[2023-03-16 16:47:18,278] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:47:18,278] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:47:18,278] [INFO] DQC Reference Directory: /var/lib/cwl/stga6ac0bd2-09e1-4657-a9cc-ca887eb5313b/dqc_reference
[2023-03-16 16:47:19,394] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:47:19,395] [INFO] Task started: Prodigal
[2023-03-16 16:47:19,395] [INFO] Running command: cat /var/lib/cwl/stg29a0583d-1492-46d9-912c-260d0c859703/OceanDNA-b22423.fa | prodigal -d OceanDNA-b22423/cds.fna -a OceanDNA-b22423/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:47:36,061] [INFO] Task succeeded: Prodigal
[2023-03-16 16:47:36,062] [INFO] Task started: HMMsearch
[2023-03-16 16:47:36,062] [INFO] Running command: hmmsearch --tblout OceanDNA-b22423/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6ac0bd2-09e1-4657-a9cc-ca887eb5313b/dqc_reference/reference_markers.hmm OceanDNA-b22423/protein.faa > /dev/null
[2023-03-16 16:47:36,616] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:47:36,616] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg29a0583d-1492-46d9-912c-260d0c859703/OceanDNA-b22423.fa]
[2023-03-16 16:47:36,689] [INFO] Query marker FASTA was written to OceanDNA-b22423/markers.fasta
[2023-03-16 16:47:36,699] [INFO] Task started: Blastn
[2023-03-16 16:47:36,699] [INFO] Running command: blastn -query OceanDNA-b22423/markers.fasta -db /var/lib/cwl/stga6ac0bd2-09e1-4657-a9cc-ca887eb5313b/dqc_reference/reference_markers.fasta -out OceanDNA-b22423/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:47:38,181] [INFO] Task succeeded: Blastn
[2023-03-16 16:47:38,189] [INFO] Selected 30 target genomes.
[2023-03-16 16:47:38,189] [INFO] Target genome list was writen to OceanDNA-b22423/target_genomes.txt
[2023-03-16 16:47:38,215] [INFO] Task started: fastANI
[2023-03-16 16:47:38,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg29a0583d-1492-46d9-912c-260d0c859703/OceanDNA-b22423.fa --refList OceanDNA-b22423/target_genomes.txt --output OceanDNA-b22423/fastani_result.tsv --threads 1
[2023-03-16 16:48:19,226] [INFO] Task succeeded: fastANI
[2023-03-16 16:48:19,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6ac0bd2-09e1-4657-a9cc-ca887eb5313b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:48:19,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6ac0bd2-09e1-4657-a9cc-ca887eb5313b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:48:19,227] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:48:19,227] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:48:19,227] [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
--------------------------------------------------------------------------------
[2023-03-16 16:48:19,227] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22423/tc_result.tsv
[2023-03-16 16:48:19,227] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:48:19,227] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:48:19,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6ac0bd2-09e1-4657-a9cc-ca887eb5313b/dqc_reference/checkm_data
[2023-03-16 16:48:19,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:48:19,244] [INFO] Task started: CheckM
[2023-03-16 16:48:19,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22423/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22423/checkm_input OceanDNA-b22423/checkm_result
[2023-03-16 16:49:16,432] [INFO] Task succeeded: CheckM
[2023-03-16 16:49:16,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.84%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:49:16,437] [INFO] ===== Completeness check finished =====
[2023-03-16 16:49:16,437] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:49:16,437] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22423/markers.fasta)
[2023-03-16 16:49:16,439] [INFO] Task started: Blastn
[2023-03-16 16:49:16,439] [INFO] Running command: blastn -query OceanDNA-b22423/markers.fasta -db /var/lib/cwl/stga6ac0bd2-09e1-4657-a9cc-ca887eb5313b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22423/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:49:17,490] [INFO] Task succeeded: Blastn
[2023-03-16 16:49:17,491] [INFO] Selected 33 target genomes.
[2023-03-16 16:49:17,491] [INFO] Target genome list was writen to OceanDNA-b22423/target_genomes_gtdb.txt
[2023-03-16 16:49:17,511] [INFO] Task started: fastANI
[2023-03-16 16:49:17,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg29a0583d-1492-46d9-912c-260d0c859703/OceanDNA-b22423.fa --refList OceanDNA-b22423/target_genomes_gtdb.txt --output OceanDNA-b22423/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:49:43,350] [INFO] Task succeeded: fastANI
[2023-03-16 16:49:43,352] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:49:43,352] [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_002723275.1	s__GCA-2723275 sp002723275	96.4189	538	559	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__GCA-2723275	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-16 16:49:43,352] [INFO] GTDB search result was written to OceanDNA-b22423/result_gtdb.tsv
[2023-03-16 16:49:43,352] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:49:43,353] [INFO] DFAST_QC result json was written to OceanDNA-b22423/dqc_result.json
[2023-03-16 16:49:43,353] [INFO] DFAST_QC completed!
[2023-03-16 16:49:43,353] [INFO] Total running time: 0h2m25s