[2023-03-15 17:39:53,959] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:39:53,960] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:39:53,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg2945d859-48b2-4c66-9d30-079f8ca8d526/dqc_reference
[2023-03-15 17:39:55,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:39:55,113] [INFO] Task started: Prodigal
[2023-03-15 17:39:55,113] [INFO] Running command: cat /var/lib/cwl/stgdd873f80-d852-4755-ace6-f0581a43cf57/OceanDNA-b17032.fa | prodigal -d OceanDNA-b17032/cds.fna -a OceanDNA-b17032/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:40:08,213] [INFO] Task succeeded: Prodigal
[2023-03-15 17:40:08,214] [INFO] Task started: HMMsearch
[2023-03-15 17:40:08,214] [INFO] Running command: hmmsearch --tblout OceanDNA-b17032/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2945d859-48b2-4c66-9d30-079f8ca8d526/dqc_reference/reference_markers.hmm OceanDNA-b17032/protein.faa > /dev/null
[2023-03-15 17:40:08,399] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:40:08,399] [INFO] Found 6/6 markers.
[2023-03-15 17:40:08,418] [INFO] Query marker FASTA was written to OceanDNA-b17032/markers.fasta
[2023-03-15 17:40:08,418] [INFO] Task started: Blastn
[2023-03-15 17:40:08,418] [INFO] Running command: blastn -query OceanDNA-b17032/markers.fasta -db /var/lib/cwl/stg2945d859-48b2-4c66-9d30-079f8ca8d526/dqc_reference/reference_markers.fasta -out OceanDNA-b17032/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:40:08,932] [INFO] Task succeeded: Blastn
[2023-03-15 17:40:08,933] [INFO] Selected 25 target genomes.
[2023-03-15 17:40:08,933] [INFO] Target genome list was writen to OceanDNA-b17032/target_genomes.txt
[2023-03-15 17:40:08,970] [INFO] Task started: fastANI
[2023-03-15 17:40:08,970] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd873f80-d852-4755-ace6-f0581a43cf57/OceanDNA-b17032.fa --refList OceanDNA-b17032/target_genomes.txt --output OceanDNA-b17032/fastani_result.tsv --threads 1
[2023-03-15 17:40:23,894] [INFO] Task succeeded: fastANI
[2023-03-15 17:40:23,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2945d859-48b2-4c66-9d30-079f8ca8d526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:40:23,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2945d859-48b2-4c66-9d30-079f8ca8d526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:40:23,895] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:40:23,895] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:40:23,895] [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
--------------------------------------------------------------------------------
[2023-03-15 17:40:23,895] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17032/tc_result.tsv
[2023-03-15 17:40:23,895] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:40:23,896] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:40:23,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2945d859-48b2-4c66-9d30-079f8ca8d526/dqc_reference/checkm_data
[2023-03-15 17:40:23,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:40:23,908] [INFO] Task started: CheckM
[2023-03-15 17:40:23,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17032/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17032/checkm_input OceanDNA-b17032/checkm_result
[2023-03-15 17:40:59,720] [INFO] Task succeeded: CheckM
[2023-03-15 17:40:59,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.46%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:40:59,722] [INFO] ===== Completeness check finished =====
[2023-03-15 17:40:59,722] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:40:59,723] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17032/markers.fasta)
[2023-03-15 17:40:59,724] [INFO] Task started: Blastn
[2023-03-15 17:40:59,724] [INFO] Running command: blastn -query OceanDNA-b17032/markers.fasta -db /var/lib/cwl/stg2945d859-48b2-4c66-9d30-079f8ca8d526/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17032/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:41:00,434] [INFO] Task succeeded: Blastn
[2023-03-15 17:41:00,435] [INFO] Selected 32 target genomes.
[2023-03-15 17:41:00,436] [INFO] Target genome list was writen to OceanDNA-b17032/target_genomes_gtdb.txt
[2023-03-15 17:41:00,783] [INFO] Task started: fastANI
[2023-03-15 17:41:00,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd873f80-d852-4755-ace6-f0581a43cf57/OceanDNA-b17032.fa --refList OceanDNA-b17032/target_genomes_gtdb.txt --output OceanDNA-b17032/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:41:17,764] [INFO] Task succeeded: fastANI
[2023-03-15 17:41:17,766] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:41:17,766] [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_902806425.1	s__Truepera sp902806425	75.7808	54	770	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__Truepera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:41:17,766] [INFO] GTDB search result was written to OceanDNA-b17032/result_gtdb.tsv
[2023-03-15 17:41:17,766] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:41:17,767] [INFO] DFAST_QC result json was written to OceanDNA-b17032/dqc_result.json
[2023-03-15 17:41:17,767] [INFO] DFAST_QC completed!
[2023-03-15 17:41:17,767] [INFO] Total running time: 0h1m24s