[2023-03-17 23:08:31,911] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,912] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b4ce28d-41f1-4484-9d3b-a80385313b8f/dqc_reference
[2023-03-17 23:08:33,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,080] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,080] [INFO] Running command: cat /var/lib/cwl/stg4d7201ab-9127-4640-91fa-225c7210e146/OceanDNA-b28152.fa | prodigal -d OceanDNA-b28152/cds.fna -a OceanDNA-b28152/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:43,268] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:43,268] [INFO] Task started: HMMsearch
[2023-03-17 23:08:43,268] [INFO] Running command: hmmsearch --tblout OceanDNA-b28152/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b4ce28d-41f1-4484-9d3b-a80385313b8f/dqc_reference/reference_markers.hmm OceanDNA-b28152/protein.faa > /dev/null
[2023-03-17 23:08:43,438] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:43,438] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4d7201ab-9127-4640-91fa-225c7210e146/OceanDNA-b28152.fa]
[2023-03-17 23:08:43,462] [INFO] Query marker FASTA was written to OceanDNA-b28152/markers.fasta
[2023-03-17 23:08:43,463] [INFO] Task started: Blastn
[2023-03-17 23:08:43,464] [INFO] Running command: blastn -query OceanDNA-b28152/markers.fasta -db /var/lib/cwl/stg7b4ce28d-41f1-4484-9d3b-a80385313b8f/dqc_reference/reference_markers.fasta -out OceanDNA-b28152/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:43,950] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:43,952] [INFO] Selected 23 target genomes.
[2023-03-17 23:08:43,952] [INFO] Target genome list was writen to OceanDNA-b28152/target_genomes.txt
[2023-03-17 23:08:43,965] [INFO] Task started: fastANI
[2023-03-17 23:08:43,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d7201ab-9127-4640-91fa-225c7210e146/OceanDNA-b28152.fa --refList OceanDNA-b28152/target_genomes.txt --output OceanDNA-b28152/fastani_result.tsv --threads 1
[2023-03-17 23:08:58,031] [INFO] Task succeeded: fastANI
[2023-03-17 23:08:58,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b4ce28d-41f1-4484-9d3b-a80385313b8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:08:58,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b4ce28d-41f1-4484-9d3b-a80385313b8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:08:58,036] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:08:58,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:08:58,037] [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
Cognatiyoonia sediminum	strain=DSM 28715	GCA_900129845.1	1508389	1508389	type	True	80.0948	261	497	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	76.6063	68	497	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	76.593	57	497	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	76.5273	53	497	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:08:58,038] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28152/tc_result.tsv
[2023-03-17 23:08:58,040] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:08:58,040] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:08:58,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b4ce28d-41f1-4484-9d3b-a80385313b8f/dqc_reference/checkm_data
[2023-03-17 23:08:58,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:08:58,130] [INFO] Task started: CheckM
[2023-03-17 23:08:58,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28152/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28152/checkm_input OceanDNA-b28152/checkm_result
[2023-03-17 23:09:29,148] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:29,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:09:29,161] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:29,161] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:29,162] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28152/markers.fasta)
[2023-03-17 23:09:29,163] [INFO] Task started: Blastn
[2023-03-17 23:09:29,163] [INFO] Running command: blastn -query OceanDNA-b28152/markers.fasta -db /var/lib/cwl/stg7b4ce28d-41f1-4484-9d3b-a80385313b8f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28152/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:29,735] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:29,741] [INFO] Selected 24 target genomes.
[2023-03-17 23:09:29,741] [INFO] Target genome list was writen to OceanDNA-b28152/target_genomes_gtdb.txt
[2023-03-17 23:09:29,754] [INFO] Task started: fastANI
[2023-03-17 23:09:29,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d7201ab-9127-4640-91fa-225c7210e146/OceanDNA-b28152.fa --refList OceanDNA-b28152/target_genomes_gtdb.txt --output OceanDNA-b28152/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:09:44,904] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:44,911] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:09:44,911] [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_900129845.1	s__Cognatiyoonia sediminum	80.0948	261	497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	76.6817	67	497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156505.1	s__Yoonia rosea	76.6063	68	497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_002797915.1	s__Yoonia maricola	76.593	57	497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	76.5758	57	497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	76.5273	53	497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169435.1	s__Yoonia sp000169435	76.4539	67	497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	76.3369	72	497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114675.1	s__Yoonia litorea	76.1747	65	497	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:09:44,913] [INFO] GTDB search result was written to OceanDNA-b28152/result_gtdb.tsv
[2023-03-17 23:09:44,913] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:09:44,916] [INFO] DFAST_QC result json was written to OceanDNA-b28152/dqc_result.json
[2023-03-17 23:09:44,916] [INFO] DFAST_QC completed!
[2023-03-17 23:09:44,916] [INFO] Total running time: 0h1m13s