[2024-01-24 14:06:05,683] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,685] [INFO] DQC Reference Directory: /var/lib/cwl/stgfadf130c-a949-4e85-816f-844e9b116a74/dqc_reference
[2024-01-24 14:06:07,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,098] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,098] [INFO] Running command: gunzip -c /var/lib/cwl/stg70c344f9-6a4b-4322-be8c-f4fdd1aa398c/GCF_001042655.1_ASM104265v1_genomic.fna.gz | prodigal -d GCF_001042655.1_ASM104265v1_genomic.fna/cds.fna -a GCF_001042655.1_ASM104265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:11,434] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:11,435] [INFO] Task started: HMMsearch
[2024-01-24 14:06:11,435] [INFO] Running command: hmmsearch --tblout GCF_001042655.1_ASM104265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfadf130c-a949-4e85-816f-844e9b116a74/dqc_reference/reference_markers.hmm GCF_001042655.1_ASM104265v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:11,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:11,714] [INFO] Found 6/6 markers.
[2024-01-24 14:06:11,745] [INFO] Query marker FASTA was written to GCF_001042655.1_ASM104265v1_genomic.fna/markers.fasta
[2024-01-24 14:06:11,746] [INFO] Task started: Blastn
[2024-01-24 14:06:11,746] [INFO] Running command: blastn -query GCF_001042655.1_ASM104265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfadf130c-a949-4e85-816f-844e9b116a74/dqc_reference/reference_markers.fasta -out GCF_001042655.1_ASM104265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:12,359] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:12,361] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:12,362] [INFO] Target genome list was writen to GCF_001042655.1_ASM104265v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:12,385] [INFO] Task started: fastANI
[2024-01-24 14:06:12,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c344f9-6a4b-4322-be8c-f4fdd1aa398c/GCF_001042655.1_ASM104265v1_genomic.fna.gz --refList GCF_001042655.1_ASM104265v1_genomic.fna/target_genomes.txt --output GCF_001042655.1_ASM104265v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:17,908] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:17,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfadf130c-a949-4e85-816f-844e9b116a74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:17,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfadf130c-a949-4e85-816f-844e9b116a74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:17,915] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 14:06:17,916] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:17,916] [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=JCM 11026	GCA_001042655.1	2702	2702	suspected-type	True	100.0	555	555	95	conclusive
Gardnerella vaginalis	strain=DSM 4944	GCA_900105405.1	2702	2702	suspected-type	True	99.9966	555	555	95	conclusive
Gardnerella vaginalis	strain=ATCC 14018	GCA_003397685.1	2702	2702	suspected-type	True	99.9961	553	555	95	conclusive
Gardnerella vaginalis	strain=NCTC10287	GCA_900637625.1	2702	2702	suspected-type	True	99.9955	555	555	95	conclusive
Gardnerella vaginalis	strain=ATCC 14018	GCA_004336685.1	2702	2702	suspected-type	True	99.9792	542	555	95	conclusive
Gardnerella vaginalis	strain=ATCC 14018	GCA_000178355.1	2702	2702	suspected-type	True	99.7766	460	555	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:06:17,917] [INFO] DFAST Taxonomy check result was written to GCF_001042655.1_ASM104265v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:17,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:17,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:17,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfadf130c-a949-4e85-816f-844e9b116a74/dqc_reference/checkm_data
[2024-01-24 14:06:17,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:17,949] [INFO] Task started: CheckM
[2024-01-24 14:06:17,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001042655.1_ASM104265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001042655.1_ASM104265v1_genomic.fna/checkm_input GCF_001042655.1_ASM104265v1_genomic.fna/checkm_result
[2024-01-24 14:06:38,565] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:38,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:38,580] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:38,580] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:38,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001042655.1_ASM104265v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:38,581] [INFO] Task started: Blastn
[2024-01-24 14:06:38,581] [INFO] Running command: blastn -query GCF_001042655.1_ASM104265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfadf130c-a949-4e85-816f-844e9b116a74/dqc_reference/reference_markers_gtdb.fasta -out GCF_001042655.1_ASM104265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:39,408] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:39,411] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:39,411] [INFO] Target genome list was writen to GCF_001042655.1_ASM104265v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:39,419] [INFO] Task started: fastANI
[2024-01-24 14:06:39,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c344f9-6a4b-4322-be8c-f4fdd1aa398c/GCF_001042655.1_ASM104265v1_genomic.fna.gz --refList GCF_001042655.1_ASM104265v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001042655.1_ASM104265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:44,780] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:44,790] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:44,791] [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	100.0	555	555	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	89.0427	435	555	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	87.913	404	555	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	84.4211	290	555	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	83.9514	304	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.706	N/A	N/A	N/A	N/A	1	-
GCF_002896555.1	s__Bifidobacterium vaginale_F	83.8852	271	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001546485.1	s__Bifidobacterium vaginale_D	83.6785	269	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.87	98.82	0.95	0.94	3	-
GCF_000263635.1	s__Bifidobacterium vaginale_C	83.4119	285	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.53	95.52	0.94	0.93	5	-
GCA_003585735.1	s__Bifidobacterium sp003585735	83.2189	308	555	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.73	99.73	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:44,794] [INFO] GTDB search result was written to GCF_001042655.1_ASM104265v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:44,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:44,800] [INFO] DFAST_QC result json was written to GCF_001042655.1_ASM104265v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:44,800] [INFO] DFAST_QC completed!
[2024-01-24 14:06:44,801] [INFO] Total running time: 0h0m39s