[2023-03-15 23:42:29,662] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,662] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fc5f743-7c33-4f9f-aaa8-7180d820d086/dqc_reference
[2023-03-15 23:42:31,285] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,285] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,285] [INFO] Running command: cat /var/lib/cwl/stg974e4786-0228-45bd-ac18-56495fa23aa3/OceanDNA-b32504.fa | prodigal -d OceanDNA-b32504/cds.fna -a OceanDNA-b32504/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:33,353] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:33,354] [INFO] Task started: HMMsearch
[2023-03-15 23:42:33,354] [INFO] Running command: hmmsearch --tblout OceanDNA-b32504/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fc5f743-7c33-4f9f-aaa8-7180d820d086/dqc_reference/reference_markers.hmm OceanDNA-b32504/protein.faa > /dev/null
[2023-03-15 23:42:33,521] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:33,522] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg974e4786-0228-45bd-ac18-56495fa23aa3/OceanDNA-b32504.fa]
[2023-03-15 23:42:33,529] [INFO] Query marker FASTA was written to OceanDNA-b32504/markers.fasta
[2023-03-15 23:42:33,531] [INFO] Task started: Blastn
[2023-03-15 23:42:33,531] [INFO] Running command: blastn -query OceanDNA-b32504/markers.fasta -db /var/lib/cwl/stg7fc5f743-7c33-4f9f-aaa8-7180d820d086/dqc_reference/reference_markers.fasta -out OceanDNA-b32504/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:36,518] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:36,519] [INFO] Selected 9 target genomes.
[2023-03-15 23:42:36,519] [INFO] Target genome list was writen to OceanDNA-b32504/target_genomes.txt
[2023-03-15 23:42:36,526] [INFO] Task started: fastANI
[2023-03-15 23:42:36,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg974e4786-0228-45bd-ac18-56495fa23aa3/OceanDNA-b32504.fa --refList OceanDNA-b32504/target_genomes.txt --output OceanDNA-b32504/fastani_result.tsv --threads 1
[2023-03-15 23:42:40,502] [INFO] Task succeeded: fastANI
[2023-03-15 23:42:40,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fc5f743-7c33-4f9f-aaa8-7180d820d086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:42:40,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fc5f743-7c33-4f9f-aaa8-7180d820d086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:42:40,503] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:42:40,503] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:42:40,503] [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 23:42:40,504] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32504/tc_result.tsv
[2023-03-15 23:42:40,504] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:42:40,504] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:42:40,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fc5f743-7c33-4f9f-aaa8-7180d820d086/dqc_reference/checkm_data
[2023-03-15 23:42:40,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:42:40,648] [INFO] Task started: CheckM
[2023-03-15 23:42:40,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32504/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32504/checkm_input OceanDNA-b32504/checkm_result
[2023-03-15 23:42:53,940] [INFO] Task succeeded: CheckM
[2023-03-15 23:42:53,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:42:53,942] [INFO] ===== Completeness check finished =====
[2023-03-15 23:42:53,942] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:42:53,942] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32504/markers.fasta)
[2023-03-15 23:42:53,944] [INFO] Task started: Blastn
[2023-03-15 23:42:53,944] [INFO] Running command: blastn -query OceanDNA-b32504/markers.fasta -db /var/lib/cwl/stg7fc5f743-7c33-4f9f-aaa8-7180d820d086/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32504/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:54,801] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:54,802] [INFO] Selected 15 target genomes.
[2023-03-15 23:42:54,802] [INFO] Target genome list was writen to OceanDNA-b32504/target_genomes_gtdb.txt
[2023-03-15 23:42:54,811] [INFO] Task started: fastANI
[2023-03-15 23:42:54,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg974e4786-0228-45bd-ac18-56495fa23aa3/OceanDNA-b32504.fa --refList OceanDNA-b32504/target_genomes_gtdb.txt --output OceanDNA-b32504/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:42:57,429] [INFO] Task succeeded: fastANI
[2023-03-15 23:42:57,430] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:42:57,431] [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_902563305.1	s__GCA-2691245 sp902563305	78.2927	62	109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:42:57,431] [INFO] GTDB search result was written to OceanDNA-b32504/result_gtdb.tsv
[2023-03-15 23:42:57,431] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:42:57,431] [INFO] DFAST_QC result json was written to OceanDNA-b32504/dqc_result.json
[2023-03-15 23:42:57,431] [INFO] DFAST_QC completed!
[2023-03-15 23:42:57,431] [INFO] Total running time: 0h0m28s