[2023-06-28 03:25:02,667] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:25:02,669] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:25:02,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c03da30-04b5-43f1-8e9c-6ac22f0f30d3/dqc_reference
[2023-06-28 03:25:03,978] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:25:03,980] [INFO] Task started: Prodigal
[2023-06-28 03:25:03,980] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaf1e5db-9f35-4b50-b3e4-51abd8402285/GCA_944358775.1_BRZ_CH_bin90_genomic.fna.gz | prodigal -d GCA_944358775.1_BRZ_CH_bin90_genomic.fna/cds.fna -a GCA_944358775.1_BRZ_CH_bin90_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:25:06,426] [INFO] Task succeeded: Prodigal
[2023-06-28 03:25:06,427] [INFO] Task started: HMMsearch
[2023-06-28 03:25:06,427] [INFO] Running command: hmmsearch --tblout GCA_944358775.1_BRZ_CH_bin90_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c03da30-04b5-43f1-8e9c-6ac22f0f30d3/dqc_reference/reference_markers.hmm GCA_944358775.1_BRZ_CH_bin90_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:25:06,670] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:25:06,672] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbaf1e5db-9f35-4b50-b3e4-51abd8402285/GCA_944358775.1_BRZ_CH_bin90_genomic.fna.gz]
[2023-06-28 03:25:06,691] [INFO] Query marker FASTA was written to GCA_944358775.1_BRZ_CH_bin90_genomic.fna/markers.fasta
[2023-06-28 03:25:06,692] [INFO] Task started: Blastn
[2023-06-28 03:25:06,692] [INFO] Running command: blastn -query GCA_944358775.1_BRZ_CH_bin90_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c03da30-04b5-43f1-8e9c-6ac22f0f30d3/dqc_reference/reference_markers.fasta -out GCA_944358775.1_BRZ_CH_bin90_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:07,316] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:07,319] [INFO] Selected 21 target genomes.
[2023-06-28 03:25:07,320] [INFO] Target genome list was writen to GCA_944358775.1_BRZ_CH_bin90_genomic.fna/target_genomes.txt
[2023-06-28 03:25:07,322] [INFO] Task started: fastANI
[2023-06-28 03:25:07,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaf1e5db-9f35-4b50-b3e4-51abd8402285/GCA_944358775.1_BRZ_CH_bin90_genomic.fna.gz --refList GCA_944358775.1_BRZ_CH_bin90_genomic.fna/target_genomes.txt --output GCA_944358775.1_BRZ_CH_bin90_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:25:17,023] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:17,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c03da30-04b5-43f1-8e9c-6ac22f0f30d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:25:17,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c03da30-04b5-43f1-8e9c-6ac22f0f30d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:25:17,026] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:25:17,026] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 03:25:17,027] [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 03:25:17,029] [INFO] DFAST Taxonomy check result was written to GCA_944358775.1_BRZ_CH_bin90_genomic.fna/tc_result.tsv
[2023-06-28 03:25:17,030] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:25:17,030] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:25:17,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c03da30-04b5-43f1-8e9c-6ac22f0f30d3/dqc_reference/checkm_data
[2023-06-28 03:25:17,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:25:17,056] [INFO] Task started: CheckM
[2023-06-28 03:25:17,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944358775.1_BRZ_CH_bin90_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944358775.1_BRZ_CH_bin90_genomic.fna/checkm_input GCA_944358775.1_BRZ_CH_bin90_genomic.fna/checkm_result
[2023-06-28 03:25:33,161] [INFO] Task succeeded: CheckM
[2023-06-28 03:25:33,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:25:33,181] [INFO] ===== Completeness check finished =====
[2023-06-28 03:25:33,182] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:25:33,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944358775.1_BRZ_CH_bin90_genomic.fna/markers.fasta)
[2023-06-28 03:25:33,182] [INFO] Task started: Blastn
[2023-06-28 03:25:33,183] [INFO] Running command: blastn -query GCA_944358775.1_BRZ_CH_bin90_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c03da30-04b5-43f1-8e9c-6ac22f0f30d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_944358775.1_BRZ_CH_bin90_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:34,166] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:34,170] [INFO] Selected 29 target genomes.
[2023-06-28 03:25:34,170] [INFO] Target genome list was writen to GCA_944358775.1_BRZ_CH_bin90_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:25:34,202] [INFO] Task started: fastANI
[2023-06-28 03:25:34,202] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaf1e5db-9f35-4b50-b3e4-51abd8402285/GCA_944358775.1_BRZ_CH_bin90_genomic.fna.gz --refList GCA_944358775.1_BRZ_CH_bin90_genomic.fna/target_genomes_gtdb.txt --output GCA_944358775.1_BRZ_CH_bin90_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:25:42,408] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:42,410] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 03:25:42,410] [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 03:25:42,412] [INFO] GTDB search result was written to GCA_944358775.1_BRZ_CH_bin90_genomic.fna/result_gtdb.tsv
[2023-06-28 03:25:42,413] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:25:42,416] [INFO] DFAST_QC result json was written to GCA_944358775.1_BRZ_CH_bin90_genomic.fna/dqc_result.json
[2023-06-28 03:25:42,416] [INFO] DFAST_QC completed!
[2023-06-28 03:25:42,416] [INFO] Total running time: 0h0m40s