[2024-01-24 13:31:57,374] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,376] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg8aa857fb-f19c-4ebe-8bc8-7954fd97b511/dqc_reference
[2024-01-24 13:31:58,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,918] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,919] [INFO] Running command: gunzip -c /var/lib/cwl/stgf608852b-9295-42a6-aa52-b39558789012/GCF_028745505.1_ASM2874550v1_genomic.fna.gz | prodigal -d GCF_028745505.1_ASM2874550v1_genomic.fna/cds.fna -a GCF_028745505.1_ASM2874550v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:11,419] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:11,419] [INFO] Task started: HMMsearch
[2024-01-24 13:32:11,419] [INFO] Running command: hmmsearch --tblout GCF_028745505.1_ASM2874550v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8aa857fb-f19c-4ebe-8bc8-7954fd97b511/dqc_reference/reference_markers.hmm GCF_028745505.1_ASM2874550v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:11,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:11,759] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf608852b-9295-42a6-aa52-b39558789012/GCF_028745505.1_ASM2874550v1_genomic.fna.gz]
[2024-01-24 13:32:11,808] [INFO] Query marker FASTA was written to GCF_028745505.1_ASM2874550v1_genomic.fna/markers.fasta
[2024-01-24 13:32:11,809] [INFO] Task started: Blastn
[2024-01-24 13:32:11,809] [INFO] Running command: blastn -query GCF_028745505.1_ASM2874550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aa857fb-f19c-4ebe-8bc8-7954fd97b511/dqc_reference/reference_markers.fasta -out GCF_028745505.1_ASM2874550v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:12,409] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:12,413] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:12,414] [INFO] Target genome list was writen to GCF_028745505.1_ASM2874550v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:12,421] [INFO] Task started: fastANI
[2024-01-24 13:32:12,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgf608852b-9295-42a6-aa52-b39558789012/GCF_028745505.1_ASM2874550v1_genomic.fna.gz --refList GCF_028745505.1_ASM2874550v1_genomic.fna/target_genomes.txt --output GCF_028745505.1_ASM2874550v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:20,751] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:20,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8aa857fb-f19c-4ebe-8bc8-7954fd97b511/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:20,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8aa857fb-f19c-4ebe-8bc8-7954fd97b511/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:20,755] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:20,755] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:20,755] [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
Lentisphaera araneosa	strain=HTCC2155	GCA_000170755.1	256847	256847	type	True	81.7335	846	1765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:20,759] [INFO] DFAST Taxonomy check result was written to GCF_028745505.1_ASM2874550v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:20,760] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:20,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:20,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8aa857fb-f19c-4ebe-8bc8-7954fd97b511/dqc_reference/checkm_data
[2024-01-24 13:32:20,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:20,814] [INFO] Task started: CheckM
[2024-01-24 13:32:20,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028745505.1_ASM2874550v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028745505.1_ASM2874550v1_genomic.fna/checkm_input GCF_028745505.1_ASM2874550v1_genomic.fna/checkm_result
[2024-01-24 13:33:01,525] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:01,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:01,546] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:01,546] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:01,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028745505.1_ASM2874550v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:01,547] [INFO] Task started: Blastn
[2024-01-24 13:33:01,547] [INFO] Running command: blastn -query GCF_028745505.1_ASM2874550v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aa857fb-f19c-4ebe-8bc8-7954fd97b511/dqc_reference/reference_markers_gtdb.fasta -out GCF_028745505.1_ASM2874550v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:02,347] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:02,350] [INFO] Selected 23 target genomes.
[2024-01-24 13:33:02,351] [INFO] Target genome list was writen to GCF_028745505.1_ASM2874550v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:02,386] [INFO] Task started: fastANI
[2024-01-24 13:33:02,386] [INFO] Running command: fastANI --query /var/lib/cwl/stgf608852b-9295-42a6-aa52-b39558789012/GCF_028745505.1_ASM2874550v1_genomic.fna.gz --refList GCF_028745505.1_ASM2874550v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028745505.1_ASM2874550v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:16,779] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:16,782] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:33:16,783] [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_000170755.1	s__Lentisphaera araneosa	81.7158	848	1765	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__Lentisphaerales;f__Lentisphaeraceae;g__Lentisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:16,784] [INFO] GTDB search result was written to GCF_028745505.1_ASM2874550v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:16,785] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:16,787] [INFO] DFAST_QC result json was written to GCF_028745505.1_ASM2874550v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:16,788] [INFO] DFAST_QC completed!
[2024-01-24 13:33:16,788] [INFO] Total running time: 0h1m19s