[2023-03-14 14:20:16,025] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:20:16,025] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:20:16,025] [INFO] DQC Reference Directory: /var/lib/cwl/stge69c9a24-2338-4ea7-af99-6e50bf1b2206/dqc_reference
[2023-03-14 14:20:18,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:20:18,682] [INFO] Task started: Prodigal
[2023-03-14 14:20:18,683] [INFO] Running command: cat /var/lib/cwl/stg0cde4e88-d264-4dab-9bff-c518a1314cbe/OceanDNA-b22416.fa | prodigal -d OceanDNA-b22416/cds.fna -a OceanDNA-b22416/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:20:52,824] [INFO] Task succeeded: Prodigal
[2023-03-14 14:20:52,824] [INFO] Task started: HMMsearch
[2023-03-14 14:20:52,824] [INFO] Running command: hmmsearch --tblout OceanDNA-b22416/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge69c9a24-2338-4ea7-af99-6e50bf1b2206/dqc_reference/reference_markers.hmm OceanDNA-b22416/protein.faa > /dev/null
[2023-03-14 14:20:53,344] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:20:53,344] [INFO] Found 6/6 markers.
[2023-03-14 14:20:53,412] [INFO] Query marker FASTA was written to OceanDNA-b22416/markers.fasta
[2023-03-14 14:20:53,420] [INFO] Task started: Blastn
[2023-03-14 14:20:53,420] [INFO] Running command: blastn -query OceanDNA-b22416/markers.fasta -db /var/lib/cwl/stge69c9a24-2338-4ea7-af99-6e50bf1b2206/dqc_reference/reference_markers.fasta -out OceanDNA-b22416/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:20:54,761] [INFO] Task succeeded: Blastn
[2023-03-14 14:20:54,763] [INFO] Selected 15 target genomes.
[2023-03-14 14:20:54,763] [INFO] Target genome list was writen to OceanDNA-b22416/target_genomes.txt
[2023-03-14 14:20:54,774] [INFO] Task started: fastANI
[2023-03-14 14:20:54,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cde4e88-d264-4dab-9bff-c518a1314cbe/OceanDNA-b22416.fa --refList OceanDNA-b22416/target_genomes.txt --output OceanDNA-b22416/fastani_result.tsv --threads 1
[2023-03-14 14:21:11,654] [INFO] Task succeeded: fastANI
[2023-03-14 14:21:11,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge69c9a24-2338-4ea7-af99-6e50bf1b2206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:21:11,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge69c9a24-2338-4ea7-af99-6e50bf1b2206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:21:11,655] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:21:11,655] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:21:11,655] [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 14:21:11,656] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22416/tc_result.tsv
[2023-03-14 14:21:11,656] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:21:11,656] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:21:11,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge69c9a24-2338-4ea7-af99-6e50bf1b2206/dqc_reference/checkm_data
[2023-03-14 14:21:11,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:21:11,866] [INFO] Task started: CheckM
[2023-03-14 14:21:11,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22416/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22416/checkm_input OceanDNA-b22416/checkm_result
[2023-03-14 14:22:38,089] [INFO] Task succeeded: CheckM
[2023-03-14 14:22:38,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 7.45%
Strain heterogeneity: 31.25%
--------------------------------------------------------------------------------
[2023-03-14 14:22:38,095] [INFO] ===== Completeness check finished =====
[2023-03-14 14:22:38,095] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:22:38,095] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22416/markers.fasta)
[2023-03-14 14:22:38,097] [INFO] Task started: Blastn
[2023-03-14 14:22:38,097] [INFO] Running command: blastn -query OceanDNA-b22416/markers.fasta -db /var/lib/cwl/stge69c9a24-2338-4ea7-af99-6e50bf1b2206/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22416/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:22:39,336] [INFO] Task succeeded: Blastn
[2023-03-14 14:22:39,338] [INFO] Selected 28 target genomes.
[2023-03-14 14:22:39,338] [INFO] Target genome list was writen to OceanDNA-b22416/target_genomes_gtdb.txt
[2023-03-14 14:22:39,371] [INFO] Task started: fastANI
[2023-03-14 14:22:39,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cde4e88-d264-4dab-9bff-c518a1314cbe/OceanDNA-b22416.fa --refList OceanDNA-b22416/target_genomes_gtdb.txt --output OceanDNA-b22416/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:23:11,009] [INFO] Task succeeded: fastANI
[2023-03-14 14:23:11,009] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:23:11,009] [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 14:23:11,010] [INFO] GTDB search result was written to OceanDNA-b22416/result_gtdb.tsv
[2023-03-14 14:23:11,011] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:23:11,013] [INFO] DFAST_QC result json was written to OceanDNA-b22416/dqc_result.json
[2023-03-14 14:23:11,013] [INFO] DFAST_QC completed!
[2023-03-14 14:23:11,013] [INFO] Total running time: 0h2m55s