[2023-06-13 03:18:00,455] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:18:00,481] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:18:00,482] [INFO] DQC Reference Directory: /var/lib/cwl/stga2bf9a7c-1ce7-43e5-8337-b758e471cd59/dqc_reference
[2023-06-13 03:18:02,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:18:02,758] [INFO] Task started: Prodigal
[2023-06-13 03:18:02,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ac49470-6aa7-4074-9da2-7253acb8cc68/GCA_022720295.1_ASM2272029v1_genomic.fna.gz | prodigal -d GCA_022720295.1_ASM2272029v1_genomic.fna/cds.fna -a GCA_022720295.1_ASM2272029v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:18:10,246] [INFO] Task succeeded: Prodigal
[2023-06-13 03:18:10,247] [INFO] Task started: HMMsearch
[2023-06-13 03:18:10,247] [INFO] Running command: hmmsearch --tblout GCA_022720295.1_ASM2272029v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2bf9a7c-1ce7-43e5-8337-b758e471cd59/dqc_reference/reference_markers.hmm GCA_022720295.1_ASM2272029v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:18:10,503] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:18:10,504] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ac49470-6aa7-4074-9da2-7253acb8cc68/GCA_022720295.1_ASM2272029v1_genomic.fna.gz]
[2023-06-13 03:18:10,541] [INFO] Query marker FASTA was written to GCA_022720295.1_ASM2272029v1_genomic.fna/markers.fasta
[2023-06-13 03:18:10,541] [INFO] Task started: Blastn
[2023-06-13 03:18:10,541] [INFO] Running command: blastn -query GCA_022720295.1_ASM2272029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2bf9a7c-1ce7-43e5-8337-b758e471cd59/dqc_reference/reference_markers.fasta -out GCA_022720295.1_ASM2272029v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:18:11,346] [INFO] Task succeeded: Blastn
[2023-06-13 03:18:11,350] [INFO] Selected 12 target genomes.
[2023-06-13 03:18:11,350] [INFO] Target genome list was writen to GCA_022720295.1_ASM2272029v1_genomic.fna/target_genomes.txt
[2023-06-13 03:18:11,354] [INFO] Task started: fastANI
[2023-06-13 03:18:11,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ac49470-6aa7-4074-9da2-7253acb8cc68/GCA_022720295.1_ASM2272029v1_genomic.fna.gz --refList GCA_022720295.1_ASM2272029v1_genomic.fna/target_genomes.txt --output GCA_022720295.1_ASM2272029v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:18:18,625] [INFO] Task succeeded: fastANI
[2023-06-13 03:18:18,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2bf9a7c-1ce7-43e5-8337-b758e471cd59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:18:18,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2bf9a7c-1ce7-43e5-8337-b758e471cd59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:18:18,635] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 03:18:18,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 03:18:18,635] [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 angulatum	strain=DSM 20098	GCA_000771205.1	1683	1683	type	True	98.7582	536	732	95	conclusive
Bifidobacterium angulatum	strain=LMG 11039	GCA_000741065.1	1683	1683	type	True	98.7568	545	732	95	conclusive
Bifidobacterium angulatum	strain=DSM 20098	GCA_000156635.1	1683	1683	type	True	98.7352	547	732	95	conclusive
Bifidobacterium angulatum	strain=JCM 7096	GCA_001025155.1	1683	1683	type	True	98.7082	551	732	95	conclusive
Bifidobacterium merycicum	strain=DSM 6492	GCA_900129045.1	78345	78345	type	True	88.0457	477	732	95	below_threshold
Bifidobacterium pongonis	strain=64T4	GCA_019331805.1	2834432	2834432	type	True	85.9336	455	732	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	80.7985	295	732	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 03:18:18,637] [INFO] DFAST Taxonomy check result was written to GCA_022720295.1_ASM2272029v1_genomic.fna/tc_result.tsv
[2023-06-13 03:18:18,638] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:18:18,638] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:18:18,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2bf9a7c-1ce7-43e5-8337-b758e471cd59/dqc_reference/checkm_data
[2023-06-13 03:18:18,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:18:18,665] [INFO] Task started: CheckM
[2023-06-13 03:18:18,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022720295.1_ASM2272029v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022720295.1_ASM2272029v1_genomic.fna/checkm_input GCA_022720295.1_ASM2272029v1_genomic.fna/checkm_result
[2023-06-13 03:18:46,052] [INFO] Task succeeded: CheckM
[2023-06-13 03:18:46,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:18:46,075] [INFO] ===== Completeness check finished =====
[2023-06-13 03:18:46,075] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:18:46,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022720295.1_ASM2272029v1_genomic.fna/markers.fasta)
[2023-06-13 03:18:46,076] [INFO] Task started: Blastn
[2023-06-13 03:18:46,076] [INFO] Running command: blastn -query GCA_022720295.1_ASM2272029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2bf9a7c-1ce7-43e5-8337-b758e471cd59/dqc_reference/reference_markers_gtdb.fasta -out GCA_022720295.1_ASM2272029v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:18:47,355] [INFO] Task succeeded: Blastn
[2023-06-13 03:18:47,363] [INFO] Selected 19 target genomes.
[2023-06-13 03:18:47,364] [INFO] Target genome list was writen to GCA_022720295.1_ASM2272029v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:18:47,370] [INFO] Task started: fastANI
[2023-06-13 03:18:47,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ac49470-6aa7-4074-9da2-7253acb8cc68/GCA_022720295.1_ASM2272029v1_genomic.fna.gz --refList GCA_022720295.1_ASM2272029v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022720295.1_ASM2272029v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:18:54,481] [INFO] Task succeeded: fastANI
[2023-06-13 03:18:54,492] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:18:54,493] [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_001025155.1	s__Bifidobacterium angulatum	98.7082	551	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.71	95.22	0.93	0.74	7	conclusive
GCF_900129045.1	s__Bifidobacterium merycicum	88.029	478	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.68	99.29	0.97	0.90	6	-
GCF_012932675.1	s__Bifidobacterium sp012932675	87.4859	500	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	80.7333	301	732	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	80.7104	304	732	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	80.6756	311	732	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	80.6091	311	732	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	80.5789	292	732	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	80.4458	295	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932445.1	s__Bifidobacterium sp012932445	80.2733	224	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 03:18:54,495] [INFO] GTDB search result was written to GCA_022720295.1_ASM2272029v1_genomic.fna/result_gtdb.tsv
[2023-06-13 03:18:54,496] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:18:54,500] [INFO] DFAST_QC result json was written to GCA_022720295.1_ASM2272029v1_genomic.fna/dqc_result.json
[2023-06-13 03:18:54,500] [INFO] DFAST_QC completed!
[2023-06-13 03:18:54,500] [INFO] Total running time: 0h0m54s