[2024-01-24 12:53:36,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dfee81a-ee68-48ea-b2f3-34637caee5c9/dqc_reference
[2024-01-24 12:53:37,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:37,847] [INFO] Task started: Prodigal
[2024-01-24 12:53:37,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fee666c-e5a1-4c79-80c1-0122e236e097/GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/cds.fna -a GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:41,923] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:41,924] [INFO] Task started: HMMsearch
[2024-01-24 12:53:41,924] [INFO] Running command: hmmsearch --tblout GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dfee81a-ee68-48ea-b2f3-34637caee5c9/dqc_reference/reference_markers.hmm GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:42,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:42,142] [INFO] Found 6/6 markers.
[2024-01-24 12:53:42,163] [INFO] Query marker FASTA was written to GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:53:42,163] [INFO] Task started: Blastn
[2024-01-24 12:53:42,163] [INFO] Running command: blastn -query GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dfee81a-ee68-48ea-b2f3-34637caee5c9/dqc_reference/reference_markers.fasta -out GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:42,782] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:42,786] [INFO] Selected 11 target genomes.
[2024-01-24 12:53:42,787] [INFO] Target genome list was writen to GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:53:42,874] [INFO] Task started: fastANI
[2024-01-24 12:53:42,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fee666c-e5a1-4c79-80c1-0122e236e097/GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna.gz --refList GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:47,902] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:47,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dfee81a-ee68-48ea-b2f3-34637caee5c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:47,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dfee81a-ee68-48ea-b2f3-34637caee5c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:47,909] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:53:47,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:47,910] [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
Gardnerella vaginalis	strain=DSM 4944	GCA_900105405.1	2702	2702	suspected-type	True	100.0	559	561	95	conclusive
Gardnerella vaginalis	strain=ATCC 14018	GCA_003397685.1	2702	2702	suspected-type	True	99.9987	552	561	95	conclusive
Gardnerella vaginalis	strain=JCM 11026	GCA_001042655.1	2702	2702	suspected-type	True	99.9946	555	561	95	conclusive
Gardnerella vaginalis	strain=NCTC10287	GCA_900637625.1	2702	2702	suspected-type	True	99.9941	556	561	95	conclusive
Gardnerella vaginalis	strain=ATCC 14018	GCA_004336685.1	2702	2702	suspected-type	True	99.9882	541	561	95	conclusive
Gardnerella vaginalis	strain=ATCC 14018	GCA_000178355.1	2702	2702	suspected-type	True	99.7677	457	561	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:53:47,911] [INFO] DFAST Taxonomy check result was written to GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:53:47,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:47,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:47,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dfee81a-ee68-48ea-b2f3-34637caee5c9/dqc_reference/checkm_data
[2024-01-24 12:53:47,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:47,931] [INFO] Task started: CheckM
[2024-01-24 12:53:47,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/checkm_input GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:54:07,055] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:07,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:07,069] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:07,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:07,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:54:07,070] [INFO] Task started: Blastn
[2024-01-24 12:54:07,070] [INFO] Running command: blastn -query GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dfee81a-ee68-48ea-b2f3-34637caee5c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:07,815] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:07,820] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:07,820] [INFO] Target genome list was writen to GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:07,839] [INFO] Task started: fastANI
[2024-01-24 12:54:07,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fee666c-e5a1-4c79-80c1-0122e236e097/GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna.gz --refList GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:13,004] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:13,021] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:13,022] [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_001042655.1	s__Bifidobacterium vaginale	99.9946	555	561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.38	95.61	0.95	0.87	50	conclusive
GCF_003397585.1	s__Bifidobacterium piotii	89.0966	429	561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.39	95.73	0.93	0.88	27	-
GCF_001546455.1	s__Bifidobacterium vaginale_B	87.8959	402	561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002896555.1	s__Bifidobacterium vaginale_F	84.107	268	561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003397705.1	s__Bifidobacterium swidsinskii	84.0461	298	561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.6629	98.35	97.96	0.94	0.90	18	-
GCA_003585845.1	s__Bifidobacterium sp003585845	83.7429	308	561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.706	N/A	N/A	N/A	N/A	1	-
GCF_001546485.1	s__Bifidobacterium vaginale_D	83.7209	270	561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.87	98.82	0.95	0.94	3	-
GCA_003585735.1	s__Bifidobacterium sp003585735	83.1752	309	561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.73	99.73	0.99	0.99	2	-
GCF_000263635.1	s__Bifidobacterium vaginale_C	83.0785	297	561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.53	95.52	0.94	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:13,024] [INFO] GTDB search result was written to GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:13,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:13,028] [INFO] DFAST_QC result json was written to GCF_900105405.1_IMG-taxon_2630968301_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:54:13,029] [INFO] DFAST_QC completed!
[2024-01-24 12:54:13,029] [INFO] Total running time: 0h0m36s