[2024-01-24 12:07:04,497] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:04,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:04,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgc229b757-ebb6-41c1-8c34-1ee10eb3d6eb/dqc_reference
[2024-01-24 12:07:05,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:05,750] [INFO] Task started: Prodigal
[2024-01-24 12:07:05,750] [INFO] Running command: gunzip -c /var/lib/cwl/stga21317e2-1281-4aab-9258-15eb219d14e4/GCF_000741535.1_Bifbou_genomic.fna.gz | prodigal -d GCF_000741535.1_Bifbou_genomic.fna/cds.fna -a GCF_000741535.1_Bifbou_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:13,397] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:13,398] [INFO] Task started: HMMsearch
[2024-01-24 12:07:13,398] [INFO] Running command: hmmsearch --tblout GCF_000741535.1_Bifbou_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc229b757-ebb6-41c1-8c34-1ee10eb3d6eb/dqc_reference/reference_markers.hmm GCF_000741535.1_Bifbou_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:13,656] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:13,657] [INFO] Found 6/6 markers.
[2024-01-24 12:07:13,682] [INFO] Query marker FASTA was written to GCF_000741535.1_Bifbou_genomic.fna/markers.fasta
[2024-01-24 12:07:13,683] [INFO] Task started: Blastn
[2024-01-24 12:07:13,683] [INFO] Running command: blastn -query GCF_000741535.1_Bifbou_genomic.fna/markers.fasta -db /var/lib/cwl/stgc229b757-ebb6-41c1-8c34-1ee10eb3d6eb/dqc_reference/reference_markers.fasta -out GCF_000741535.1_Bifbou_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:14,571] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:14,575] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:14,576] [INFO] Target genome list was writen to GCF_000741535.1_Bifbou_genomic.fna/target_genomes.txt
[2024-01-24 12:07:14,587] [INFO] Task started: fastANI
[2024-01-24 12:07:14,587] [INFO] Running command: fastANI --query /var/lib/cwl/stga21317e2-1281-4aab-9258-15eb219d14e4/GCF_000741535.1_Bifbou_genomic.fna.gz --refList GCF_000741535.1_Bifbou_genomic.fna/target_genomes.txt --output GCF_000741535.1_Bifbou_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:21,979] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:21,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc229b757-ebb6-41c1-8c34-1ee10eb3d6eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:21,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc229b757-ebb6-41c1-8c34-1ee10eb3d6eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:21,994] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:07:21,994] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:21,994] [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=LMG 10736	GCA_000741535.1	78343	78343	type	True	100.0	713	714	95	conclusive
Bifidobacterium boum	strain=DSM 20432	GCA_000771385.1	78343	78343	type	True	99.9944	705	714	95	conclusive
Bifidobacterium boum	strain=DSM 20432	GCA_000687615.1	78343	78343	type	True	99.9918	702	714	95	conclusive
Bifidobacterium porcinum	strain=DSM 17755	GCA_000771045.1	212365	212365	type	True	86.5064	520	714	95	below_threshold
Bifidobacterium apri	strain=DSM 100238	GCA_009299485.1	1769423	1769423	type	True	86.3138	538	714	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=LMG 21395	GCA_000741455.1	79262	246618	type	True	85.9863	527	714	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000426425.1	79262	246618	type	True	85.9566	524	714	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000687635.1	78346	78346	type	True	79.8606	246	714	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.5474	179	714	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:21,996] [INFO] DFAST Taxonomy check result was written to GCF_000741535.1_Bifbou_genomic.fna/tc_result.tsv
[2024-01-24 12:07:21,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:21,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:21,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc229b757-ebb6-41c1-8c34-1ee10eb3d6eb/dqc_reference/checkm_data
[2024-01-24 12:07:21,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:22,021] [INFO] Task started: CheckM
[2024-01-24 12:07:22,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000741535.1_Bifbou_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000741535.1_Bifbou_genomic.fna/checkm_input GCF_000741535.1_Bifbou_genomic.fna/checkm_result
[2024-01-24 12:07:51,466] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:51,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:51,489] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:51,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:51,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000741535.1_Bifbou_genomic.fna/markers.fasta)
[2024-01-24 12:07:51,490] [INFO] Task started: Blastn
[2024-01-24 12:07:51,491] [INFO] Running command: blastn -query GCF_000741535.1_Bifbou_genomic.fna/markers.fasta -db /var/lib/cwl/stgc229b757-ebb6-41c1-8c34-1ee10eb3d6eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000741535.1_Bifbou_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:52,741] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:52,745] [INFO] Selected 12 target genomes.
[2024-01-24 12:07:52,745] [INFO] Target genome list was writen to GCF_000741535.1_Bifbou_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:52,761] [INFO] Task started: fastANI
[2024-01-24 12:07:52,761] [INFO] Running command: fastANI --query /var/lib/cwl/stga21317e2-1281-4aab-9258-15eb219d14e4/GCF_000741535.1_Bifbou_genomic.fna.gz --refList GCF_000741535.1_Bifbou_genomic.fna/target_genomes_gtdb.txt --output GCF_000741535.1_Bifbou_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:58,428] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:58,445] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:58,445] [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	100.0	713	714	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	94.8657	606	714	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	86.6426	538	714	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	86.3316	537	714	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	79.9764	244	714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_000010425.1	s__Bifidobacterium adolescentis	79.7393	254	714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	79.7366	257	714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667685.1	s__Bifidobacterium aerophilum	79.7102	247	714	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	79.6766	207	714	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_001042635.1	s__Bifidobacterium scardovii	79.3552	261	714	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	78.9973	216	714	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	78.9918	217	714	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 12:07:58,447] [INFO] GTDB search result was written to GCF_000741535.1_Bifbou_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:58,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:58,451] [INFO] DFAST_QC result json was written to GCF_000741535.1_Bifbou_genomic.fna/dqc_result.json
[2024-01-24 12:07:58,451] [INFO] DFAST_QC completed!
[2024-01-24 12:07:58,451] [INFO] Total running time: 0h0m54s