[2024-01-24 12:15:03,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fec8800-adff-483d-b1dd-da53a455f240/dqc_reference
[2024-01-24 12:15:05,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,319] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,319] [INFO] Running command: gunzip -c /var/lib/cwl/stg130af834-eff1-41b8-83b8-81e645448eaf/GCF_000741375.1_Bifsae_genomic.fna.gz | prodigal -d GCF_000741375.1_Bifsae_genomic.fna/cds.fna -a GCF_000741375.1_Bifsae_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:12,801] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:12,802] [INFO] Task started: HMMsearch
[2024-01-24 12:15:12,802] [INFO] Running command: hmmsearch --tblout GCF_000741375.1_Bifsae_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fec8800-adff-483d-b1dd-da53a455f240/dqc_reference/reference_markers.hmm GCF_000741375.1_Bifsae_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:13,029] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:13,030] [INFO] Found 6/6 markers.
[2024-01-24 12:15:13,052] [INFO] Query marker FASTA was written to GCF_000741375.1_Bifsae_genomic.fna/markers.fasta
[2024-01-24 12:15:13,052] [INFO] Task started: Blastn
[2024-01-24 12:15:13,052] [INFO] Running command: blastn -query GCF_000741375.1_Bifsae_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fec8800-adff-483d-b1dd-da53a455f240/dqc_reference/reference_markers.fasta -out GCF_000741375.1_Bifsae_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:14,099] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:14,102] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:14,103] [INFO] Target genome list was writen to GCF_000741375.1_Bifsae_genomic.fna/target_genomes.txt
[2024-01-24 12:15:14,107] [INFO] Task started: fastANI
[2024-01-24 12:15:14,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg130af834-eff1-41b8-83b8-81e645448eaf/GCF_000741375.1_Bifsae_genomic.fna.gz --refList GCF_000741375.1_Bifsae_genomic.fna/target_genomes.txt --output GCF_000741375.1_Bifsae_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:21,428] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:21,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fec8800-adff-483d-b1dd-da53a455f240/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:21,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fec8800-adff-483d-b1dd-da53a455f240/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:21,439] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:15:21,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:21,439] [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 pullorum subsp. saeculare	strain=LMG 14934	GCA_000741375.1	78257	78448	type	True	100.0	745	747	95	conclusive
Bifidobacterium pullorum subsp. saeculare	strain=DSM 6531	GCA_000770965.1	78257	78448	type	True	99.9692	723	747	95	conclusive
Bifidobacterium pullorum subsp. gallinarum	strain=DSM 20670	GCA_000771505.1	78344	78448	type	True	97.0145	592	747	95	conclusive
Bifidobacterium pullorum subsp. gallinarum	strain=LMG 11586	GCA_000741215.1	78344	78448	type	True	96.8201	614	747	95	conclusive
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	85.2519	523	747	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	82.2286	382	747	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.9958	391	747	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.8326	403	747	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.7851	281	747	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.4588	95	747	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.3424	82	747	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:21,441] [INFO] DFAST Taxonomy check result was written to GCF_000741375.1_Bifsae_genomic.fna/tc_result.tsv
[2024-01-24 12:15:21,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:21,442] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:21,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fec8800-adff-483d-b1dd-da53a455f240/dqc_reference/checkm_data
[2024-01-24 12:15:21,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:21,469] [INFO] Task started: CheckM
[2024-01-24 12:15:21,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000741375.1_Bifsae_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000741375.1_Bifsae_genomic.fna/checkm_input GCF_000741375.1_Bifsae_genomic.fna/checkm_result
[2024-01-24 12:15:49,287] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:49,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:49,310] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:49,311] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:49,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000741375.1_Bifsae_genomic.fna/markers.fasta)
[2024-01-24 12:15:49,312] [INFO] Task started: Blastn
[2024-01-24 12:15:49,312] [INFO] Running command: blastn -query GCF_000741375.1_Bifsae_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fec8800-adff-483d-b1dd-da53a455f240/dqc_reference/reference_markers_gtdb.fasta -out GCF_000741375.1_Bifsae_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:50,872] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:50,877] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:50,877] [INFO] Target genome list was writen to GCF_000741375.1_Bifsae_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:50,886] [INFO] Task started: fastANI
[2024-01-24 12:15:50,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg130af834-eff1-41b8-83b8-81e645448eaf/GCF_000741375.1_Bifsae_genomic.fna.gz --refList GCF_000741375.1_Bifsae_genomic.fna/target_genomes_gtdb.txt --output GCF_000741375.1_Bifsae_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:59,434] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:59,461] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:59,462] [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_000741215.1	s__Bifidobacterium pullorum_B	96.8529	613	747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	conclusive
GCF_000771405.1	s__Bifidobacterium pullorum	90.6721	564	747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_003952945.1	s__Bifidobacterium samirii	82.2655	408	747	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	82.2186	429	747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_018555385.1	s__Bifidobacterium sp018555385	82.2135	382	747	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	82.2083	399	747	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	82.0698	391	747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008698235.1	s__Bifidobacterium rousetti	82.0676	381	747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_018555355.1	s__Bifidobacterium sp018555355	81.9486	405	747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_009299505.1	s__Bifidobacterium ramosum	81.9439	383	747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000741175.1	s__Bifidobacterium callitrichos	81.9368	398	747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_012932365.1	s__Bifidobacterium sp012932365	81.7745	368	747	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	81.7631	381	747	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	81.7187	385	747	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	81.5369	387	747	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	81.4253	369	747	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 12:15:59,463] [INFO] GTDB search result was written to GCF_000741375.1_Bifsae_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:59,464] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:59,468] [INFO] DFAST_QC result json was written to GCF_000741375.1_Bifsae_genomic.fna/dqc_result.json
[2024-01-24 12:15:59,469] [INFO] DFAST_QC completed!
[2024-01-24 12:15:59,469] [INFO] Total running time: 0h0m56s