[2023-03-19 00:33:19,075] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,075] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,075] [INFO] DQC Reference Directory: /var/lib/cwl/stg43547c2c-fc4e-4624-95fe-6951252790cb/dqc_reference
[2023-03-19 00:33:20,348] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,348] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,349] [INFO] Running command: cat /var/lib/cwl/stg4523408d-f986-4f92-83bb-c9510d72b1cd/OceanDNA-b32536.fa | prodigal -d OceanDNA-b32536/cds.fna -a OceanDNA-b32536/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:22,462] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:22,463] [INFO] Task started: HMMsearch
[2023-03-19 00:33:22,463] [INFO] Running command: hmmsearch --tblout OceanDNA-b32536/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43547c2c-fc4e-4624-95fe-6951252790cb/dqc_reference/reference_markers.hmm OceanDNA-b32536/protein.faa > /dev/null
[2023-03-19 00:33:22,645] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:22,646] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4523408d-f986-4f92-83bb-c9510d72b1cd/OceanDNA-b32536.fa]
[2023-03-19 00:33:22,655] [INFO] Query marker FASTA was written to OceanDNA-b32536/markers.fasta
[2023-03-19 00:33:22,657] [INFO] Task started: Blastn
[2023-03-19 00:33:22,657] [INFO] Running command: blastn -query OceanDNA-b32536/markers.fasta -db /var/lib/cwl/stg43547c2c-fc4e-4624-95fe-6951252790cb/dqc_reference/reference_markers.fasta -out OceanDNA-b32536/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:23,145] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:23,146] [INFO] Selected 16 target genomes.
[2023-03-19 00:33:23,147] [INFO] Target genome list was writen to OceanDNA-b32536/target_genomes.txt
[2023-03-19 00:33:23,157] [INFO] Task started: fastANI
[2023-03-19 00:33:23,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg4523408d-f986-4f92-83bb-c9510d72b1cd/OceanDNA-b32536.fa --refList OceanDNA-b32536/target_genomes.txt --output OceanDNA-b32536/fastani_result.tsv --threads 1
[2023-03-19 00:33:30,237] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:30,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43547c2c-fc4e-4624-95fe-6951252790cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:30,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43547c2c-fc4e-4624-95fe-6951252790cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:30,238] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:30,238] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:33:30,238] [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
--------------------------------------------------------------------------------
[2023-03-19 00:33:30,240] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32536/tc_result.tsv
[2023-03-19 00:33:30,240] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:30,240] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:30,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43547c2c-fc4e-4624-95fe-6951252790cb/dqc_reference/checkm_data
[2023-03-19 00:33:30,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:30,247] [INFO] Task started: CheckM
[2023-03-19 00:33:30,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32536/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32536/checkm_input OceanDNA-b32536/checkm_result
[2023-03-19 00:33:44,905] [INFO] Task succeeded: CheckM
[2023-03-19 00:33:44,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:33:44,915] [INFO] ===== Completeness check finished =====
[2023-03-19 00:33:44,915] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:33:44,915] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32536/markers.fasta)
[2023-03-19 00:33:44,917] [INFO] Task started: Blastn
[2023-03-19 00:33:44,917] [INFO] Running command: blastn -query OceanDNA-b32536/markers.fasta -db /var/lib/cwl/stg43547c2c-fc4e-4624-95fe-6951252790cb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32536/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:45,556] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:45,566] [INFO] Selected 17 target genomes.
[2023-03-19 00:33:45,566] [INFO] Target genome list was writen to OceanDNA-b32536/target_genomes_gtdb.txt
[2023-03-19 00:33:45,649] [INFO] Task started: fastANI
[2023-03-19 00:33:45,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg4523408d-f986-4f92-83bb-c9510d72b1cd/OceanDNA-b32536.fa --refList OceanDNA-b32536/target_genomes_gtdb.txt --output OceanDNA-b32536/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:33:48,774] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:48,774] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:33:48,774] [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
--------------------------------------------------------------------------------
[2023-03-19 00:33:48,778] [INFO] GTDB search result was written to OceanDNA-b32536/result_gtdb.tsv
[2023-03-19 00:33:48,785] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:33:48,790] [INFO] DFAST_QC result json was written to OceanDNA-b32536/dqc_result.json
[2023-03-19 00:33:48,790] [INFO] DFAST_QC completed!
[2023-03-19 00:33:48,790] [INFO] Total running time: 0h0m30s