[2023-03-16 06:46:39,279] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:46:39,279] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:46:39,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg71b8f314-c9fc-4856-b0aa-8ea7f9fe7330/dqc_reference
[2023-03-16 06:46:40,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:46:40,379] [INFO] Task started: Prodigal
[2023-03-16 06:46:40,380] [INFO] Running command: cat /var/lib/cwl/stgb6daa5b6-aa89-451f-ad73-ac89d3a0ebed/OceanDNA-b34222.fa | prodigal -d OceanDNA-b34222/cds.fna -a OceanDNA-b34222/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:46:46,260] [INFO] Task succeeded: Prodigal
[2023-03-16 06:46:46,260] [INFO] Task started: HMMsearch
[2023-03-16 06:46:46,260] [INFO] Running command: hmmsearch --tblout OceanDNA-b34222/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71b8f314-c9fc-4856-b0aa-8ea7f9fe7330/dqc_reference/reference_markers.hmm OceanDNA-b34222/protein.faa > /dev/null
[2023-03-16 06:46:46,401] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:46:46,401] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb6daa5b6-aa89-451f-ad73-ac89d3a0ebed/OceanDNA-b34222.fa]
[2023-03-16 06:46:46,413] [INFO] Query marker FASTA was written to OceanDNA-b34222/markers.fasta
[2023-03-16 06:46:46,413] [INFO] Task started: Blastn
[2023-03-16 06:46:46,413] [INFO] Running command: blastn -query OceanDNA-b34222/markers.fasta -db /var/lib/cwl/stg71b8f314-c9fc-4856-b0aa-8ea7f9fe7330/dqc_reference/reference_markers.fasta -out OceanDNA-b34222/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:46:46,886] [INFO] Task succeeded: Blastn
[2023-03-16 06:46:46,887] [INFO] Selected 26 target genomes.
[2023-03-16 06:46:46,887] [INFO] Target genome list was writen to OceanDNA-b34222/target_genomes.txt
[2023-03-16 06:46:47,105] [INFO] Task started: fastANI
[2023-03-16 06:46:47,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6daa5b6-aa89-451f-ad73-ac89d3a0ebed/OceanDNA-b34222.fa --refList OceanDNA-b34222/target_genomes.txt --output OceanDNA-b34222/fastani_result.tsv --threads 1
[2023-03-16 06:47:01,729] [INFO] Task succeeded: fastANI
[2023-03-16 06:47:01,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71b8f314-c9fc-4856-b0aa-8ea7f9fe7330/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:47:01,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71b8f314-c9fc-4856-b0aa-8ea7f9fe7330/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:47:01,730] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:47:01,730] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:47:01,730] [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 06:47:01,730] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34222/tc_result.tsv
[2023-03-16 06:47:01,730] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:47:01,730] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:47:01,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71b8f314-c9fc-4856-b0aa-8ea7f9fe7330/dqc_reference/checkm_data
[2023-03-16 06:47:01,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:47:01,766] [INFO] Task started: CheckM
[2023-03-16 06:47:01,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34222/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34222/checkm_input OceanDNA-b34222/checkm_result
[2023-03-16 06:47:22,370] [INFO] Task succeeded: CheckM
[2023-03-16 06:47:22,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:47:22,373] [INFO] ===== Completeness check finished =====
[2023-03-16 06:47:22,373] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:47:22,373] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34222/markers.fasta)
[2023-03-16 06:47:22,374] [INFO] Task started: Blastn
[2023-03-16 06:47:22,374] [INFO] Running command: blastn -query OceanDNA-b34222/markers.fasta -db /var/lib/cwl/stg71b8f314-c9fc-4856-b0aa-8ea7f9fe7330/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34222/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:47:22,883] [INFO] Task succeeded: Blastn
[2023-03-16 06:47:22,884] [INFO] Selected 26 target genomes.
[2023-03-16 06:47:22,884] [INFO] Target genome list was writen to OceanDNA-b34222/target_genomes_gtdb.txt
[2023-03-16 06:47:22,974] [INFO] Task started: fastANI
[2023-03-16 06:47:22,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6daa5b6-aa89-451f-ad73-ac89d3a0ebed/OceanDNA-b34222.fa --refList OceanDNA-b34222/target_genomes_gtdb.txt --output OceanDNA-b34222/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:47:38,213] [INFO] Task succeeded: fastANI
[2023-03-16 06:47:38,214] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:47:38,214] [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
--------------------------------------------------------------------------------
[2023-03-16 06:47:38,214] [INFO] GTDB search result was written to OceanDNA-b34222/result_gtdb.tsv
[2023-03-16 06:47:38,214] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:47:38,214] [INFO] DFAST_QC result json was written to OceanDNA-b34222/dqc_result.json
[2023-03-16 06:47:38,215] [INFO] DFAST_QC completed!
[2023-03-16 06:47:38,215] [INFO] Total running time: 0h0m59s