[2023-03-16 19:34:13,603] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:34:13,603] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:34:13,603] [INFO] DQC Reference Directory: /var/lib/cwl/stgb515388b-9de6-479a-8478-c734c3b63608/dqc_reference
[2023-03-16 19:34:14,919] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:34:14,920] [INFO] Task started: Prodigal
[2023-03-16 19:34:14,920] [INFO] Running command: cat /var/lib/cwl/stg5c573ef2-fe6b-4584-b730-c6c40e073404/OceanDNA-b22848.fa | prodigal -d OceanDNA-b22848/cds.fna -a OceanDNA-b22848/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:34:56,665] [INFO] Task succeeded: Prodigal
[2023-03-16 19:34:56,665] [INFO] Task started: HMMsearch
[2023-03-16 19:34:56,665] [INFO] Running command: hmmsearch --tblout OceanDNA-b22848/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb515388b-9de6-479a-8478-c734c3b63608/dqc_reference/reference_markers.hmm OceanDNA-b22848/protein.faa > /dev/null
[2023-03-16 19:34:56,955] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:34:56,955] [INFO] Found 6/6 markers.
[2023-03-16 19:34:56,994] [INFO] Query marker FASTA was written to OceanDNA-b22848/markers.fasta
[2023-03-16 19:34:56,995] [INFO] Task started: Blastn
[2023-03-16 19:34:56,996] [INFO] Running command: blastn -query OceanDNA-b22848/markers.fasta -db /var/lib/cwl/stgb515388b-9de6-479a-8478-c734c3b63608/dqc_reference/reference_markers.fasta -out OceanDNA-b22848/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:34:57,558] [INFO] Task succeeded: Blastn
[2023-03-16 19:34:57,559] [INFO] Selected 20 target genomes.
[2023-03-16 19:34:57,559] [INFO] Target genome list was writen to OceanDNA-b22848/target_genomes.txt
[2023-03-16 19:34:57,566] [INFO] Task started: fastANI
[2023-03-16 19:34:57,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c573ef2-fe6b-4584-b730-c6c40e073404/OceanDNA-b22848.fa --refList OceanDNA-b22848/target_genomes.txt --output OceanDNA-b22848/fastani_result.tsv --threads 1
[2023-03-16 19:35:14,969] [INFO] Task succeeded: fastANI
[2023-03-16 19:35:14,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb515388b-9de6-479a-8478-c734c3b63608/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:35:14,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb515388b-9de6-479a-8478-c734c3b63608/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:35:15,040] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 19:35:15,040] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 19:35:15,040] [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
Symmachiella dynata	strain=Mal52	GCA_007747995.1	2527995	2527995	type	True	96.4678	2041	2153	95	conclusive
Symmachiella macrocystis	strain=CA54	GCA_007860075.1	2527985	2527985	type	True	90.9823	1912	2153	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:35:15,040] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22848/tc_result.tsv
[2023-03-16 19:35:15,040] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:35:15,041] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:35:15,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb515388b-9de6-479a-8478-c734c3b63608/dqc_reference/checkm_data
[2023-03-16 19:35:15,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:35:15,298] [INFO] Task started: CheckM
[2023-03-16 19:35:15,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22848/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22848/checkm_input OceanDNA-b22848/checkm_result
[2023-03-16 19:37:12,945] [INFO] Task succeeded: CheckM
[2023-03-16 19:37:12,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:37:12,948] [INFO] ===== Completeness check finished =====
[2023-03-16 19:37:12,949] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:37:12,949] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22848/markers.fasta)
[2023-03-16 19:37:12,950] [INFO] Task started: Blastn
[2023-03-16 19:37:12,950] [INFO] Running command: blastn -query OceanDNA-b22848/markers.fasta -db /var/lib/cwl/stgb515388b-9de6-479a-8478-c734c3b63608/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22848/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:37:13,630] [INFO] Task succeeded: Blastn
[2023-03-16 19:37:13,631] [INFO] Selected 24 target genomes.
[2023-03-16 19:37:13,631] [INFO] Target genome list was writen to OceanDNA-b22848/target_genomes_gtdb.txt
[2023-03-16 19:37:13,649] [INFO] Task started: fastANI
[2023-03-16 19:37:13,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c573ef2-fe6b-4584-b730-c6c40e073404/OceanDNA-b22848.fa --refList OceanDNA-b22848/target_genomes_gtdb.txt --output OceanDNA-b22848/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:37:38,153] [INFO] Task succeeded: fastANI
[2023-03-16 19:37:38,156] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:37:38,156] [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_007747995.1	s__Symmachiella dynata	96.4678	2041	2153	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Mal52;g__Symmachiella	95.0	96.81	96.81	0.94	0.94	2	conclusive
GCF_007860075.1	s__Symmachiella macrocystis	90.9823	1912	2153	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Mal52;g__Symmachiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:37:38,156] [INFO] GTDB search result was written to OceanDNA-b22848/result_gtdb.tsv
[2023-03-16 19:37:38,156] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:37:38,157] [INFO] DFAST_QC result json was written to OceanDNA-b22848/dqc_result.json
[2023-03-16 19:37:38,157] [INFO] DFAST_QC completed!
[2023-03-16 19:37:38,157] [INFO] Total running time: 0h3m25s