[2023-03-16 09:06:46,893] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:06:46,893] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:06:46,893] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcc8655e-c93c-4349-add0-d3439c9b49bc/dqc_reference
[2023-03-16 09:06:47,984] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:06:47,984] [INFO] Task started: Prodigal
[2023-03-16 09:06:47,984] [INFO] Running command: cat /var/lib/cwl/stgd26ecf95-565e-4988-8d67-1ceaeab1b35d/OceanDNA-b17063.fa | prodigal -d OceanDNA-b17063/cds.fna -a OceanDNA-b17063/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:06:51,593] [INFO] Task succeeded: Prodigal
[2023-03-16 09:06:51,593] [INFO] Task started: HMMsearch
[2023-03-16 09:06:51,593] [INFO] Running command: hmmsearch --tblout OceanDNA-b17063/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcc8655e-c93c-4349-add0-d3439c9b49bc/dqc_reference/reference_markers.hmm OceanDNA-b17063/protein.faa > /dev/null
[2023-03-16 09:06:51,770] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:06:51,770] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd26ecf95-565e-4988-8d67-1ceaeab1b35d/OceanDNA-b17063.fa]
[2023-03-16 09:06:51,778] [INFO] Query marker FASTA was written to OceanDNA-b17063/markers.fasta
[2023-03-16 09:06:51,779] [INFO] Task started: Blastn
[2023-03-16 09:06:51,779] [INFO] Running command: blastn -query OceanDNA-b17063/markers.fasta -db /var/lib/cwl/stgfcc8655e-c93c-4349-add0-d3439c9b49bc/dqc_reference/reference_markers.fasta -out OceanDNA-b17063/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:06:52,629] [INFO] Task succeeded: Blastn
[2023-03-16 09:06:52,630] [INFO] Selected 11 target genomes.
[2023-03-16 09:06:52,630] [INFO] Target genome list was writen to OceanDNA-b17063/target_genomes.txt
[2023-03-16 09:06:52,680] [INFO] Task started: fastANI
[2023-03-16 09:06:52,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgd26ecf95-565e-4988-8d67-1ceaeab1b35d/OceanDNA-b17063.fa --refList OceanDNA-b17063/target_genomes.txt --output OceanDNA-b17063/fastani_result.tsv --threads 1
[2023-03-16 09:06:57,849] [INFO] Task succeeded: fastANI
[2023-03-16 09:06:57,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcc8655e-c93c-4349-add0-d3439c9b49bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:06:57,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcc8655e-c93c-4349-add0-d3439c9b49bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:06:57,849] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:06:57,849] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:06:57,849] [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
--------------------------------------------------------------------------------
[2023-03-16 09:06:57,850] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17063/tc_result.tsv
[2023-03-16 09:06:57,850] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:06:57,850] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:06:57,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcc8655e-c93c-4349-add0-d3439c9b49bc/dqc_reference/checkm_data
[2023-03-16 09:06:58,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:06:58,255] [INFO] Task started: CheckM
[2023-03-16 09:06:58,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17063/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17063/checkm_input OceanDNA-b17063/checkm_result
[2023-03-16 09:07:21,721] [INFO] Task succeeded: CheckM
[2023-03-16 09:07:21,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:07:21,729] [INFO] ===== Completeness check finished =====
[2023-03-16 09:07:21,729] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:07:21,729] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17063/markers.fasta)
[2023-03-16 09:07:21,730] [INFO] Task started: Blastn
[2023-03-16 09:07:21,731] [INFO] Running command: blastn -query OceanDNA-b17063/markers.fasta -db /var/lib/cwl/stgfcc8655e-c93c-4349-add0-d3439c9b49bc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17063/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:07:23,389] [INFO] Task succeeded: Blastn
[2023-03-16 09:07:23,391] [INFO] Selected 16 target genomes.
[2023-03-16 09:07:23,391] [INFO] Target genome list was writen to OceanDNA-b17063/target_genomes_gtdb.txt
[2023-03-16 09:07:23,825] [INFO] Task started: fastANI
[2023-03-16 09:07:23,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgd26ecf95-565e-4988-8d67-1ceaeab1b35d/OceanDNA-b17063.fa --refList OceanDNA-b17063/target_genomes_gtdb.txt --output OceanDNA-b17063/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:07:27,398] [INFO] Task succeeded: fastANI
[2023-03-16 09:07:27,399] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:07:27,399] [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
--------------------------------------------------------------------------------
[2023-03-16 09:07:27,399] [INFO] GTDB search result was written to OceanDNA-b17063/result_gtdb.tsv
[2023-03-16 09:07:27,400] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:07:27,400] [INFO] DFAST_QC result json was written to OceanDNA-b17063/dqc_result.json
[2023-03-16 09:07:27,400] [INFO] DFAST_QC completed!
[2023-03-16 09:07:27,400] [INFO] Total running time: 0h0m41s