[2023-03-18 20:13:32,253] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,253] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ced4958-7911-4836-ad02-d5cda5e4801d/dqc_reference
[2023-03-18 20:13:33,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,436] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,436] [INFO] Running command: cat /var/lib/cwl/stg0c15c4aa-4272-4b75-9051-ff269103d9f9/OceanDNA-b3634.fa | prodigal -d OceanDNA-b3634/cds.fna -a OceanDNA-b3634/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:59,765] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:59,765] [INFO] Task started: HMMsearch
[2023-03-18 20:13:59,765] [INFO] Running command: hmmsearch --tblout OceanDNA-b3634/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ced4958-7911-4836-ad02-d5cda5e4801d/dqc_reference/reference_markers.hmm OceanDNA-b3634/protein.faa > /dev/null
[2023-03-18 20:13:59,997] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:59,998] [INFO] Found 6/6 markers.
[2023-03-18 20:14:00,025] [INFO] Query marker FASTA was written to OceanDNA-b3634/markers.fasta
[2023-03-18 20:14:00,025] [INFO] Task started: Blastn
[2023-03-18 20:14:00,025] [INFO] Running command: blastn -query OceanDNA-b3634/markers.fasta -db /var/lib/cwl/stg5ced4958-7911-4836-ad02-d5cda5e4801d/dqc_reference/reference_markers.fasta -out OceanDNA-b3634/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:00,585] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:00,585] [INFO] Selected 25 target genomes.
[2023-03-18 20:14:00,586] [INFO] Target genome list was writen to OceanDNA-b3634/target_genomes.txt
[2023-03-18 20:14:00,599] [INFO] Task started: fastANI
[2023-03-18 20:14:00,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c15c4aa-4272-4b75-9051-ff269103d9f9/OceanDNA-b3634.fa --refList OceanDNA-b3634/target_genomes.txt --output OceanDNA-b3634/fastani_result.tsv --threads 1
[2023-03-18 20:14:16,798] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:16,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ced4958-7911-4836-ad02-d5cda5e4801d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:16,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ced4958-7911-4836-ad02-d5cda5e4801d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:16,799] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:16,799] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:14:16,799] [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 20:14:16,807] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3634/tc_result.tsv
[2023-03-18 20:14:16,807] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:16,807] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:16,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ced4958-7911-4836-ad02-d5cda5e4801d/dqc_reference/checkm_data
[2023-03-18 20:14:16,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:16,816] [INFO] Task started: CheckM
[2023-03-18 20:14:16,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3634/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3634/checkm_input OceanDNA-b3634/checkm_result
[2023-03-18 20:15:24,245] [INFO] Task succeeded: CheckM
[2023-03-18 20:15:24,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:15:24,248] [INFO] ===== Completeness check finished =====
[2023-03-18 20:15:24,248] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:15:24,248] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3634/markers.fasta)
[2023-03-18 20:15:24,249] [INFO] Task started: Blastn
[2023-03-18 20:15:24,249] [INFO] Running command: blastn -query OceanDNA-b3634/markers.fasta -db /var/lib/cwl/stg5ced4958-7911-4836-ad02-d5cda5e4801d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3634/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:15:24,958] [INFO] Task succeeded: Blastn
[2023-03-18 20:15:24,959] [INFO] Selected 34 target genomes.
[2023-03-18 20:15:24,960] [INFO] Target genome list was writen to OceanDNA-b3634/target_genomes_gtdb.txt
[2023-03-18 20:15:25,793] [INFO] Task started: fastANI
[2023-03-18 20:15:25,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c15c4aa-4272-4b75-9051-ff269103d9f9/OceanDNA-b3634.fa --refList OceanDNA-b3634/target_genomes_gtdb.txt --output OceanDNA-b3634/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:50,423] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:50,425] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:15:50,425] [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
GCA_013214265.1	s__DT-110 sp013214265	99.6123	1035	1169	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__DT-110	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 20:15:50,425] [INFO] GTDB search result was written to OceanDNA-b3634/result_gtdb.tsv
[2023-03-18 20:15:50,425] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:50,426] [INFO] DFAST_QC result json was written to OceanDNA-b3634/dqc_result.json
[2023-03-18 20:15:50,426] [INFO] DFAST_QC completed!
[2023-03-18 20:15:50,426] [INFO] Total running time: 0h2m18s