[2023-03-17 01:23:45,130] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,130] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,130] [INFO] DQC Reference Directory: /var/lib/cwl/stga8917bf5-34d3-421b-95ec-0224f5e88520/dqc_reference
[2023-03-17 01:23:46,318] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,319] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,319] [INFO] Running command: cat /var/lib/cwl/stgc5ff26c2-6b64-4abc-891c-54faf86438f6/OceanDNA-b237.fa | prodigal -d OceanDNA-b237/cds.fna -a OceanDNA-b237/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:23:55,594] [INFO] Task succeeded: Prodigal
[2023-03-17 01:23:55,594] [INFO] Task started: HMMsearch
[2023-03-17 01:23:55,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b237/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8917bf5-34d3-421b-95ec-0224f5e88520/dqc_reference/reference_markers.hmm OceanDNA-b237/protein.faa > /dev/null
[2023-03-17 01:23:55,773] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:23:55,774] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc5ff26c2-6b64-4abc-891c-54faf86438f6/OceanDNA-b237.fa]
[2023-03-17 01:23:55,788] [INFO] Query marker FASTA was written to OceanDNA-b237/markers.fasta
[2023-03-17 01:23:55,788] [INFO] Task started: Blastn
[2023-03-17 01:23:55,788] [INFO] Running command: blastn -query OceanDNA-b237/markers.fasta -db /var/lib/cwl/stga8917bf5-34d3-421b-95ec-0224f5e88520/dqc_reference/reference_markers.fasta -out OceanDNA-b237/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:23:56,318] [INFO] Task succeeded: Blastn
[2023-03-17 01:23:56,319] [INFO] Selected 13 target genomes.
[2023-03-17 01:23:56,319] [INFO] Target genome list was writen to OceanDNA-b237/target_genomes.txt
[2023-03-17 01:23:56,327] [INFO] Task started: fastANI
[2023-03-17 01:23:56,327] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ff26c2-6b64-4abc-891c-54faf86438f6/OceanDNA-b237.fa --refList OceanDNA-b237/target_genomes.txt --output OceanDNA-b237/fastani_result.tsv --threads 1
[2023-03-17 01:24:02,977] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:02,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8917bf5-34d3-421b-95ec-0224f5e88520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:24:02,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8917bf5-34d3-421b-95ec-0224f5e88520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:24:02,978] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:24:02,978] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 01:24:02,978] [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
--------------------------------------------------------------------------------
[2023-03-17 01:24:02,979] [INFO] DFAST Taxonomy check result was written to OceanDNA-b237/tc_result.tsv
[2023-03-17 01:24:02,979] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:24:02,979] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:24:02,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8917bf5-34d3-421b-95ec-0224f5e88520/dqc_reference/checkm_data
[2023-03-17 01:24:02,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:24:02,985] [INFO] Task started: CheckM
[2023-03-17 01:24:02,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b237/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b237/checkm_input OceanDNA-b237/checkm_result
[2023-03-17 01:24:30,957] [INFO] Task succeeded: CheckM
[2023-03-17 01:24:30,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:24:30,960] [INFO] ===== Completeness check finished =====
[2023-03-17 01:24:30,960] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:24:30,960] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b237/markers.fasta)
[2023-03-17 01:24:30,960] [INFO] Task started: Blastn
[2023-03-17 01:24:30,960] [INFO] Running command: blastn -query OceanDNA-b237/markers.fasta -db /var/lib/cwl/stga8917bf5-34d3-421b-95ec-0224f5e88520/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b237/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:31,797] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:31,798] [INFO] Selected 21 target genomes.
[2023-03-17 01:24:31,798] [INFO] Target genome list was writen to OceanDNA-b237/target_genomes_gtdb.txt
[2023-03-17 01:24:32,453] [INFO] Task started: fastANI
[2023-03-17 01:24:32,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ff26c2-6b64-4abc-891c-54faf86438f6/OceanDNA-b237.fa --refList OceanDNA-b237/target_genomes_gtdb.txt --output OceanDNA-b237/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:24:44,986] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:44,988] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:24:44,988] [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_012963185.1	s__DTWD01 sp012963185	91.8052	318	506	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__DTWD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:24:44,989] [INFO] GTDB search result was written to OceanDNA-b237/result_gtdb.tsv
[2023-03-17 01:24:44,989] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:24:44,989] [INFO] DFAST_QC result json was written to OceanDNA-b237/dqc_result.json
[2023-03-17 01:24:44,989] [INFO] DFAST_QC completed!
[2023-03-17 01:24:44,989] [INFO] Total running time: 0h0m60s