[2024-01-24 14:15:32,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:32,295] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:32,295] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf835516-b87f-47f9-bd4a-705b1ca476f5/dqc_reference
[2024-01-24 14:15:33,571] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:33,573] [INFO] Task started: Prodigal
[2024-01-24 14:15:33,573] [INFO] Running command: gunzip -c /var/lib/cwl/stgc07c04bb-a457-4de0-bd25-2995de7e328d/GCF_009193355.1_ASM919335v1_genomic.fna.gz | prodigal -d GCF_009193355.1_ASM919335v1_genomic.fna/cds.fna -a GCF_009193355.1_ASM919335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:43,456] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:43,457] [INFO] Task started: HMMsearch
[2024-01-24 14:15:43,457] [INFO] Running command: hmmsearch --tblout GCF_009193355.1_ASM919335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf835516-b87f-47f9-bd4a-705b1ca476f5/dqc_reference/reference_markers.hmm GCF_009193355.1_ASM919335v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:43,744] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:43,745] [INFO] Found 6/6 markers.
[2024-01-24 14:15:43,772] [INFO] Query marker FASTA was written to GCF_009193355.1_ASM919335v1_genomic.fna/markers.fasta
[2024-01-24 14:15:43,773] [INFO] Task started: Blastn
[2024-01-24 14:15:43,773] [INFO] Running command: blastn -query GCF_009193355.1_ASM919335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf835516-b87f-47f9-bd4a-705b1ca476f5/dqc_reference/reference_markers.fasta -out GCF_009193355.1_ASM919335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:44,860] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:44,863] [INFO] Selected 21 target genomes.
[2024-01-24 14:15:44,864] [INFO] Target genome list was writen to GCF_009193355.1_ASM919335v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:44,883] [INFO] Task started: fastANI
[2024-01-24 14:15:44,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07c04bb-a457-4de0-bd25-2995de7e328d/GCF_009193355.1_ASM919335v1_genomic.fna.gz --refList GCF_009193355.1_ASM919335v1_genomic.fna/target_genomes.txt --output GCF_009193355.1_ASM919335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:57,599] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:57,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf835516-b87f-47f9-bd4a-705b1ca476f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:57,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf835516-b87f-47f9-bd4a-705b1ca476f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:57,617] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:57,617] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:57,618] [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 leontopitheci	strain=LMG 31471	GCA_009193355.1	2650774	2650774	type	True	100.0	960	966	95	conclusive
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	83.6597	491	966	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	83.6018	497	966	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	83.5455	501	966	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	83.5335	511	966	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	83.3785	508	966	95	below_threshold
Bifidobacterium bifidum	strain=NCTC13001	GCA_900637095.1	1681	1681	type	True	83.3301	492	966	95	below_threshold
Bifidobacterium bifidum	strain=JCM 1255	GCA_001025135.1	1681	1681	type	True	83.2639	487	966	95	below_threshold
Bifidobacterium bifidum	strain=LMG 11041	GCA_000741085.1	1681	1681	type	True	83.2195	493	966	95	below_threshold
Bifidobacterium bifidum	strain=DSM 20456	GCA_000771485.1	1681	1681	type	True	83.0975	492	966	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	82.902	439	966	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	82.8532	450	966	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	82.8159	454	966	95	below_threshold
Bifidobacterium aesculapii	strain=DSM 26737	GCA_001417815.1	1329411	1329411	type	True	82.7665	481	966	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.2723	473	966	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	82.125	418	966	95	below_threshold
Bifidobacterium pluvialisilvae	strain=82T24	GCA_019331695.1	2834436	2834436	type	True	81.7509	400	966	95	below_threshold
Bifidobacterium primatium	strain=TRE 1	GCA_002802875.1	2045438	2045438	type	True	81.6665	418	966	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.8359	299	966	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.3222	144	966	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.2852	124	966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:57,619] [INFO] DFAST Taxonomy check result was written to GCF_009193355.1_ASM919335v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:57,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:57,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:57,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf835516-b87f-47f9-bd4a-705b1ca476f5/dqc_reference/checkm_data
[2024-01-24 14:15:57,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:57,654] [INFO] Task started: CheckM
[2024-01-24 14:15:57,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009193355.1_ASM919335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009193355.1_ASM919335v1_genomic.fna/checkm_input GCF_009193355.1_ASM919335v1_genomic.fna/checkm_result
[2024-01-24 14:16:31,028] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:31,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:31,049] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:31,049] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:31,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009193355.1_ASM919335v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:31,050] [INFO] Task started: Blastn
[2024-01-24 14:16:31,050] [INFO] Running command: blastn -query GCF_009193355.1_ASM919335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf835516-b87f-47f9-bd4a-705b1ca476f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009193355.1_ASM919335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:32,652] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:32,657] [INFO] Selected 12 target genomes.
[2024-01-24 14:16:32,657] [INFO] Target genome list was writen to GCF_009193355.1_ASM919335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:32,667] [INFO] Task started: fastANI
[2024-01-24 14:16:32,667] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07c04bb-a457-4de0-bd25-2995de7e328d/GCF_009193355.1_ASM919335v1_genomic.fna.gz --refList GCF_009193355.1_ASM919335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009193355.1_ASM919335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:40,833] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:40,846] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:40,847] [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_009193355.1	s__Bifidobacterium leontopitheci	100.0	960	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	83.6123	493	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	83.6021	497	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	83.4961	504	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555635.1	s__Bifidobacterium sp018555635	83.2957	519	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001025135.1	s__Bifidobacterium bifidum	83.2639	487	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.04	98.27	0.95	0.91	128	-
GCF_009299505.1	s__Bifidobacterium ramosum	83.1955	523	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003952945.1	s__Bifidobacterium samirii	82.8971	439	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	82.7867	466	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_001417815.1	s__Bifidobacterium aesculapii	82.7413	483	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	81.9746	392	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002802875.1	s__Galliscardovia primatium	81.6774	417	966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:40,848] [INFO] GTDB search result was written to GCF_009193355.1_ASM919335v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:40,849] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:40,853] [INFO] DFAST_QC result json was written to GCF_009193355.1_ASM919335v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:40,853] [INFO] DFAST_QC completed!
[2024-01-24 14:16:40,853] [INFO] Total running time: 0h1m9s