[2023-03-14 11:36:02,657] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:36:02,659] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:36:02,659] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9a00e4c-69a7-45f5-9441-e67d75af373c/dqc_reference
[2023-03-14 11:36:04,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:36:04,406] [INFO] Task started: Prodigal
[2023-03-14 11:36:04,406] [INFO] Running command: cat /var/lib/cwl/stg121a6629-d867-4e66-b33f-5598fa6bb2ce/OceanDNA-b32485.fa | prodigal -d OceanDNA-b32485/cds.fna -a OceanDNA-b32485/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:36:06,863] [INFO] Task succeeded: Prodigal
[2023-03-14 11:36:06,863] [INFO] Task started: HMMsearch
[2023-03-14 11:36:06,863] [INFO] Running command: hmmsearch --tblout OceanDNA-b32485/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9a00e4c-69a7-45f5-9441-e67d75af373c/dqc_reference/reference_markers.hmm OceanDNA-b32485/protein.faa > /dev/null
[2023-03-14 11:36:07,089] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:36:07,090] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg121a6629-d867-4e66-b33f-5598fa6bb2ce/OceanDNA-b32485.fa]
[2023-03-14 11:36:07,102] [INFO] Query marker FASTA was written to OceanDNA-b32485/markers.fasta
[2023-03-14 11:36:07,103] [INFO] Task started: Blastn
[2023-03-14 11:36:07,103] [INFO] Running command: blastn -query OceanDNA-b32485/markers.fasta -db /var/lib/cwl/stgb9a00e4c-69a7-45f5-9441-e67d75af373c/dqc_reference/reference_markers.fasta -out OceanDNA-b32485/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:10,017] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:10,019] [INFO] Selected 5 target genomes.
[2023-03-14 11:36:10,019] [INFO] Target genome list was writen to OceanDNA-b32485/target_genomes.txt
[2023-03-14 11:36:10,022] [INFO] Task started: fastANI
[2023-03-14 11:36:10,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg121a6629-d867-4e66-b33f-5598fa6bb2ce/OceanDNA-b32485.fa --refList OceanDNA-b32485/target_genomes.txt --output OceanDNA-b32485/fastani_result.tsv --threads 1
[2023-03-14 11:36:12,393] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:12,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9a00e4c-69a7-45f5-9441-e67d75af373c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:36:12,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9a00e4c-69a7-45f5-9441-e67d75af373c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:36:12,394] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:36:12,394] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:36:12,394] [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
--------------------------------------------------------------------------------
[2023-03-14 11:36:12,394] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32485/tc_result.tsv
[2023-03-14 11:36:12,394] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:36:12,394] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:36:12,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9a00e4c-69a7-45f5-9441-e67d75af373c/dqc_reference/checkm_data
[2023-03-14 11:36:12,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:36:12,406] [INFO] Task started: CheckM
[2023-03-14 11:36:12,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32485/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32485/checkm_input OceanDNA-b32485/checkm_result
[2023-03-14 11:36:29,197] [INFO] Task succeeded: CheckM
[2023-03-14 11:36:29,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:36:29,200] [INFO] ===== Completeness check finished =====
[2023-03-14 11:36:29,200] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:36:29,200] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32485/markers.fasta)
[2023-03-14 11:36:29,201] [INFO] Task started: Blastn
[2023-03-14 11:36:29,201] [INFO] Running command: blastn -query OceanDNA-b32485/markers.fasta -db /var/lib/cwl/stgb9a00e4c-69a7-45f5-9441-e67d75af373c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32485/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:29,929] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:29,930] [INFO] Selected 16 target genomes.
[2023-03-14 11:36:29,930] [INFO] Target genome list was writen to OceanDNA-b32485/target_genomes_gtdb.txt
[2023-03-14 11:36:30,044] [INFO] Task started: fastANI
[2023-03-14 11:36:30,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg121a6629-d867-4e66-b33f-5598fa6bb2ce/OceanDNA-b32485.fa --refList OceanDNA-b32485/target_genomes_gtdb.txt --output OceanDNA-b32485/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:36:33,134] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:33,134] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:36:33,134] [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
--------------------------------------------------------------------------------
[2023-03-14 11:36:33,134] [INFO] GTDB search result was written to OceanDNA-b32485/result_gtdb.tsv
[2023-03-14 11:36:33,135] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:36:33,135] [INFO] DFAST_QC result json was written to OceanDNA-b32485/dqc_result.json
[2023-03-14 11:36:33,135] [INFO] DFAST_QC completed!
[2023-03-14 11:36:33,135] [INFO] Total running time: 0h0m30s