[2023-03-16 21:45:15,258] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:15,258] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:15,258] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fc8f227-8bbe-42ac-b34b-d9da40f8d1b2/dqc_reference
[2023-03-16 21:45:16,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:16,436] [INFO] Task started: Prodigal
[2023-03-16 21:45:16,437] [INFO] Running command: cat /var/lib/cwl/stg38b253d3-d416-47a6-ac41-99fb295688c9/OceanDNA-b11613.fa | prodigal -d OceanDNA-b11613/cds.fna -a OceanDNA-b11613/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:31,198] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:31,199] [INFO] Task started: HMMsearch
[2023-03-16 21:45:31,199] [INFO] Running command: hmmsearch --tblout OceanDNA-b11613/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fc8f227-8bbe-42ac-b34b-d9da40f8d1b2/dqc_reference/reference_markers.hmm OceanDNA-b11613/protein.faa > /dev/null
[2023-03-16 21:45:31,399] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:31,399] [INFO] Found 6/6 markers.
[2023-03-16 21:45:31,418] [INFO] Query marker FASTA was written to OceanDNA-b11613/markers.fasta
[2023-03-16 21:45:31,418] [INFO] Task started: Blastn
[2023-03-16 21:45:31,418] [INFO] Running command: blastn -query OceanDNA-b11613/markers.fasta -db /var/lib/cwl/stg7fc8f227-8bbe-42ac-b34b-d9da40f8d1b2/dqc_reference/reference_markers.fasta -out OceanDNA-b11613/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:31,942] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:31,943] [INFO] Selected 33 target genomes.
[2023-03-16 21:45:31,943] [INFO] Target genome list was writen to OceanDNA-b11613/target_genomes.txt
[2023-03-16 21:45:31,965] [INFO] Task started: fastANI
[2023-03-16 21:45:31,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg38b253d3-d416-47a6-ac41-99fb295688c9/OceanDNA-b11613.fa --refList OceanDNA-b11613/target_genomes.txt --output OceanDNA-b11613/fastani_result.tsv --threads 1
[2023-03-16 21:45:54,158] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:54,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fc8f227-8bbe-42ac-b34b-d9da40f8d1b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:54,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fc8f227-8bbe-42ac-b34b-d9da40f8d1b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:54,159] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:54,159] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 21:45:54,159] [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 21:45:54,159] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11613/tc_result.tsv
[2023-03-16 21:45:54,160] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:54,160] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:54,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fc8f227-8bbe-42ac-b34b-d9da40f8d1b2/dqc_reference/checkm_data
[2023-03-16 21:45:54,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:54,167] [INFO] Task started: CheckM
[2023-03-16 21:45:54,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11613/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11613/checkm_input OceanDNA-b11613/checkm_result
[2023-03-16 21:46:36,187] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:36,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.35%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:36,191] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:36,191] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:36,191] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11613/markers.fasta)
[2023-03-16 21:46:36,191] [INFO] Task started: Blastn
[2023-03-16 21:46:36,191] [INFO] Running command: blastn -query OceanDNA-b11613/markers.fasta -db /var/lib/cwl/stg7fc8f227-8bbe-42ac-b34b-d9da40f8d1b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11613/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:37,001] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:37,002] [INFO] Selected 33 target genomes.
[2023-03-16 21:46:37,002] [INFO] Target genome list was writen to OceanDNA-b11613/target_genomes_gtdb.txt
[2023-03-16 21:46:37,101] [INFO] Task started: fastANI
[2023-03-16 21:46:37,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg38b253d3-d416-47a6-ac41-99fb295688c9/OceanDNA-b11613.fa --refList OceanDNA-b11613/target_genomes_gtdb.txt --output OceanDNA-b11613/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:53,795] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:53,797] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:46:53,798] [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_016124575.1	s__RI-182 sp016124575	87.1782	316	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__RI-182	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:53,798] [INFO] GTDB search result was written to OceanDNA-b11613/result_gtdb.tsv
[2023-03-16 21:46:53,798] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:53,798] [INFO] DFAST_QC result json was written to OceanDNA-b11613/dqc_result.json
[2023-03-16 21:46:53,798] [INFO] DFAST_QC completed!
[2023-03-16 21:46:53,798] [INFO] Total running time: 0h1m39s