[2024-01-24 13:35:27,555] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,556] [INFO] DQC Reference Directory: /var/lib/cwl/stgc61e00c4-46d3-4e53-a48d-3a846df1b2ce/dqc_reference
[2024-01-24 13:35:28,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,824] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,825] [INFO] Running command: gunzip -c /var/lib/cwl/stge02d7526-16f6-43f1-9199-f8c020a8374c/GCF_000771385.1_DSM-20432_genomic.fna.gz | prodigal -d GCF_000771385.1_DSM-20432_genomic.fna/cds.fna -a GCF_000771385.1_DSM-20432_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:36,238] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:36,239] [INFO] Task started: HMMsearch
[2024-01-24 13:35:36,239] [INFO] Running command: hmmsearch --tblout GCF_000771385.1_DSM-20432_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc61e00c4-46d3-4e53-a48d-3a846df1b2ce/dqc_reference/reference_markers.hmm GCF_000771385.1_DSM-20432_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:36,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:36,479] [INFO] Found 6/6 markers.
[2024-01-24 13:35:36,505] [INFO] Query marker FASTA was written to GCF_000771385.1_DSM-20432_genomic.fna/markers.fasta
[2024-01-24 13:35:36,506] [INFO] Task started: Blastn
[2024-01-24 13:35:36,506] [INFO] Running command: blastn -query GCF_000771385.1_DSM-20432_genomic.fna/markers.fasta -db /var/lib/cwl/stgc61e00c4-46d3-4e53-a48d-3a846df1b2ce/dqc_reference/reference_markers.fasta -out GCF_000771385.1_DSM-20432_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:37,408] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:37,412] [INFO] Selected 13 target genomes.
[2024-01-24 13:35:37,413] [INFO] Target genome list was writen to GCF_000771385.1_DSM-20432_genomic.fna/target_genomes.txt
[2024-01-24 13:35:37,453] [INFO] Task started: fastANI
[2024-01-24 13:35:37,453] [INFO] Running command: fastANI --query /var/lib/cwl/stge02d7526-16f6-43f1-9199-f8c020a8374c/GCF_000771385.1_DSM-20432_genomic.fna.gz --refList GCF_000771385.1_DSM-20432_genomic.fna/target_genomes.txt --output GCF_000771385.1_DSM-20432_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:35:44,441] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:44,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc61e00c4-46d3-4e53-a48d-3a846df1b2ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:35:44,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc61e00c4-46d3-4e53-a48d-3a846df1b2ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:35:44,453] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:35:44,454] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:35:44,454] [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
Bifidobacterium boum	strain=DSM 20432	GCA_000771385.1	78343	78343	type	True	100.0	707	709	95	conclusive
Bifidobacterium boum	strain=DSM 20432	GCA_000687615.1	78343	78343	type	True	99.9961	701	709	95	conclusive
Bifidobacterium boum	strain=LMG 10736	GCA_000741535.1	78343	78343	type	True	99.9959	702	709	95	conclusive
Bifidobacterium porcinum	strain=DSM 17755	GCA_000771045.1	212365	212365	type	True	86.4208	519	709	95	below_threshold
Bifidobacterium apri	strain=DSM 100238	GCA_009299485.1	1769423	1769423	type	True	86.395	533	709	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000426425.1	79262	246618	type	True	85.908	513	709	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=LMG 21395	GCA_000741455.1	79262	246618	type	True	85.7973	525	709	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000687635.1	78346	78346	type	True	79.7939	242	709	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.2776	185	709	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:35:44,456] [INFO] DFAST Taxonomy check result was written to GCF_000771385.1_DSM-20432_genomic.fna/tc_result.tsv
[2024-01-24 13:35:44,456] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:35:44,456] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:35:44,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc61e00c4-46d3-4e53-a48d-3a846df1b2ce/dqc_reference/checkm_data
[2024-01-24 13:35:44,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:35:44,482] [INFO] Task started: CheckM
[2024-01-24 13:35:44,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771385.1_DSM-20432_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771385.1_DSM-20432_genomic.fna/checkm_input GCF_000771385.1_DSM-20432_genomic.fna/checkm_result
[2024-01-24 13:36:11,839] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:11,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:11,861] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:11,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:11,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771385.1_DSM-20432_genomic.fna/markers.fasta)
[2024-01-24 13:36:11,862] [INFO] Task started: Blastn
[2024-01-24 13:36:11,862] [INFO] Running command: blastn -query GCF_000771385.1_DSM-20432_genomic.fna/markers.fasta -db /var/lib/cwl/stgc61e00c4-46d3-4e53-a48d-3a846df1b2ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771385.1_DSM-20432_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:13,126] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:13,130] [INFO] Selected 12 target genomes.
[2024-01-24 13:36:13,130] [INFO] Target genome list was writen to GCF_000771385.1_DSM-20432_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:13,156] [INFO] Task started: fastANI
[2024-01-24 13:36:13,156] [INFO] Running command: fastANI --query /var/lib/cwl/stge02d7526-16f6-43f1-9199-f8c020a8374c/GCF_000771385.1_DSM-20432_genomic.fna.gz --refList GCF_000771385.1_DSM-20432_genomic.fna/target_genomes_gtdb.txt --output GCF_000771385.1_DSM-20432_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:18,989] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:19,004] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:19,004] [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_000741535.1	s__Bifidobacterium boum	99.9959	702	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.80	97.54	0.95	0.91	9	conclusive
GCA_000741495.1	s__Bifidobacterium thermophilum_A	94.9045	599	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000771265.1	s__Bifidobacterium thermophilum	86.665	528	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.72	95.35	0.90	0.87	15	-
GCF_009299485.1	s__Bifidobacterium apri	86.395	533	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000770925.1	s__Bifidobacterium ruminantium	79.8808	243	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_010667685.1	s__Bifidobacterium aerophilum	79.6501	256	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	79.6036	260	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002451435.1	s__Bifidobacterium sp002451435	79.5961	199	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_000010425.1	s__Bifidobacterium adolescentis	79.5877	260	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_001042635.1	s__Bifidobacterium scardovii	79.3666	260	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_018555455.1	s__Bifidobacterium sp018555455	78.9617	212	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932365.1	s__Bifidobacterium sp012932365	78.8199	222	709	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:19,006] [INFO] GTDB search result was written to GCF_000771385.1_DSM-20432_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:19,006] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:19,009] [INFO] DFAST_QC result json was written to GCF_000771385.1_DSM-20432_genomic.fna/dqc_result.json
[2024-01-24 13:36:19,009] [INFO] DFAST_QC completed!
[2024-01-24 13:36:19,009] [INFO] Total running time: 0h0m51s