[2023-06-05 01:05:03,962] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:05:03,964] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:05:03,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c00e635-571d-478d-90b9-68f9ce3c1022/dqc_reference
[2023-06-05 01:05:05,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:05:05,413] [INFO] Task started: Prodigal
[2023-06-05 01:05:05,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ee96080-cb4b-40e0-b7f3-7487cb31373b/GCA_934417455.1_ERR7738447_bin.216_genomic.fna.gz | prodigal -d GCA_934417455.1_ERR7738447_bin.216_genomic.fna/cds.fna -a GCA_934417455.1_ERR7738447_bin.216_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:05:09,008] [INFO] Task succeeded: Prodigal
[2023-06-05 01:05:09,009] [INFO] Task started: HMMsearch
[2023-06-05 01:05:09,009] [INFO] Running command: hmmsearch --tblout GCA_934417455.1_ERR7738447_bin.216_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c00e635-571d-478d-90b9-68f9ce3c1022/dqc_reference/reference_markers.hmm GCA_934417455.1_ERR7738447_bin.216_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:05:09,211] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:05:09,213] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4ee96080-cb4b-40e0-b7f3-7487cb31373b/GCA_934417455.1_ERR7738447_bin.216_genomic.fna.gz]
[2023-06-05 01:05:09,234] [INFO] Query marker FASTA was written to GCA_934417455.1_ERR7738447_bin.216_genomic.fna/markers.fasta
[2023-06-05 01:05:09,234] [INFO] Task started: Blastn
[2023-06-05 01:05:09,234] [INFO] Running command: blastn -query GCA_934417455.1_ERR7738447_bin.216_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c00e635-571d-478d-90b9-68f9ce3c1022/dqc_reference/reference_markers.fasta -out GCA_934417455.1_ERR7738447_bin.216_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:05:09,793] [INFO] Task succeeded: Blastn
[2023-06-05 01:05:09,798] [INFO] Selected 10 target genomes.
[2023-06-05 01:05:09,798] [INFO] Target genome list was writen to GCA_934417455.1_ERR7738447_bin.216_genomic.fna/target_genomes.txt
[2023-06-05 01:05:09,802] [INFO] Task started: fastANI
[2023-06-05 01:05:09,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee96080-cb4b-40e0-b7f3-7487cb31373b/GCA_934417455.1_ERR7738447_bin.216_genomic.fna.gz --refList GCA_934417455.1_ERR7738447_bin.216_genomic.fna/target_genomes.txt --output GCA_934417455.1_ERR7738447_bin.216_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:05:13,036] [INFO] Task succeeded: fastANI
[2023-06-05 01:05:13,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c00e635-571d-478d-90b9-68f9ce3c1022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:05:13,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c00e635-571d-478d-90b9-68f9ce3c1022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:05:13,038] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:05:13,038] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 01:05:13,038] [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
--------------------------------------------------------------------------------
[2023-06-05 01:05:13,041] [INFO] DFAST Taxonomy check result was written to GCA_934417455.1_ERR7738447_bin.216_genomic.fna/tc_result.tsv
[2023-06-05 01:05:13,041] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:05:13,041] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:05:13,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c00e635-571d-478d-90b9-68f9ce3c1022/dqc_reference/checkm_data
[2023-06-05 01:05:13,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:05:13,067] [INFO] Task started: CheckM
[2023-06-05 01:05:13,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934417455.1_ERR7738447_bin.216_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934417455.1_ERR7738447_bin.216_genomic.fna/checkm_input GCA_934417455.1_ERR7738447_bin.216_genomic.fna/checkm_result
[2023-06-05 01:05:32,359] [INFO] Task succeeded: CheckM
[2023-06-05 01:05:32,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.24%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:05:32,382] [INFO] ===== Completeness check finished =====
[2023-06-05 01:05:32,382] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:05:32,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934417455.1_ERR7738447_bin.216_genomic.fna/markers.fasta)
[2023-06-05 01:05:32,383] [INFO] Task started: Blastn
[2023-06-05 01:05:32,383] [INFO] Running command: blastn -query GCA_934417455.1_ERR7738447_bin.216_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c00e635-571d-478d-90b9-68f9ce3c1022/dqc_reference/reference_markers_gtdb.fasta -out GCA_934417455.1_ERR7738447_bin.216_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:05:33,134] [INFO] Task succeeded: Blastn
[2023-06-05 01:05:33,139] [INFO] Selected 15 target genomes.
[2023-06-05 01:05:33,139] [INFO] Target genome list was writen to GCA_934417455.1_ERR7738447_bin.216_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:05:33,202] [INFO] Task started: fastANI
[2023-06-05 01:05:33,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee96080-cb4b-40e0-b7f3-7487cb31373b/GCA_934417455.1_ERR7738447_bin.216_genomic.fna.gz --refList GCA_934417455.1_ERR7738447_bin.216_genomic.fna/target_genomes_gtdb.txt --output GCA_934417455.1_ERR7738447_bin.216_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:05:38,118] [INFO] Task succeeded: fastANI
[2023-06-05 01:05:38,120] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 01:05:38,121] [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
--------------------------------------------------------------------------------
[2023-06-05 01:05:38,123] [INFO] GTDB search result was written to GCA_934417455.1_ERR7738447_bin.216_genomic.fna/result_gtdb.tsv
[2023-06-05 01:05:38,123] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:05:38,125] [INFO] DFAST_QC result json was written to GCA_934417455.1_ERR7738447_bin.216_genomic.fna/dqc_result.json
[2023-06-05 01:05:38,125] [INFO] DFAST_QC completed!
[2023-06-05 01:05:38,125] [INFO] Total running time: 0h0m34s