[2023-03-16 10:25:31,275] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:25:31,275] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:25:31,275] [INFO] DQC Reference Directory: /var/lib/cwl/stga961d62a-d3ce-4bd1-952a-ef10c7444d51/dqc_reference
[2023-03-16 10:25:32,442] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:25:32,443] [INFO] Task started: Prodigal
[2023-03-16 10:25:32,443] [INFO] Running command: cat /var/lib/cwl/stg0c95ae94-d708-4f07-8c58-a3283e597f5b/OceanDNA-b28260.fa | prodigal -d OceanDNA-b28260/cds.fna -a OceanDNA-b28260/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:25:38,522] [INFO] Task succeeded: Prodigal
[2023-03-16 10:25:38,522] [INFO] Task started: HMMsearch
[2023-03-16 10:25:38,522] [INFO] Running command: hmmsearch --tblout OceanDNA-b28260/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga961d62a-d3ce-4bd1-952a-ef10c7444d51/dqc_reference/reference_markers.hmm OceanDNA-b28260/protein.faa > /dev/null
[2023-03-16 10:25:38,677] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:25:38,678] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0c95ae94-d708-4f07-8c58-a3283e597f5b/OceanDNA-b28260.fa]
[2023-03-16 10:25:38,692] [INFO] Query marker FASTA was written to OceanDNA-b28260/markers.fasta
[2023-03-16 10:25:38,692] [INFO] Task started: Blastn
[2023-03-16 10:25:38,692] [INFO] Running command: blastn -query OceanDNA-b28260/markers.fasta -db /var/lib/cwl/stga961d62a-d3ce-4bd1-952a-ef10c7444d51/dqc_reference/reference_markers.fasta -out OceanDNA-b28260/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:25:39,195] [INFO] Task succeeded: Blastn
[2023-03-16 10:25:39,196] [INFO] Selected 14 target genomes.
[2023-03-16 10:25:39,196] [INFO] Target genome list was writen to OceanDNA-b28260/target_genomes.txt
[2023-03-16 10:25:39,224] [INFO] Task started: fastANI
[2023-03-16 10:25:39,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c95ae94-d708-4f07-8c58-a3283e597f5b/OceanDNA-b28260.fa --refList OceanDNA-b28260/target_genomes.txt --output OceanDNA-b28260/fastani_result.tsv --threads 1
[2023-03-16 10:25:44,642] [INFO] Task succeeded: fastANI
[2023-03-16 10:25:44,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga961d62a-d3ce-4bd1-952a-ef10c7444d51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:25:44,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga961d62a-d3ce-4bd1-952a-ef10c7444d51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:25:44,643] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:25:44,643] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:25:44,643] [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 10:25:44,644] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28260/tc_result.tsv
[2023-03-16 10:25:44,644] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:25:44,644] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:25:44,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga961d62a-d3ce-4bd1-952a-ef10c7444d51/dqc_reference/checkm_data
[2023-03-16 10:25:44,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:25:44,669] [INFO] Task started: CheckM
[2023-03-16 10:25:44,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28260/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28260/checkm_input OceanDNA-b28260/checkm_result
[2023-03-16 10:26:12,342] [INFO] Task succeeded: CheckM
[2023-03-16 10:26:12,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:26:12,345] [INFO] ===== Completeness check finished =====
[2023-03-16 10:26:12,345] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:26:12,345] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28260/markers.fasta)
[2023-03-16 10:26:12,367] [INFO] Task started: Blastn
[2023-03-16 10:26:12,367] [INFO] Running command: blastn -query OceanDNA-b28260/markers.fasta -db /var/lib/cwl/stga961d62a-d3ce-4bd1-952a-ef10c7444d51/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28260/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:26:13,257] [INFO] Task succeeded: Blastn
[2023-03-16 10:26:13,258] [INFO] Selected 23 target genomes.
[2023-03-16 10:26:13,258] [INFO] Target genome list was writen to OceanDNA-b28260/target_genomes_gtdb.txt
[2023-03-16 10:26:13,319] [INFO] Task started: fastANI
[2023-03-16 10:26:13,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c95ae94-d708-4f07-8c58-a3283e597f5b/OceanDNA-b28260.fa --refList OceanDNA-b28260/target_genomes_gtdb.txt --output OceanDNA-b28260/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:26:20,558] [INFO] Task succeeded: fastANI
[2023-03-16 10:26:20,561] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:26:20,561] [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_902586855.1	s__CACIIZ01 sp902586855	77.7476	62	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699695.2	s__CACIIZ01 sp002699695	77.6684	113	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599445.1	s__CACIIZ01 sp902599445	77.4725	90	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:26:20,561] [INFO] GTDB search result was written to OceanDNA-b28260/result_gtdb.tsv
[2023-03-16 10:26:20,561] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:26:20,562] [INFO] DFAST_QC result json was written to OceanDNA-b28260/dqc_result.json
[2023-03-16 10:26:20,562] [INFO] DFAST_QC completed!
[2023-03-16 10:26:20,562] [INFO] Total running time: 0h0m49s