[2023-06-28 16:48:03,123] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:48:03,125] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:48:03,125] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4d34bd6-c479-4d33-b761-f4b5947350d0/dqc_reference
[2023-06-28 16:48:04,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:48:04,413] [INFO] Task started: Prodigal
[2023-06-28 16:48:04,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a47c57e-c40d-49da-a219-33f9b6bfb4d3/GCA_027080695.1_ASM2708069v1_genomic.fna.gz | prodigal -d GCA_027080695.1_ASM2708069v1_genomic.fna/cds.fna -a GCA_027080695.1_ASM2708069v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:48:08,921] [INFO] Task succeeded: Prodigal
[2023-06-28 16:48:08,922] [INFO] Task started: HMMsearch
[2023-06-28 16:48:08,922] [INFO] Running command: hmmsearch --tblout GCA_027080695.1_ASM2708069v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4d34bd6-c479-4d33-b761-f4b5947350d0/dqc_reference/reference_markers.hmm GCA_027080695.1_ASM2708069v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:48:09,169] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:48:09,171] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7a47c57e-c40d-49da-a219-33f9b6bfb4d3/GCA_027080695.1_ASM2708069v1_genomic.fna.gz]
[2023-06-28 16:48:09,199] [INFO] Query marker FASTA was written to GCA_027080695.1_ASM2708069v1_genomic.fna/markers.fasta
[2023-06-28 16:48:09,199] [INFO] Task started: Blastn
[2023-06-28 16:48:09,200] [INFO] Running command: blastn -query GCA_027080695.1_ASM2708069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4d34bd6-c479-4d33-b761-f4b5947350d0/dqc_reference/reference_markers.fasta -out GCA_027080695.1_ASM2708069v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:48:09,781] [INFO] Task succeeded: Blastn
[2023-06-28 16:48:09,786] [INFO] Selected 30 target genomes.
[2023-06-28 16:48:09,786] [INFO] Target genome list was writen to GCA_027080695.1_ASM2708069v1_genomic.fna/target_genomes.txt
[2023-06-28 16:48:09,792] [INFO] Task started: fastANI
[2023-06-28 16:48:09,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a47c57e-c40d-49da-a219-33f9b6bfb4d3/GCA_027080695.1_ASM2708069v1_genomic.fna.gz --refList GCA_027080695.1_ASM2708069v1_genomic.fna/target_genomes.txt --output GCA_027080695.1_ASM2708069v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:48:25,772] [INFO] Task succeeded: fastANI
[2023-06-28 16:48:25,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4d34bd6-c479-4d33-b761-f4b5947350d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:48:25,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4d34bd6-c479-4d33-b761-f4b5947350d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:48:25,776] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:48:25,776] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:48:25,776] [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
--------------------------------------------------------------------------------
[2023-06-28 16:48:25,778] [INFO] DFAST Taxonomy check result was written to GCA_027080695.1_ASM2708069v1_genomic.fna/tc_result.tsv
[2023-06-28 16:48:25,779] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:48:25,779] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:48:25,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4d34bd6-c479-4d33-b761-f4b5947350d0/dqc_reference/checkm_data
[2023-06-28 16:48:25,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:48:25,814] [INFO] Task started: CheckM
[2023-06-28 16:48:25,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027080695.1_ASM2708069v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027080695.1_ASM2708069v1_genomic.fna/checkm_input GCA_027080695.1_ASM2708069v1_genomic.fna/checkm_result
[2023-06-28 16:48:47,154] [INFO] Task succeeded: CheckM
[2023-06-28 16:48:47,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:48:47,179] [INFO] ===== Completeness check finished =====
[2023-06-28 16:48:47,180] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:48:47,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027080695.1_ASM2708069v1_genomic.fna/markers.fasta)
[2023-06-28 16:48:47,181] [INFO] Task started: Blastn
[2023-06-28 16:48:47,181] [INFO] Running command: blastn -query GCA_027080695.1_ASM2708069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4d34bd6-c479-4d33-b761-f4b5947350d0/dqc_reference/reference_markers_gtdb.fasta -out GCA_027080695.1_ASM2708069v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:48:47,974] [INFO] Task succeeded: Blastn
[2023-06-28 16:48:47,979] [INFO] Selected 33 target genomes.
[2023-06-28 16:48:47,979] [INFO] Target genome list was writen to GCA_027080695.1_ASM2708069v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:48:48,027] [INFO] Task started: fastANI
[2023-06-28 16:48:48,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a47c57e-c40d-49da-a219-33f9b6bfb4d3/GCA_027080695.1_ASM2708069v1_genomic.fna.gz --refList GCA_027080695.1_ASM2708069v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027080695.1_ASM2708069v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:49:03,257] [INFO] Task succeeded: fastANI
[2023-06-28 16:49:03,260] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:49:03,260] [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
--------------------------------------------------------------------------------
[2023-06-28 16:49:03,263] [INFO] GTDB search result was written to GCA_027080695.1_ASM2708069v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:49:03,264] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:49:03,266] [INFO] DFAST_QC result json was written to GCA_027080695.1_ASM2708069v1_genomic.fna/dqc_result.json
[2023-06-28 16:49:03,267] [INFO] DFAST_QC completed!
[2023-06-28 16:49:03,267] [INFO] Total running time: 0h1m0s