[2023-03-17 10:08:39,087] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:08:39,087] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:08:39,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg0084fa74-3cb7-43ae-b7d9-4c89687cf618/dqc_reference
[2023-03-17 10:08:40,197] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:08:40,198] [INFO] Task started: Prodigal
[2023-03-17 10:08:40,198] [INFO] Running command: cat /var/lib/cwl/stgce6eef11-8462-4ca9-9eb6-be0421e19b86/OceanDNA-b32865.fa | prodigal -d OceanDNA-b32865/cds.fna -a OceanDNA-b32865/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:08:47,652] [INFO] Task succeeded: Prodigal
[2023-03-17 10:08:47,652] [INFO] Task started: HMMsearch
[2023-03-17 10:08:47,652] [INFO] Running command: hmmsearch --tblout OceanDNA-b32865/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0084fa74-3cb7-43ae-b7d9-4c89687cf618/dqc_reference/reference_markers.hmm OceanDNA-b32865/protein.faa > /dev/null
[2023-03-17 10:08:47,832] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:08:47,832] [INFO] Found 6/6 markers.
[2023-03-17 10:08:47,846] [INFO] Query marker FASTA was written to OceanDNA-b32865/markers.fasta
[2023-03-17 10:08:47,846] [INFO] Task started: Blastn
[2023-03-17 10:08:47,846] [INFO] Running command: blastn -query OceanDNA-b32865/markers.fasta -db /var/lib/cwl/stg0084fa74-3cb7-43ae-b7d9-4c89687cf618/dqc_reference/reference_markers.fasta -out OceanDNA-b32865/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:08:48,400] [INFO] Task succeeded: Blastn
[2023-03-17 10:08:48,401] [INFO] Selected 20 target genomes.
[2023-03-17 10:08:48,401] [INFO] Target genome list was writen to OceanDNA-b32865/target_genomes.txt
[2023-03-17 10:08:48,445] [INFO] Task started: fastANI
[2023-03-17 10:08:48,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgce6eef11-8462-4ca9-9eb6-be0421e19b86/OceanDNA-b32865.fa --refList OceanDNA-b32865/target_genomes.txt --output OceanDNA-b32865/fastani_result.tsv --threads 1
[2023-03-17 10:08:58,247] [INFO] Task succeeded: fastANI
[2023-03-17 10:08:58,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0084fa74-3cb7-43ae-b7d9-4c89687cf618/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:08:58,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0084fa74-3cb7-43ae-b7d9-4c89687cf618/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:08:58,248] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:08:58,248] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:08:58,248] [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 10:08:58,248] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32865/tc_result.tsv
[2023-03-17 10:08:58,248] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:08:58,248] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:08:58,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0084fa74-3cb7-43ae-b7d9-4c89687cf618/dqc_reference/checkm_data
[2023-03-17 10:08:58,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:08:58,255] [INFO] Task started: CheckM
[2023-03-17 10:08:58,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32865/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32865/checkm_input OceanDNA-b32865/checkm_result
[2023-03-17 10:09:22,175] [INFO] Task succeeded: CheckM
[2023-03-17 10:09:22,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.88%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-17 10:09:22,195] [INFO] ===== Completeness check finished =====
[2023-03-17 10:09:22,195] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:09:22,195] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32865/markers.fasta)
[2023-03-17 10:09:22,196] [INFO] Task started: Blastn
[2023-03-17 10:09:22,196] [INFO] Running command: blastn -query OceanDNA-b32865/markers.fasta -db /var/lib/cwl/stg0084fa74-3cb7-43ae-b7d9-4c89687cf618/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32865/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:09:23,122] [INFO] Task succeeded: Blastn
[2023-03-17 10:09:23,123] [INFO] Selected 35 target genomes.
[2023-03-17 10:09:23,123] [INFO] Target genome list was writen to OceanDNA-b32865/target_genomes_gtdb.txt
[2023-03-17 10:09:23,205] [INFO] Task started: fastANI
[2023-03-17 10:09:23,206] [INFO] Running command: fastANI --query /var/lib/cwl/stgce6eef11-8462-4ca9-9eb6-be0421e19b86/OceanDNA-b32865.fa --refList OceanDNA-b32865/target_genomes_gtdb.txt --output OceanDNA-b32865/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:09:36,826] [INFO] Task succeeded: fastANI
[2023-03-17 10:09:36,826] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:09:36,826] [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
--------------------------------------------------------------------------------
[2023-03-17 10:09:36,827] [INFO] GTDB search result was written to OceanDNA-b32865/result_gtdb.tsv
[2023-03-17 10:09:36,827] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:09:36,827] [INFO] DFAST_QC result json was written to OceanDNA-b32865/dqc_result.json
[2023-03-17 10:09:36,828] [INFO] DFAST_QC completed!
[2023-03-17 10:09:36,828] [INFO] Total running time: 0h0m58s