[2023-03-15 09:48:16,563] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,563] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg84b97a95-0711-466f-977f-fdd6d26d24b6/dqc_reference
[2023-03-15 09:48:18,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,228] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,228] [INFO] Running command: cat /var/lib/cwl/stg5aca072d-44e8-4816-b09d-989e6d23a3d6/OceanDNA-b11544.fa | prodigal -d OceanDNA-b11544/cds.fna -a OceanDNA-b11544/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:37,991] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:37,992] [INFO] Task started: HMMsearch
[2023-03-15 09:48:37,992] [INFO] Running command: hmmsearch --tblout OceanDNA-b11544/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84b97a95-0711-466f-977f-fdd6d26d24b6/dqc_reference/reference_markers.hmm OceanDNA-b11544/protein.faa > /dev/null
[2023-03-15 09:48:38,186] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:38,187] [INFO] Found 6/6 markers.
[2023-03-15 09:48:38,205] [INFO] Query marker FASTA was written to OceanDNA-b11544/markers.fasta
[2023-03-15 09:48:38,206] [INFO] Task started: Blastn
[2023-03-15 09:48:38,206] [INFO] Running command: blastn -query OceanDNA-b11544/markers.fasta -db /var/lib/cwl/stg84b97a95-0711-466f-977f-fdd6d26d24b6/dqc_reference/reference_markers.fasta -out OceanDNA-b11544/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:38,742] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:38,743] [INFO] Selected 25 target genomes.
[2023-03-15 09:48:38,743] [INFO] Target genome list was writen to OceanDNA-b11544/target_genomes.txt
[2023-03-15 09:48:38,756] [INFO] Task started: fastANI
[2023-03-15 09:48:38,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aca072d-44e8-4816-b09d-989e6d23a3d6/OceanDNA-b11544.fa --refList OceanDNA-b11544/target_genomes.txt --output OceanDNA-b11544/fastani_result.tsv --threads 1
[2023-03-15 09:48:53,944] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:53,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84b97a95-0711-466f-977f-fdd6d26d24b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:53,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84b97a95-0711-466f-977f-fdd6d26d24b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:53,948] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:53,948] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:48:53,948] [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
Luteibaculum oceani	strain=JCM 18817	GCA_007995015.1	1294296	1294296	type	True	77.4409	173	986	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:48:53,948] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11544/tc_result.tsv
[2023-03-15 09:48:53,948] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:53,948] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:53,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84b97a95-0711-466f-977f-fdd6d26d24b6/dqc_reference/checkm_data
[2023-03-15 09:48:53,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:53,967] [INFO] Task started: CheckM
[2023-03-15 09:48:53,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11544/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11544/checkm_input OceanDNA-b11544/checkm_result
[2023-03-15 09:49:43,900] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:43,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:43,903] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:43,903] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:43,903] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11544/markers.fasta)
[2023-03-15 09:49:43,904] [INFO] Task started: Blastn
[2023-03-15 09:49:43,904] [INFO] Running command: blastn -query OceanDNA-b11544/markers.fasta -db /var/lib/cwl/stg84b97a95-0711-466f-977f-fdd6d26d24b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11544/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:44,642] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:44,643] [INFO] Selected 28 target genomes.
[2023-03-15 09:49:44,643] [INFO] Target genome list was writen to OceanDNA-b11544/target_genomes_gtdb.txt
[2023-03-15 09:49:45,099] [INFO] Task started: fastANI
[2023-03-15 09:49:45,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aca072d-44e8-4816-b09d-989e6d23a3d6/OceanDNA-b11544.fa --refList OceanDNA-b11544/target_genomes_gtdb.txt --output OceanDNA-b11544/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:50:00,171] [INFO] Task succeeded: fastANI
[2023-03-15 09:50:00,173] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:50:00,173] [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_007995015.1	s__Luteibaculum oceani	77.4281	173	986	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Luteibaculaceae;g__Luteibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:50:00,173] [INFO] GTDB search result was written to OceanDNA-b11544/result_gtdb.tsv
[2023-03-15 09:50:00,173] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:50:00,173] [INFO] DFAST_QC result json was written to OceanDNA-b11544/dqc_result.json
[2023-03-15 09:50:00,174] [INFO] DFAST_QC completed!
[2023-03-15 09:50:00,174] [INFO] Total running time: 0h1m44s