[2023-03-15 15:18:22,052] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,052] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,052] [INFO] DQC Reference Directory: /var/lib/cwl/stgec7b2348-78bc-4026-a40d-e667f950d13a/dqc_reference
[2023-03-15 15:18:23,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,207] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,207] [INFO] Running command: cat /var/lib/cwl/stga8f44bcc-0e3d-46c2-8b5f-75279ef0eb97/OceanDNA-b22873.fa | prodigal -d OceanDNA-b22873/cds.fna -a OceanDNA-b22873/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:43,837] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:43,838] [INFO] Task started: HMMsearch
[2023-03-15 15:18:43,838] [INFO] Running command: hmmsearch --tblout OceanDNA-b22873/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec7b2348-78bc-4026-a40d-e667f950d13a/dqc_reference/reference_markers.hmm OceanDNA-b22873/protein.faa > /dev/null
[2023-03-15 15:18:44,102] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:44,103] [INFO] Found 6/6 markers.
[2023-03-15 15:18:44,174] [INFO] Query marker FASTA was written to OceanDNA-b22873/markers.fasta
[2023-03-15 15:18:44,176] [INFO] Task started: Blastn
[2023-03-15 15:18:44,176] [INFO] Running command: blastn -query OceanDNA-b22873/markers.fasta -db /var/lib/cwl/stgec7b2348-78bc-4026-a40d-e667f950d13a/dqc_reference/reference_markers.fasta -out OceanDNA-b22873/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:44,707] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:44,710] [INFO] Selected 26 target genomes.
[2023-03-15 15:18:44,711] [INFO] Target genome list was writen to OceanDNA-b22873/target_genomes.txt
[2023-03-15 15:18:44,729] [INFO] Task started: fastANI
[2023-03-15 15:18:44,729] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f44bcc-0e3d-46c2-8b5f-75279ef0eb97/OceanDNA-b22873.fa --refList OceanDNA-b22873/target_genomes.txt --output OceanDNA-b22873/fastani_result.tsv --threads 1
[2023-03-15 15:19:08,709] [INFO] Task succeeded: fastANI
[2023-03-15 15:19:08,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec7b2348-78bc-4026-a40d-e667f950d13a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:19:08,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec7b2348-78bc-4026-a40d-e667f950d13a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:19:08,713] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:19:08,713] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:19:08,713] [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
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.8731	81	814	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:19:08,714] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22873/tc_result.tsv
[2023-03-15 15:19:08,715] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:19:08,715] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:19:08,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec7b2348-78bc-4026-a40d-e667f950d13a/dqc_reference/checkm_data
[2023-03-15 15:19:08,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:19:08,727] [INFO] Task started: CheckM
[2023-03-15 15:19:08,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22873/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22873/checkm_input OceanDNA-b22873/checkm_result
[2023-03-15 15:20:02,628] [INFO] Task succeeded: CheckM
[2023-03-15 15:20:02,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:20:02,633] [INFO] ===== Completeness check finished =====
[2023-03-15 15:20:02,633] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:20:02,633] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22873/markers.fasta)
[2023-03-15 15:20:02,635] [INFO] Task started: Blastn
[2023-03-15 15:20:02,635] [INFO] Running command: blastn -query OceanDNA-b22873/markers.fasta -db /var/lib/cwl/stgec7b2348-78bc-4026-a40d-e667f950d13a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22873/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:20:03,379] [INFO] Task succeeded: Blastn
[2023-03-15 15:20:03,383] [INFO] Selected 32 target genomes.
[2023-03-15 15:20:03,384] [INFO] Target genome list was writen to OceanDNA-b22873/target_genomes_gtdb.txt
[2023-03-15 15:20:03,406] [INFO] Task started: fastANI
[2023-03-15 15:20:03,406] [INFO] Running command: fastANI --query /var/lib/cwl/stga8f44bcc-0e3d-46c2-8b5f-75279ef0eb97/OceanDNA-b22873.fa --refList OceanDNA-b22873/target_genomes_gtdb.txt --output OceanDNA-b22873/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:20:32,014] [INFO] Task succeeded: fastANI
[2023-03-15 15:20:32,017] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:20:32,017] [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_014238335.1	s__Fuerstia sp014238335	75.9826	61	814	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983935.1	s__Fuerstia marisgermanicae	75.8731	81	814	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:20:32,020] [INFO] GTDB search result was written to OceanDNA-b22873/result_gtdb.tsv
[2023-03-15 15:20:32,021] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:20:32,024] [INFO] DFAST_QC result json was written to OceanDNA-b22873/dqc_result.json
[2023-03-15 15:20:32,024] [INFO] DFAST_QC completed!
[2023-03-15 15:20:32,024] [INFO] Total running time: 0h2m10s