[2023-06-17 18:03:36,855] [INFO] DFAST_QC pipeline started.
[2023-06-17 18:03:36,858] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 18:03:36,858] [INFO] DQC Reference Directory: /var/lib/cwl/stg17221871-6371-449d-9b69-6ca21f96db6d/dqc_reference
[2023-06-17 18:03:38,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 18:03:38,271] [INFO] Task started: Prodigal
[2023-06-17 18:03:38,271] [INFO] Running command: gunzip -c /var/lib/cwl/stg02a01cc8-8099-42e7-9155-8eb91cb94462/GCA_028716045.1_ASM2871604v1_genomic.fna.gz | prodigal -d GCA_028716045.1_ASM2871604v1_genomic.fna/cds.fna -a GCA_028716045.1_ASM2871604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 18:03:42,268] [INFO] Task succeeded: Prodigal
[2023-06-17 18:03:42,268] [INFO] Task started: HMMsearch
[2023-06-17 18:03:42,268] [INFO] Running command: hmmsearch --tblout GCA_028716045.1_ASM2871604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17221871-6371-449d-9b69-6ca21f96db6d/dqc_reference/reference_markers.hmm GCA_028716045.1_ASM2871604v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 18:03:42,434] [INFO] Task succeeded: HMMsearch
[2023-06-17 18:03:42,435] [INFO] Found 6/6 markers.
[2023-06-17 18:03:42,447] [INFO] Query marker FASTA was written to GCA_028716045.1_ASM2871604v1_genomic.fna/markers.fasta
[2023-06-17 18:03:42,447] [INFO] Task started: Blastn
[2023-06-17 18:03:42,447] [INFO] Running command: blastn -query GCA_028716045.1_ASM2871604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17221871-6371-449d-9b69-6ca21f96db6d/dqc_reference/reference_markers.fasta -out GCA_028716045.1_ASM2871604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:03:43,147] [INFO] Task succeeded: Blastn
[2023-06-17 18:03:43,152] [INFO] Selected 18 target genomes.
[2023-06-17 18:03:43,153] [INFO] Target genome list was writen to GCA_028716045.1_ASM2871604v1_genomic.fna/target_genomes.txt
[2023-06-17 18:03:43,154] [INFO] Task started: fastANI
[2023-06-17 18:03:43,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg02a01cc8-8099-42e7-9155-8eb91cb94462/GCA_028716045.1_ASM2871604v1_genomic.fna.gz --refList GCA_028716045.1_ASM2871604v1_genomic.fna/target_genomes.txt --output GCA_028716045.1_ASM2871604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 18:03:53,915] [INFO] Task succeeded: fastANI
[2023-06-17 18:03:53,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17221871-6371-449d-9b69-6ca21f96db6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 18:03:53,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17221871-6371-449d-9b69-6ca21f96db6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 18:03:53,918] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 18:03:53,918] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 18:03:53,918] [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
--------------------------------------------------------------------------------
[2023-06-17 18:03:53,920] [INFO] DFAST Taxonomy check result was written to GCA_028716045.1_ASM2871604v1_genomic.fna/tc_result.tsv
[2023-06-17 18:03:53,921] [INFO] ===== Taxonomy check completed =====
[2023-06-17 18:03:53,921] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 18:03:53,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17221871-6371-449d-9b69-6ca21f96db6d/dqc_reference/checkm_data
[2023-06-17 18:03:53,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 18:03:53,936] [INFO] Task started: CheckM
[2023-06-17 18:03:53,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028716045.1_ASM2871604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028716045.1_ASM2871604v1_genomic.fna/checkm_input GCA_028716045.1_ASM2871604v1_genomic.fna/checkm_result
[2023-06-17 18:04:11,653] [INFO] Task succeeded: CheckM
[2023-06-17 18:04:11,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 18:04:11,670] [INFO] ===== Completeness check finished =====
[2023-06-17 18:04:11,671] [INFO] ===== Start GTDB Search =====
[2023-06-17 18:04:11,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028716045.1_ASM2871604v1_genomic.fna/markers.fasta)
[2023-06-17 18:04:11,671] [INFO] Task started: Blastn
[2023-06-17 18:04:11,671] [INFO] Running command: blastn -query GCA_028716045.1_ASM2871604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17221871-6371-449d-9b69-6ca21f96db6d/dqc_reference/reference_markers_gtdb.fasta -out GCA_028716045.1_ASM2871604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:04:12,455] [INFO] Task succeeded: Blastn
[2023-06-17 18:04:12,459] [INFO] Selected 19 target genomes.
[2023-06-17 18:04:12,459] [INFO] Target genome list was writen to GCA_028716045.1_ASM2871604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 18:04:12,468] [INFO] Task started: fastANI
[2023-06-17 18:04:12,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg02a01cc8-8099-42e7-9155-8eb91cb94462/GCA_028716045.1_ASM2871604v1_genomic.fna.gz --refList GCA_028716045.1_ASM2871604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028716045.1_ASM2871604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 18:04:16,833] [INFO] Task succeeded: fastANI
[2023-06-17 18:04:16,835] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 18:04:16,835] [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
--------------------------------------------------------------------------------
[2023-06-17 18:04:16,837] [INFO] GTDB search result was written to GCA_028716045.1_ASM2871604v1_genomic.fna/result_gtdb.tsv
[2023-06-17 18:04:16,837] [INFO] ===== GTDB Search completed =====
[2023-06-17 18:04:16,839] [INFO] DFAST_QC result json was written to GCA_028716045.1_ASM2871604v1_genomic.fna/dqc_result.json
[2023-06-17 18:04:16,840] [INFO] DFAST_QC completed!
[2023-06-17 18:04:16,840] [INFO] Total running time: 0h0m40s