[2023-06-28 10:47:06,597] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:47:06,623] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:47:06,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgeee43bbe-6a5d-4929-8dc3-c3be5a435519/dqc_reference
[2023-06-28 10:47:07,856] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:47:07,856] [INFO] Task started: Prodigal
[2023-06-28 10:47:07,857] [INFO] Running command: gunzip -c /var/lib/cwl/stga0d20cda-8c51-4556-821c-f8b0a6b3269e/GCA_027428455.1_ASM2742845v1_genomic.fna.gz | prodigal -d GCA_027428455.1_ASM2742845v1_genomic.fna/cds.fna -a GCA_027428455.1_ASM2742845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:47:10,526] [INFO] Task succeeded: Prodigal
[2023-06-28 10:47:10,526] [INFO] Task started: HMMsearch
[2023-06-28 10:47:10,527] [INFO] Running command: hmmsearch --tblout GCA_027428455.1_ASM2742845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeee43bbe-6a5d-4929-8dc3-c3be5a435519/dqc_reference/reference_markers.hmm GCA_027428455.1_ASM2742845v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:47:10,847] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:47:10,848] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga0d20cda-8c51-4556-821c-f8b0a6b3269e/GCA_027428455.1_ASM2742845v1_genomic.fna.gz]
[2023-06-28 10:47:10,867] [INFO] Query marker FASTA was written to GCA_027428455.1_ASM2742845v1_genomic.fna/markers.fasta
[2023-06-28 10:47:10,868] [INFO] Task started: Blastn
[2023-06-28 10:47:10,868] [INFO] Running command: blastn -query GCA_027428455.1_ASM2742845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeee43bbe-6a5d-4929-8dc3-c3be5a435519/dqc_reference/reference_markers.fasta -out GCA_027428455.1_ASM2742845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:11,951] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:11,955] [INFO] Selected 15 target genomes.
[2023-06-28 10:47:11,956] [INFO] Target genome list was writen to GCA_027428455.1_ASM2742845v1_genomic.fna/target_genomes.txt
[2023-06-28 10:47:11,961] [INFO] Task started: fastANI
[2023-06-28 10:47:11,961] [INFO] Running command: fastANI --query /var/lib/cwl/stga0d20cda-8c51-4556-821c-f8b0a6b3269e/GCA_027428455.1_ASM2742845v1_genomic.fna.gz --refList GCA_027428455.1_ASM2742845v1_genomic.fna/target_genomes.txt --output GCA_027428455.1_ASM2742845v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:47:18,672] [INFO] Task succeeded: fastANI
[2023-06-28 10:47:18,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeee43bbe-6a5d-4929-8dc3-c3be5a435519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:47:18,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeee43bbe-6a5d-4929-8dc3-c3be5a435519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:47:18,675] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:47:18,675] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:47:18,675] [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 10:47:18,678] [INFO] DFAST Taxonomy check result was written to GCA_027428455.1_ASM2742845v1_genomic.fna/tc_result.tsv
[2023-06-28 10:47:18,679] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:47:18,679] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:47:18,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeee43bbe-6a5d-4929-8dc3-c3be5a435519/dqc_reference/checkm_data
[2023-06-28 10:47:18,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:47:18,699] [INFO] Task started: CheckM
[2023-06-28 10:47:18,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027428455.1_ASM2742845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027428455.1_ASM2742845v1_genomic.fna/checkm_input GCA_027428455.1_ASM2742845v1_genomic.fna/checkm_result
[2023-06-28 10:47:34,438] [INFO] Task succeeded: CheckM
[2023-06-28 10:47:34,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:47:34,464] [INFO] ===== Completeness check finished =====
[2023-06-28 10:47:34,464] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:47:34,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027428455.1_ASM2742845v1_genomic.fna/markers.fasta)
[2023-06-28 10:47:34,465] [INFO] Task started: Blastn
[2023-06-28 10:47:34,465] [INFO] Running command: blastn -query GCA_027428455.1_ASM2742845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeee43bbe-6a5d-4929-8dc3-c3be5a435519/dqc_reference/reference_markers_gtdb.fasta -out GCA_027428455.1_ASM2742845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:35,221] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:35,229] [INFO] Selected 18 target genomes.
[2023-06-28 10:47:35,230] [INFO] Target genome list was writen to GCA_027428455.1_ASM2742845v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:47:35,246] [INFO] Task started: fastANI
[2023-06-28 10:47:35,246] [INFO] Running command: fastANI --query /var/lib/cwl/stga0d20cda-8c51-4556-821c-f8b0a6b3269e/GCA_027428455.1_ASM2742845v1_genomic.fna.gz --refList GCA_027428455.1_ASM2742845v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027428455.1_ASM2742845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:47:40,711] [INFO] Task succeeded: fastANI
[2023-06-28 10:47:40,715] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:47:40,715] [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 10:47:40,721] [INFO] GTDB search result was written to GCA_027428455.1_ASM2742845v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:47:40,723] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:47:40,727] [INFO] DFAST_QC result json was written to GCA_027428455.1_ASM2742845v1_genomic.fna/dqc_result.json
[2023-06-28 10:47:40,728] [INFO] DFAST_QC completed!
[2023-06-28 10:47:40,728] [INFO] Total running time: 0h0m34s