[2023-03-18 01:59:39,765] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,766] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg702c83c0-3de4-457f-9c21-52d88ac239a6/dqc_reference
[2023-03-18 01:59:40,996] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,997] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,997] [INFO] Running command: cat /var/lib/cwl/stgdd936f17-31dd-44ce-b1fc-181245a07a83/OceanDNA-b37368.fa | prodigal -d OceanDNA-b37368/cds.fna -a OceanDNA-b37368/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:59:50,052] [INFO] Task succeeded: Prodigal
[2023-03-18 01:59:50,052] [INFO] Task started: HMMsearch
[2023-03-18 01:59:50,052] [INFO] Running command: hmmsearch --tblout OceanDNA-b37368/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg702c83c0-3de4-457f-9c21-52d88ac239a6/dqc_reference/reference_markers.hmm OceanDNA-b37368/protein.faa > /dev/null
[2023-03-18 01:59:50,242] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:59:50,242] [INFO] Found 6/6 markers.
[2023-03-18 01:59:50,272] [INFO] Query marker FASTA was written to OceanDNA-b37368/markers.fasta
[2023-03-18 01:59:50,274] [INFO] Task started: Blastn
[2023-03-18 01:59:50,274] [INFO] Running command: blastn -query OceanDNA-b37368/markers.fasta -db /var/lib/cwl/stg702c83c0-3de4-457f-9c21-52d88ac239a6/dqc_reference/reference_markers.fasta -out OceanDNA-b37368/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:59:50,836] [INFO] Task succeeded: Blastn
[2023-03-18 01:59:50,838] [INFO] Selected 18 target genomes.
[2023-03-18 01:59:50,838] [INFO] Target genome list was writen to OceanDNA-b37368/target_genomes.txt
[2023-03-18 01:59:50,850] [INFO] Task started: fastANI
[2023-03-18 01:59:50,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd936f17-31dd-44ce-b1fc-181245a07a83/OceanDNA-b37368.fa --refList OceanDNA-b37368/target_genomes.txt --output OceanDNA-b37368/fastani_result.tsv --threads 1
[2023-03-18 02:00:00,243] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:00,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg702c83c0-3de4-457f-9c21-52d88ac239a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:00:00,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg702c83c0-3de4-457f-9c21-52d88ac239a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:00:00,244] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:00:00,244] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:00:00,244] [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 02:00:00,245] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37368/tc_result.tsv
[2023-03-18 02:00:00,246] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:00:00,246] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:00:00,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg702c83c0-3de4-457f-9c21-52d88ac239a6/dqc_reference/checkm_data
[2023-03-18 02:00:00,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:00:00,279] [INFO] Task started: CheckM
[2023-03-18 02:00:00,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37368/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37368/checkm_input OceanDNA-b37368/checkm_result
[2023-03-18 02:00:27,782] [INFO] Task succeeded: CheckM
[2023-03-18 02:00:27,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:00:27,815] [INFO] ===== Completeness check finished =====
[2023-03-18 02:00:27,815] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:00:27,816] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37368/markers.fasta)
[2023-03-18 02:00:27,817] [INFO] Task started: Blastn
[2023-03-18 02:00:27,817] [INFO] Running command: blastn -query OceanDNA-b37368/markers.fasta -db /var/lib/cwl/stg702c83c0-3de4-457f-9c21-52d88ac239a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37368/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:28,734] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:28,739] [INFO] Selected 19 target genomes.
[2023-03-18 02:00:28,739] [INFO] Target genome list was writen to OceanDNA-b37368/target_genomes_gtdb.txt
[2023-03-18 02:00:28,776] [INFO] Task started: fastANI
[2023-03-18 02:00:28,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd936f17-31dd-44ce-b1fc-181245a07a83/OceanDNA-b37368.fa --refList OceanDNA-b37368/target_genomes_gtdb.txt --output OceanDNA-b37368/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:00:38,835] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:38,837] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:00:38,838] [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_002708765.1	s__UBA9659 sp002708765	99.7669	514	553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 02:00:38,840] [INFO] GTDB search result was written to OceanDNA-b37368/result_gtdb.tsv
[2023-03-18 02:00:38,843] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:00:38,845] [INFO] DFAST_QC result json was written to OceanDNA-b37368/dqc_result.json
[2023-03-18 02:00:38,846] [INFO] DFAST_QC completed!
[2023-03-18 02:00:38,846] [INFO] Total running time: 0h0m59s