[2024-01-24 11:58:54,312] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:54,314] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:54,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c50a27f-39be-43af-8480-7e088e316c01/dqc_reference
[2024-01-24 11:58:57,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:57,423] [INFO] Task started: Prodigal
[2024-01-24 11:58:57,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg24bf9038-0a6e-49ec-9a6b-3fe71e28ece2/GCF_017378515.1_ASM1737851v1_genomic.fna.gz | prodigal -d GCF_017378515.1_ASM1737851v1_genomic.fna/cds.fna -a GCF_017378515.1_ASM1737851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:06,391] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:06,391] [INFO] Task started: HMMsearch
[2024-01-24 11:59:06,392] [INFO] Running command: hmmsearch --tblout GCF_017378515.1_ASM1737851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c50a27f-39be-43af-8480-7e088e316c01/dqc_reference/reference_markers.hmm GCF_017378515.1_ASM1737851v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:06,643] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:06,644] [INFO] Found 6/6 markers.
[2024-01-24 11:59:06,669] [INFO] Query marker FASTA was written to GCF_017378515.1_ASM1737851v1_genomic.fna/markers.fasta
[2024-01-24 11:59:06,669] [INFO] Task started: Blastn
[2024-01-24 11:59:06,669] [INFO] Running command: blastn -query GCF_017378515.1_ASM1737851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c50a27f-39be-43af-8480-7e088e316c01/dqc_reference/reference_markers.fasta -out GCF_017378515.1_ASM1737851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:07,448] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:07,452] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:07,453] [INFO] Target genome list was writen to GCF_017378515.1_ASM1737851v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:07,474] [INFO] Task started: fastANI
[2024-01-24 11:59:07,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg24bf9038-0a6e-49ec-9a6b-3fe71e28ece2/GCF_017378515.1_ASM1737851v1_genomic.fna.gz --refList GCF_017378515.1_ASM1737851v1_genomic.fna/target_genomes.txt --output GCF_017378515.1_ASM1737851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:16,338] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:16,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c50a27f-39be-43af-8480-7e088e316c01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:16,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c50a27f-39be-43af-8480-7e088e316c01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:16,354] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:59:16,354] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:16,354] [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 saguini	strain=DSMZ 23967	GCA_017378515.1	762210	762210	type	True	100.0	907	913	95	conclusive
Bifidobacterium saguini	strain=DSM 23967	GCA_000771625.1	762210	762210	type	True	99.977	876	913	95	conclusive
Bifidobacterium saguini	strain=DSM 23967	GCA_000741715.1	762210	762210	type	True	99.964	880	913	95	conclusive
Bifidobacterium imperatoris	strain=Tam1G	GCA_002860405.1	2020965	2020965	type	True	94.1097	716	913	95	below_threshold
Bifidobacterium felsineum	strain=TRE H	GCA_002802915.1	2045440	2045440	type	True	86.7033	615	913	95	below_threshold
Bifidobacterium colobi	strain=LC6	GCA_018555455.1	2809026	2809026	type	True	86.2215	637	913	95	below_threshold
Bifidobacterium cebidarum	strain=LMG 31469	GCA_009193305.1	2650773	2650773	type	True	85.8751	602	913	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.951	511	913	95	below_threshold
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	82.4029	466	913	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.8733	324	913	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:16,356] [INFO] DFAST Taxonomy check result was written to GCF_017378515.1_ASM1737851v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:16,356] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:16,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:16,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c50a27f-39be-43af-8480-7e088e316c01/dqc_reference/checkm_data
[2024-01-24 11:59:16,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:16,389] [INFO] Task started: CheckM
[2024-01-24 11:59:16,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017378515.1_ASM1737851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017378515.1_ASM1737851v1_genomic.fna/checkm_input GCF_017378515.1_ASM1737851v1_genomic.fna/checkm_result
[2024-01-24 11:59:47,966] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:47,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:47,989] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:47,989] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:47,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017378515.1_ASM1737851v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:47,990] [INFO] Task started: Blastn
[2024-01-24 11:59:47,990] [INFO] Running command: blastn -query GCF_017378515.1_ASM1737851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c50a27f-39be-43af-8480-7e088e316c01/dqc_reference/reference_markers_gtdb.fasta -out GCF_017378515.1_ASM1737851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:49,017] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:49,021] [INFO] Selected 9 target genomes.
[2024-01-24 11:59:49,021] [INFO] Target genome list was writen to GCF_017378515.1_ASM1737851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:49,029] [INFO] Task started: fastANI
[2024-01-24 11:59:49,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg24bf9038-0a6e-49ec-9a6b-3fe71e28ece2/GCF_017378515.1_ASM1737851v1_genomic.fna.gz --refList GCF_017378515.1_ASM1737851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017378515.1_ASM1737851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:54,267] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:54,290] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:54,292] [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_000741715.1	s__Bifidobacterium saguini	99.97	879	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.97	3	conclusive
GCF_002860405.1	s__Bifidobacterium imperatoris	94.1097	716	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002802915.1	s__Bifidobacterium felsineum	86.7118	614	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.66	98.66	0.97	0.97	2	-
GCF_018555455.1	s__Bifidobacterium sp018555455	86.2215	637	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193305.1	s__Bifidobacterium cebidarum	85.8751	602	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802865.1	s__Bifidobacterium scaligerum	83.6786	510	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932375.1	s__Bifidobacterium sp012932375	83.5266	520	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259745.1	s__Bifidobacterium myosotis	82.3778	468	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	80.7012	259	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:54,295] [INFO] GTDB search result was written to GCF_017378515.1_ASM1737851v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:54,296] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:54,299] [INFO] DFAST_QC result json was written to GCF_017378515.1_ASM1737851v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:54,299] [INFO] DFAST_QC completed!
[2024-01-24 11:59:54,299] [INFO] Total running time: 0h0m60s