8d31102240b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:34,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d870b5d-fad5-43b9-979e-8d31102240b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:34,814] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:34,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:34,815] [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
Thermus tengchongensis	strain=YIM 77924	GCA_021462405.1	1214928	1214928	type	True	100.0	776	779	95	conclusive
Thermus caliditerrae	strain=YIM 77925	GCA_021462525.1	1330700	1330700	type	True	93.5813	641	779	95	below_threshold
Thermus caldilimi	strain=YIM 78456	GCA_004684245.1	2483360	2483360	type	True	90.482	634	779	95	below_threshold
Thermus tenuipuniceus	strain=YIM 76954	GCA_002964845.1	2078690	2078690	type	True	89.9863	613	779	95	below_threshold
Thermus brevis	strain=SYSU G05001	GCA_019430925.1	2862456	2862456	type	True	89.8833	630	779	95	below_threshold
Thermus antranikianii	strain=DSM 12462	GCA_000423905.1	88190	88190	type	True	89.5546	607	779	95	below_threshold
Thermus scotoductus	strain=DSM 8553	GCA_000381045.1	37636	37636	suspected-type	True	89.4736	535	779	95	below_threshold
Thermus amyloliquefaciens	strain=YIM 77409	GCA_000744885.1	1449080	1449080	type	True	89.4029	611	779	95	below_threshold
Thermus caldifontis	strain=YIM 73026	GCA_003336745.1	1930763	1930763	type	True	87.1866	585	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:34,816] [INFO] DFAST Taxonomy check result was written to GCF_021462405.1_ASM2146240v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:34,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:34,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:34,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d870b5d-fad5-43b9-979e-8d31102240b2/dqc_reference/checkm_data
[2024-01-24 11:26:34,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:34,844] [INFO] Task started: CheckM
[2024-01-24 11:26:34,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021462405.1_ASM2146240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021462405.1_ASM2146240v1_genomic.fna/checkm_input GCF_021462405.1_ASM2146240v1_genomic.fna/checkm_result
[2024-01-24 11:27:14,760] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:14,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:14,786] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:14,786] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:14,787] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021462405.1_ASM2146240v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:14,787] [INFO] Task started: Blastn
[2024-01-24 11:27:14,788] [INFO] Running command: blastn -query GCF_021462405.1_ASM2146240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d870b5d-fad5-43b9-979e-8d31102240b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_021462405.1_ASM2146240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:15,532] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:15,535] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:15,536] [INFO] Target genome list was writen to GCF_021462405.1_ASM2146240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:15,542] [INFO] Task started: fastANI
[2024-01-24 11:27:15,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaafb8b5-d117-411f-9773-d28e3b394e16/GCF_021462405.1_ASM2146240v1_genomic.fna.gz --refList GCF_021462405.1_ASM2146240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021462405.1_ASM2146240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:20,300] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:20,308] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:20,308] [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_000744175.1	s__Thermus tengchongensis	97.7693	684	779	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.07	97.71	0.89	0.87	3	conclusive
GCF_000745065.1	s__Thermus caliditerrae	92.7957	640	779	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684245.1	s__Thermus caldilimi	90.482	634	779	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964845.1	s__Thermus tenuipuniceus	89.9863	613	779	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423905.1	s__Thermus antranikianii	89.5392	608	779	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.31	98.31	0.92	0.92	2	-
GCF_000381045.1	s__Thermus scotoductus	89.5015	534	779	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	97.38	95.93	0.81	0.76	44	-
GCF_000744885.1	s__Thermus amyloliquefaciens	89.4095	610	779	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336745.1	s__Thermus caldifontis	87.1863	585	779	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:20,310] [INFO] GTDB search result was written to GCF_021462405.1_ASM2146240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:20,310] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:20,314] [INFO] DFAST_QC result json was written to GCF_021462405.1_ASM2146240v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:20,314] [INFO] DFAST_QC completed!
[2024-01-24 11:27:20,314] [INFO] Total running time: 0h1m8s