[2023-03-18 20:40:39,443] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,455] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg08a36f33-ac9e-49d5-a8b3-f32a65635c7b/dqc_reference
[2023-03-18 20:40:41,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,209] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,209] [INFO] Running command: cat /var/lib/cwl/stgc24ffa03-f345-4161-82ad-c13e305d3e9b/OceanDNA-b33968.fa | prodigal -d OceanDNA-b33968/cds.fna -a OceanDNA-b33968/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:44,350] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:44,350] [INFO] Task started: HMMsearch
[2023-03-18 20:40:44,350] [INFO] Running command: hmmsearch --tblout OceanDNA-b33968/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08a36f33-ac9e-49d5-a8b3-f32a65635c7b/dqc_reference/reference_markers.hmm OceanDNA-b33968/protein.faa > /dev/null
[2023-03-18 20:40:44,623] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:44,623] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc24ffa03-f345-4161-82ad-c13e305d3e9b/OceanDNA-b33968.fa]
[2023-03-18 20:40:44,631] [INFO] Query marker FASTA was written to OceanDNA-b33968/markers.fasta
[2023-03-18 20:40:44,632] [INFO] Task started: Blastn
[2023-03-18 20:40:44,632] [INFO] Running command: blastn -query OceanDNA-b33968/markers.fasta -db /var/lib/cwl/stg08a36f33-ac9e-49d5-a8b3-f32a65635c7b/dqc_reference/reference_markers.fasta -out OceanDNA-b33968/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:47,500] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:47,501] [INFO] Selected 11 target genomes.
[2023-03-18 20:40:47,501] [INFO] Target genome list was writen to OceanDNA-b33968/target_genomes.txt
[2023-03-18 20:40:47,508] [INFO] Task started: fastANI
[2023-03-18 20:40:47,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgc24ffa03-f345-4161-82ad-c13e305d3e9b/OceanDNA-b33968.fa --refList OceanDNA-b33968/target_genomes.txt --output OceanDNA-b33968/fastani_result.tsv --threads 1
[2023-03-18 20:40:52,069] [INFO] Task succeeded: fastANI
[2023-03-18 20:40:52,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08a36f33-ac9e-49d5-a8b3-f32a65635c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:40:52,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08a36f33-ac9e-49d5-a8b3-f32a65635c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:40:52,070] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:40:52,070] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:40:52,070] [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 20:40:52,070] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33968/tc_result.tsv
[2023-03-18 20:40:52,070] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:40:52,070] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:40:52,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08a36f33-ac9e-49d5-a8b3-f32a65635c7b/dqc_reference/checkm_data
[2023-03-18 20:40:52,073] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:40:52,077] [INFO] Task started: CheckM
[2023-03-18 20:40:52,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33968/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33968/checkm_input OceanDNA-b33968/checkm_result
[2023-03-18 20:41:13,010] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:13,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.40%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:13,012] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:13,012] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:13,012] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33968/markers.fasta)
[2023-03-18 20:41:13,014] [INFO] Task started: Blastn
[2023-03-18 20:41:13,014] [INFO] Running command: blastn -query OceanDNA-b33968/markers.fasta -db /var/lib/cwl/stg08a36f33-ac9e-49d5-a8b3-f32a65635c7b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33968/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:14,138] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:14,139] [INFO] Selected 19 target genomes.
[2023-03-18 20:41:14,139] [INFO] Target genome list was writen to OceanDNA-b33968/target_genomes_gtdb.txt
[2023-03-18 20:41:14,276] [INFO] Task started: fastANI
[2023-03-18 20:41:14,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgc24ffa03-f345-4161-82ad-c13e305d3e9b/OceanDNA-b33968.fa --refList OceanDNA-b33968/target_genomes_gtdb.txt --output OceanDNA-b33968/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:41:17,974] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:17,976] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:41:17,976] [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_905618945.1	s__BACL14 sp905618945	80.7369	118	201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:41:17,976] [INFO] GTDB search result was written to OceanDNA-b33968/result_gtdb.tsv
[2023-03-18 20:41:17,976] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:41:17,977] [INFO] DFAST_QC result json was written to OceanDNA-b33968/dqc_result.json
[2023-03-18 20:41:17,977] [INFO] DFAST_QC completed!
[2023-03-18 20:41:17,977] [INFO] Total running time: 0h0m39s