[2023-03-18 10:46:22,166] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:46:22,166] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:46:22,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f42a56d-7c83-4b1c-a074-e61d32fe82f1/dqc_reference
[2023-03-18 10:46:23,297] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:46:23,298] [INFO] Task started: Prodigal
[2023-03-18 10:46:23,298] [INFO] Running command: cat /var/lib/cwl/stg57a5b097-2454-42a4-89b8-617103522ec9/OceanDNA-b20340.fa | prodigal -d OceanDNA-b20340/cds.fna -a OceanDNA-b20340/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:46:32,240] [INFO] Task succeeded: Prodigal
[2023-03-18 10:46:32,240] [INFO] Task started: HMMsearch
[2023-03-18 10:46:32,240] [INFO] Running command: hmmsearch --tblout OceanDNA-b20340/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f42a56d-7c83-4b1c-a074-e61d32fe82f1/dqc_reference/reference_markers.hmm OceanDNA-b20340/protein.faa > /dev/null
[2023-03-18 10:46:32,403] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:46:32,404] [INFO] Found 6/6 markers.
[2023-03-18 10:46:32,419] [INFO] Query marker FASTA was written to OceanDNA-b20340/markers.fasta
[2023-03-18 10:46:32,420] [INFO] Task started: Blastn
[2023-03-18 10:46:32,420] [INFO] Running command: blastn -query OceanDNA-b20340/markers.fasta -db /var/lib/cwl/stg4f42a56d-7c83-4b1c-a074-e61d32fe82f1/dqc_reference/reference_markers.fasta -out OceanDNA-b20340/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:46:32,945] [INFO] Task succeeded: Blastn
[2023-03-18 10:46:32,946] [INFO] Selected 15 target genomes.
[2023-03-18 10:46:32,946] [INFO] Target genome list was writen to OceanDNA-b20340/target_genomes.txt
[2023-03-18 10:46:32,954] [INFO] Task started: fastANI
[2023-03-18 10:46:32,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg57a5b097-2454-42a4-89b8-617103522ec9/OceanDNA-b20340.fa --refList OceanDNA-b20340/target_genomes.txt --output OceanDNA-b20340/fastani_result.tsv --threads 1
[2023-03-18 10:46:38,087] [INFO] Task succeeded: fastANI
[2023-03-18 10:46:38,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f42a56d-7c83-4b1c-a074-e61d32fe82f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:46:38,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f42a56d-7c83-4b1c-a074-e61d32fe82f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:46:38,088] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:46:38,088] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:46:38,088] [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
--------------------------------------------------------------------------------
[2023-03-18 10:46:38,089] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20340/tc_result.tsv
[2023-03-18 10:46:38,090] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:46:38,091] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:46:38,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f42a56d-7c83-4b1c-a074-e61d32fe82f1/dqc_reference/checkm_data
[2023-03-18 10:46:38,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:46:38,098] [INFO] Task started: CheckM
[2023-03-18 10:46:38,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20340/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20340/checkm_input OceanDNA-b20340/checkm_result
[2023-03-18 10:47:05,732] [INFO] Task succeeded: CheckM
[2023-03-18 10:47:05,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.76%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 10:47:05,749] [INFO] ===== Completeness check finished =====
[2023-03-18 10:47:05,749] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:47:05,749] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20340/markers.fasta)
[2023-03-18 10:47:05,750] [INFO] Task started: Blastn
[2023-03-18 10:47:05,750] [INFO] Running command: blastn -query OceanDNA-b20340/markers.fasta -db /var/lib/cwl/stg4f42a56d-7c83-4b1c-a074-e61d32fe82f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20340/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:47:06,533] [INFO] Task succeeded: Blastn
[2023-03-18 10:47:06,534] [INFO] Selected 25 target genomes.
[2023-03-18 10:47:06,534] [INFO] Target genome list was writen to OceanDNA-b20340/target_genomes_gtdb.txt
[2023-03-18 10:47:06,582] [INFO] Task started: fastANI
[2023-03-18 10:47:06,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg57a5b097-2454-42a4-89b8-617103522ec9/OceanDNA-b20340.fa --refList OceanDNA-b20340/target_genomes_gtdb.txt --output OceanDNA-b20340/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:47:14,156] [INFO] Task succeeded: fastANI
[2023-03-18 10:47:14,156] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:47:14,156] [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
--------------------------------------------------------------------------------
[2023-03-18 10:47:14,157] [INFO] GTDB search result was written to OceanDNA-b20340/result_gtdb.tsv
[2023-03-18 10:47:14,158] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:47:14,159] [INFO] DFAST_QC result json was written to OceanDNA-b20340/dqc_result.json
[2023-03-18 10:47:14,160] [INFO] DFAST_QC completed!
[2023-03-18 10:47:14,160] [INFO] Total running time: 0h0m52s