[2023-03-16 10:35:17,584] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:35:17,584] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:35:17,584] [INFO] DQC Reference Directory: /var/lib/cwl/stge1cf5c28-b344-42af-9158-fb6418c2b668/dqc_reference
[2023-03-16 10:35:18,774] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:35:18,774] [INFO] Task started: Prodigal
[2023-03-16 10:35:18,774] [INFO] Running command: cat /var/lib/cwl/stgd2169ed3-1cc0-40ab-9009-e87c125f251e/OceanDNA-b38543.fa | prodigal -d OceanDNA-b38543/cds.fna -a OceanDNA-b38543/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:35:32,890] [INFO] Task succeeded: Prodigal
[2023-03-16 10:35:32,890] [INFO] Task started: HMMsearch
[2023-03-16 10:35:32,890] [INFO] Running command: hmmsearch --tblout OceanDNA-b38543/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1cf5c28-b344-42af-9158-fb6418c2b668/dqc_reference/reference_markers.hmm OceanDNA-b38543/protein.faa > /dev/null
[2023-03-16 10:35:33,346] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:35:33,346] [INFO] Found 6/6 markers.
[2023-03-16 10:35:33,364] [INFO] Query marker FASTA was written to OceanDNA-b38543/markers.fasta
[2023-03-16 10:35:33,368] [INFO] Task started: Blastn
[2023-03-16 10:35:33,368] [INFO] Running command: blastn -query OceanDNA-b38543/markers.fasta -db /var/lib/cwl/stge1cf5c28-b344-42af-9158-fb6418c2b668/dqc_reference/reference_markers.fasta -out OceanDNA-b38543/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:35:34,093] [INFO] Task succeeded: Blastn
[2023-03-16 10:35:34,094] [INFO] Selected 30 target genomes.
[2023-03-16 10:35:34,094] [INFO] Target genome list was writen to OceanDNA-b38543/target_genomes.txt
[2023-03-16 10:35:34,116] [INFO] Task started: fastANI
[2023-03-16 10:35:34,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2169ed3-1cc0-40ab-9009-e87c125f251e/OceanDNA-b38543.fa --refList OceanDNA-b38543/target_genomes.txt --output OceanDNA-b38543/fastani_result.tsv --threads 1
[2023-03-16 10:35:57,232] [INFO] Task succeeded: fastANI
[2023-03-16 10:35:57,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1cf5c28-b344-42af-9158-fb6418c2b668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:35:57,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1cf5c28-b344-42af-9158-fb6418c2b668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:35:57,236] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:35:57,236] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:35:57,236] [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	81.5616	458	728	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:35:57,236] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38543/tc_result.tsv
[2023-03-16 10:35:57,236] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:35:57,236] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:35:57,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1cf5c28-b344-42af-9158-fb6418c2b668/dqc_reference/checkm_data
[2023-03-16 10:35:57,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:35:57,246] [INFO] Task started: CheckM
[2023-03-16 10:35:57,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38543/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38543/checkm_input OceanDNA-b38543/checkm_result
[2023-03-16 10:36:37,765] [INFO] Task succeeded: CheckM
[2023-03-16 10:36:37,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:36:37,768] [INFO] ===== Completeness check finished =====
[2023-03-16 10:36:37,768] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:36:37,768] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38543/markers.fasta)
[2023-03-16 10:36:37,770] [INFO] Task started: Blastn
[2023-03-16 10:36:37,770] [INFO] Running command: blastn -query OceanDNA-b38543/markers.fasta -db /var/lib/cwl/stge1cf5c28-b344-42af-9158-fb6418c2b668/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38543/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:36:39,180] [INFO] Task succeeded: Blastn
[2023-03-16 10:36:39,181] [INFO] Selected 24 target genomes.
[2023-03-16 10:36:39,181] [INFO] Target genome list was writen to OceanDNA-b38543/target_genomes_gtdb.txt
[2023-03-16 10:36:39,217] [INFO] Task started: fastANI
[2023-03-16 10:36:39,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2169ed3-1cc0-40ab-9009-e87c125f251e/OceanDNA-b38543.fa --refList OceanDNA-b38543/target_genomes_gtdb.txt --output OceanDNA-b38543/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:36:52,830] [INFO] Task succeeded: fastANI
[2023-03-16 10:36:52,834] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:36:52,834] [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_018066805.1	s__Paraperlucidibaca sp018066805	98.9364	611	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Paraperlucidibaca	95.0	99.79	99.73	0.97	0.96	3	conclusive
GCF_003387535.1	s__Paraperlucidibaca baekdonensis	81.5616	458	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Paraperlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676655.1	s__Perlucidibaca aquatica	77.3129	153	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342025.1	s__Perlucidibaca sp002342025	77.0013	119	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943415.1	s__Perlucidibaca sp002943415	76.6948	94	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:36:52,834] [INFO] GTDB search result was written to OceanDNA-b38543/result_gtdb.tsv
[2023-03-16 10:36:52,834] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:36:52,835] [INFO] DFAST_QC result json was written to OceanDNA-b38543/dqc_result.json
[2023-03-16 10:36:52,835] [INFO] DFAST_QC completed!
[2023-03-16 10:36:52,835] [INFO] Total running time: 0h1m35s