[2024-01-24 10:47:54,168] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,173] [INFO] DQC Reference Directory: /var/lib/cwl/stga102a13a-884e-4ca7-80c7-72e2089213ae/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,344] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg9790a2b9-a2ee-4d10-8751-29d26591d9bf/GCF_003951975.1_ASM395197v1_genomic.fna.gz | prodigal -d GCF_003951975.1_ASM395197v1_genomic.fna/cds.fna -a GCF_003951975.1_ASM395197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:09,134] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:09,134] [INFO] Task started: HMMsearch
[2024-01-24 10:48:09,135] [INFO] Running command: hmmsearch --tblout GCF_003951975.1_ASM395197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga102a13a-884e-4ca7-80c7-72e2089213ae/dqc_reference/reference_markers.hmm GCF_003951975.1_ASM395197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:09,359] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:09,360] [INFO] Found 6/6 markers.
[2024-01-24 10:48:09,392] [INFO] Query marker FASTA was written to GCF_003951975.1_ASM395197v1_genomic.fna/markers.fasta
[2024-01-24 10:48:09,393] [INFO] Task started: Blastn
[2024-01-24 10:48:09,393] [INFO] Running command: blastn -query GCF_003951975.1_ASM395197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga102a13a-884e-4ca7-80c7-72e2089213ae/dqc_reference/reference_markers.fasta -out GCF_003951975.1_ASM395197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:10,319] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:10,323] [INFO] Selected 23 target genomes.
[2024-01-24 10:48:10,323] [INFO] Target genome list was writen to GCF_003951975.1_ASM395197v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:10,349] [INFO] Task started: fastANI
[2024-01-24 10:48:10,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg9790a2b9-a2ee-4d10-8751-29d26591d9bf/GCF_003951975.1_ASM395197v1_genomic.fna.gz --refList GCF_003951975.1_ASM395197v1_genomic.fna/target_genomes.txt --output GCF_003951975.1_ASM395197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:20,982] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:20,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga102a13a-884e-4ca7-80c7-72e2089213ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:20,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga102a13a-884e-4ca7-80c7-72e2089213ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:20,995] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:20,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:20,996] [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 dolichotidis	strain=2036B	GCA_003951975.1	2306976	2306976	type	True	100.0	636	636	95	conclusive
Bifidobacterium gallicum	strain=DSM 20093	GCA_000173375.1	78342	78342	type	True	78.9176	176	636	95	below_threshold
Bifidobacterium gallicum	strain=DSM 20093	GCA_000771165.1	78342	78342	type	True	78.8884	171	636	95	below_threshold
Bifidobacterium gallicum	strain=LMG 11596	GCA_000741205.1	78342	78342	type	True	78.8351	174	636	95	below_threshold
Bifidobacterium magnum	strain=DSM 20222	GCA_000771365.1	1692	1692	type	True	78.323	128	636	95	below_threshold
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	78.0015	83	636	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	77.9565	84	636	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=JCM 19995	GCA_017132755.1	1931217	216816	type	True	77.9377	87	636	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000771145.1	1690	1694	type	True	77.918	103	636	95	below_threshold
Bifidobacterium cebidarum	strain=LMG 31469	GCA_009193305.1	2650773	2650773	type	True	77.9003	92	636	95	below_threshold
Bifidobacterium imperatoris	strain=Tam1G	GCA_002860405.1	2020965	2020965	type	True	77.6507	110	636	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	77.559	93	636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:20,998] [INFO] DFAST Taxonomy check result was written to GCF_003951975.1_ASM395197v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:20,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:20,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:20,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga102a13a-884e-4ca7-80c7-72e2089213ae/dqc_reference/checkm_data
[2024-01-24 10:48:21,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:21,022] [INFO] Task started: CheckM
[2024-01-24 10:48:21,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003951975.1_ASM395197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003951975.1_ASM395197v1_genomic.fna/checkm_input GCF_003951975.1_ASM395197v1_genomic.fna/checkm_result
[2024-01-24 10:48:44,223] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:44,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:44,247] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:44,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:44,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003951975.1_ASM395197v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:44,248] [INFO] Task started: Blastn
[2024-01-24 10:48:44,248] [INFO] Running command: blastn -query GCF_003951975.1_ASM395197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga102a13a-884e-4ca7-80c7-72e2089213ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_003951975.1_ASM395197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:45,385] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:45,390] [INFO] Selected 23 target genomes.
[2024-01-24 10:48:45,391] [INFO] Target genome list was writen to GCF_003951975.1_ASM395197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:45,416] [INFO] Task started: fastANI
[2024-01-24 10:48:45,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg9790a2b9-a2ee-4d10-8751-29d26591d9bf/GCF_003951975.1_ASM395197v1_genomic.fna.gz --refList GCF_003951975.1_ASM395197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003951975.1_ASM395197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:56,181] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:56,200] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:56,200] [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_003951975.1	s__Bifidobacterium dolichotidis	100.0	636	636	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_000741205.1	s__Bifidobacterium gallicum	78.8351	174	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	1.00	0.99	4	-
GCF_000741255.1	s__Bifidobacterium magnum	78.2814	131	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.98	3	-
GCF_000741135.1	s__Bifidobacterium choerinum	78.1237	100	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_001042635.1	s__Bifidobacterium scardovii	78.031	85	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000196555.1	s__Bifidobacterium longum	77.9588	88	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_009193305.1	s__Bifidobacterium cebidarum	77.9387	91	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000522505.1	s__Bifidobacterium moukalabense	77.928	93	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_003952005.1	s__Galliscardovia callimiconis	77.8634	72	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_000741295.1	s__Bifidobacterium globosum	77.855	107	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.22	96.02	0.90	0.78	79	-
GCF_004155535.1	s__Bifidobacterium pseudolongum_C	77.8339	106	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555335.1	s__Bifidobacterium sp018555335	77.7257	94	636	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	77.7255	76	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009727065.1	s__Bifidobacterium canis	77.7076	116	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.79	99.79	0.97	0.97	2	-
GCF_002860405.1	s__Bifidobacterium imperatoris	77.6804	109	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000269965.1	s__Bifidobacterium infantis	77.5117	90	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_000741575.1	s__Bifidobacterium cuniculi	77.3287	99	636	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:56,202] [INFO] GTDB search result was written to GCF_003951975.1_ASM395197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:56,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:56,209] [INFO] DFAST_QC result json was written to GCF_003951975.1_ASM395197v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:56,209] [INFO] DFAST_QC completed!
[2024-01-24 10:48:56,209] [INFO] Total running time: 0h1m2s