[2023-03-16 04:52:20,124] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:52:20,124] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:52:20,125] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bd5b86b-30c9-4661-8129-d39d295a441f/dqc_reference
[2023-03-16 04:52:21,246] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:52:21,247] [INFO] Task started: Prodigal
[2023-03-16 04:52:21,247] [INFO] Running command: cat /var/lib/cwl/stg83e3ffa9-50d9-4bad-a6aa-6df7fe4d87c0/OceanDNA-b38527.fa | prodigal -d OceanDNA-b38527/cds.fna -a OceanDNA-b38527/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:52:35,864] [INFO] Task succeeded: Prodigal
[2023-03-16 04:52:35,865] [INFO] Task started: HMMsearch
[2023-03-16 04:52:35,865] [INFO] Running command: hmmsearch --tblout OceanDNA-b38527/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bd5b86b-30c9-4661-8129-d39d295a441f/dqc_reference/reference_markers.hmm OceanDNA-b38527/protein.faa > /dev/null
[2023-03-16 04:52:36,044] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:52:36,045] [INFO] Found 6/6 markers.
[2023-03-16 04:52:36,060] [INFO] Query marker FASTA was written to OceanDNA-b38527/markers.fasta
[2023-03-16 04:52:36,060] [INFO] Task started: Blastn
[2023-03-16 04:52:36,061] [INFO] Running command: blastn -query OceanDNA-b38527/markers.fasta -db /var/lib/cwl/stg1bd5b86b-30c9-4661-8129-d39d295a441f/dqc_reference/reference_markers.fasta -out OceanDNA-b38527/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:52:36,667] [INFO] Task succeeded: Blastn
[2023-03-16 04:52:36,668] [INFO] Selected 35 target genomes.
[2023-03-16 04:52:36,668] [INFO] Target genome list was writen to OceanDNA-b38527/target_genomes.txt
[2023-03-16 04:52:36,685] [INFO] Task started: fastANI
[2023-03-16 04:52:36,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e3ffa9-50d9-4bad-a6aa-6df7fe4d87c0/OceanDNA-b38527.fa --refList OceanDNA-b38527/target_genomes.txt --output OceanDNA-b38527/fastani_result.tsv --threads 1
[2023-03-16 04:52:56,351] [INFO] Task succeeded: fastANI
[2023-03-16 04:52:56,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bd5b86b-30c9-4661-8129-d39d295a441f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:52:56,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bd5b86b-30c9-4661-8129-d39d295a441f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:52:56,354] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:52:56,354] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:52:56,354] [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
Paraperlucidibaca baekdonensis	strain=DSM 26022	GCA_003387535.1	748120	748120	type	True	77.353	140	810	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:52:56,355] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38527/tc_result.tsv
[2023-03-16 04:52:56,355] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:52:56,355] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:52:56,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bd5b86b-30c9-4661-8129-d39d295a441f/dqc_reference/checkm_data
[2023-03-16 04:52:56,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:52:56,359] [INFO] Task started: CheckM
[2023-03-16 04:52:56,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38527/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38527/checkm_input OceanDNA-b38527/checkm_result
[2023-03-16 04:53:35,655] [INFO] Task succeeded: CheckM
[2023-03-16 04:53:35,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:53:35,657] [INFO] ===== Completeness check finished =====
[2023-03-16 04:53:35,657] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:53:35,658] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38527/markers.fasta)
[2023-03-16 04:53:35,658] [INFO] Task started: Blastn
[2023-03-16 04:53:35,658] [INFO] Running command: blastn -query OceanDNA-b38527/markers.fasta -db /var/lib/cwl/stg1bd5b86b-30c9-4661-8129-d39d295a441f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38527/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:53:36,647] [INFO] Task succeeded: Blastn
[2023-03-16 04:53:36,648] [INFO] Selected 32 target genomes.
[2023-03-16 04:53:36,648] [INFO] Target genome list was writen to OceanDNA-b38527/target_genomes_gtdb.txt
[2023-03-16 04:53:36,670] [INFO] Task started: fastANI
[2023-03-16 04:53:36,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e3ffa9-50d9-4bad-a6aa-6df7fe4d87c0/OceanDNA-b38527.fa --refList OceanDNA-b38527/target_genomes_gtdb.txt --output OceanDNA-b38527/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:53:53,926] [INFO] Task succeeded: fastANI
[2023-03-16 04:53:53,929] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:53:53,929] [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
GCF_001676655.1	s__Perlucidibaca aquatica	77.5599	116	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387535.1	s__Paraperlucidibaca baekdonensis	77.353	140	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Paraperlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066805.1	s__Paraperlucidibaca sp018066805	77.2921	111	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Paraperlucidibaca	95.0	99.79	99.73	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-16 04:53:53,929] [INFO] GTDB search result was written to OceanDNA-b38527/result_gtdb.tsv
[2023-03-16 04:53:53,929] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:53:53,930] [INFO] DFAST_QC result json was written to OceanDNA-b38527/dqc_result.json
[2023-03-16 04:53:53,930] [INFO] DFAST_QC completed!
[2023-03-16 04:53:53,930] [INFO] Total running time: 0h1m34s