[2023-06-13 19:58:33,053] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:58:33,056] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:58:33,056] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d06fd81-4955-4f22-b8fe-de27ee5ee4b1/dqc_reference
[2023-06-13 19:58:34,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:58:34,294] [INFO] Task started: Prodigal
[2023-06-13 19:58:34,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg28a71fd6-7e53-491f-be14-3138d0da1b35/GCA_022486765.1_ASM2248676v1_genomic.fna.gz | prodigal -d GCA_022486765.1_ASM2248676v1_genomic.fna/cds.fna -a GCA_022486765.1_ASM2248676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:58:41,181] [INFO] Task succeeded: Prodigal
[2023-06-13 19:58:41,181] [INFO] Task started: HMMsearch
[2023-06-13 19:58:41,182] [INFO] Running command: hmmsearch --tblout GCA_022486765.1_ASM2248676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d06fd81-4955-4f22-b8fe-de27ee5ee4b1/dqc_reference/reference_markers.hmm GCA_022486765.1_ASM2248676v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:58:41,415] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:58:41,417] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28a71fd6-7e53-491f-be14-3138d0da1b35/GCA_022486765.1_ASM2248676v1_genomic.fna.gz]
[2023-06-13 19:58:41,438] [INFO] Query marker FASTA was written to GCA_022486765.1_ASM2248676v1_genomic.fna/markers.fasta
[2023-06-13 19:58:41,439] [INFO] Task started: Blastn
[2023-06-13 19:58:41,439] [INFO] Running command: blastn -query GCA_022486765.1_ASM2248676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d06fd81-4955-4f22-b8fe-de27ee5ee4b1/dqc_reference/reference_markers.fasta -out GCA_022486765.1_ASM2248676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:58:42,279] [INFO] Task succeeded: Blastn
[2023-06-13 19:58:42,284] [INFO] Selected 12 target genomes.
[2023-06-13 19:58:42,285] [INFO] Target genome list was writen to GCA_022486765.1_ASM2248676v1_genomic.fna/target_genomes.txt
[2023-06-13 19:58:42,287] [INFO] Task started: fastANI
[2023-06-13 19:58:42,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a71fd6-7e53-491f-be14-3138d0da1b35/GCA_022486765.1_ASM2248676v1_genomic.fna.gz --refList GCA_022486765.1_ASM2248676v1_genomic.fna/target_genomes.txt --output GCA_022486765.1_ASM2248676v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:58:47,831] [INFO] Task succeeded: fastANI
[2023-06-13 19:58:47,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d06fd81-4955-4f22-b8fe-de27ee5ee4b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:58:47,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d06fd81-4955-4f22-b8fe-de27ee5ee4b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:58:47,846] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:58:47,846] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 19:58:47,846] [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 subtile	strain=LMG 11597	GCA_000741775.1	77635	77635	type	True	83.6304	472	692	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000426405.1	77635	77635	type	True	83.6094	469	692	95	below_threshold
Bifidobacterium subtile	strain=DSM 20096	GCA_000771185.1	77635	77635	type	True	83.4724	476	692	95	below_threshold
Bifidobacterium tibiigranuli	strain=TMW 2.2057	GCA_009371885.1	2172043	2172043	type	True	83.0743	450	692	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	79.6669	242	692	95	below_threshold
Bifidobacterium mongoliense	strain=DSM 21395	GCA_000771525.1	518643	518643	type	True	79.2539	222	692	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	79.2499	231	692	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000741165.1	762212	762212	type	True	78.8878	233	692	95	below_threshold
Bifidobacterium cuniculi	strain=LMG 10738	GCA_000741575.1	1688	1688	type	True	78.6988	173	692	95	below_threshold
Bifidobacterium cuniculi	strain=DSM 20435	GCA_000771465.1	1688	1688	type	True	78.6886	158	692	95	below_threshold
Bifidobacterium merycicum	strain=DSM 6492	GCA_900129045.1	78345	78345	type	True	78.5441	195	692	95	below_threshold
Bifidobacterium criceti	strain=Ham19E	GCA_002286935.1	1960969	1960969	type	True	78.2518	162	692	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:58:47,848] [INFO] DFAST Taxonomy check result was written to GCA_022486765.1_ASM2248676v1_genomic.fna/tc_result.tsv
[2023-06-13 19:58:47,849] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:58:47,849] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:58:47,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d06fd81-4955-4f22-b8fe-de27ee5ee4b1/dqc_reference/checkm_data
[2023-06-13 19:58:47,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:58:47,874] [INFO] Task started: CheckM
[2023-06-13 19:58:47,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022486765.1_ASM2248676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022486765.1_ASM2248676v1_genomic.fna/checkm_input GCA_022486765.1_ASM2248676v1_genomic.fna/checkm_result
[2023-06-13 19:59:13,240] [INFO] Task succeeded: CheckM
[2023-06-13 19:59:13,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:59:13,266] [INFO] ===== Completeness check finished =====
[2023-06-13 19:59:13,266] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:59:13,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022486765.1_ASM2248676v1_genomic.fna/markers.fasta)
[2023-06-13 19:59:13,267] [INFO] Task started: Blastn
[2023-06-13 19:59:13,267] [INFO] Running command: blastn -query GCA_022486765.1_ASM2248676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d06fd81-4955-4f22-b8fe-de27ee5ee4b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_022486765.1_ASM2248676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:59:14,428] [INFO] Task succeeded: Blastn
[2023-06-13 19:59:14,433] [INFO] Selected 15 target genomes.
[2023-06-13 19:59:14,434] [INFO] Target genome list was writen to GCA_022486765.1_ASM2248676v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:59:14,437] [INFO] Task started: fastANI
[2023-06-13 19:59:14,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a71fd6-7e53-491f-be14-3138d0da1b35/GCA_022486765.1_ASM2248676v1_genomic.fna.gz --refList GCA_022486765.1_ASM2248676v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022486765.1_ASM2248676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:59:21,513] [INFO] Task succeeded: fastANI
[2023-06-13 19:59:21,540] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 19:59:21,540] [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_000741775.1	s__Bifidobacterium subtile	83.6603	470	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	4	-
GCF_009371885.1	s__Bifidobacterium tibiigranuli	83.0806	450	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001042635.1	s__Bifidobacterium scardovii	79.7151	253	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000741285.1	s__Bifidobacterium mongoliense	79.3956	222	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_003952945.1	s__Bifidobacterium samirii	79.3281	224	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	79.2695	230	692	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	79.0249	233	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899725.1	s__Bifidobacterium pullorum_C	78.9614	217	692	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	78.9085	241	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741165.1	s__Bifidobacterium biavatii	78.9068	232	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000741575.1	s__Bifidobacterium cuniculi	78.6988	173	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_009078285.1	s__Bifidobacterium jacchi	78.6696	207	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129045.1	s__Bifidobacterium merycicum	78.5657	194	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.68	99.29	0.97	0.90	6	-
GCF_001025155.1	s__Bifidobacterium angulatum	78.4717	168	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.71	95.22	0.93	0.74	7	-
GCF_002286935.1	s__Bifidobacterium criceti	78.2632	163	692	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.26	97.26	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-13 19:59:21,542] [INFO] GTDB search result was written to GCA_022486765.1_ASM2248676v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:59:21,543] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:59:21,547] [INFO] DFAST_QC result json was written to GCA_022486765.1_ASM2248676v1_genomic.fna/dqc_result.json
[2023-06-13 19:59:21,548] [INFO] DFAST_QC completed!
[2023-06-13 19:59:21,548] [INFO] Total running time: 0h0m48s