[2023-03-18 01:54:19,436] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:54:19,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:54:19,437] [INFO] DQC Reference Directory: /var/lib/cwl/stga1bdc88b-9272-4b71-8f99-ead1f2521281/dqc_reference
[2023-03-18 01:54:20,520] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:54:20,520] [INFO] Task started: Prodigal
[2023-03-18 01:54:20,520] [INFO] Running command: cat /var/lib/cwl/stg32402957-30cc-4b77-b052-cf15aff1ab9b/OceanDNA-b21554.fa | prodigal -d OceanDNA-b21554/cds.fna -a OceanDNA-b21554/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:54:28,539] [INFO] Task succeeded: Prodigal
[2023-03-18 01:54:28,540] [INFO] Task started: HMMsearch
[2023-03-18 01:54:28,540] [INFO] Running command: hmmsearch --tblout OceanDNA-b21554/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1bdc88b-9272-4b71-8f99-ead1f2521281/dqc_reference/reference_markers.hmm OceanDNA-b21554/protein.faa > /dev/null
[2023-03-18 01:54:28,715] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:54:28,715] [INFO] Found 6/6 markers.
[2023-03-18 01:54:28,729] [INFO] Query marker FASTA was written to OceanDNA-b21554/markers.fasta
[2023-03-18 01:54:28,730] [INFO] Task started: Blastn
[2023-03-18 01:54:28,730] [INFO] Running command: blastn -query OceanDNA-b21554/markers.fasta -db /var/lib/cwl/stga1bdc88b-9272-4b71-8f99-ead1f2521281/dqc_reference/reference_markers.fasta -out OceanDNA-b21554/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:29,234] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:29,235] [INFO] Selected 11 target genomes.
[2023-03-18 01:54:29,235] [INFO] Target genome list was writen to OceanDNA-b21554/target_genomes.txt
[2023-03-18 01:54:29,241] [INFO] Task started: fastANI
[2023-03-18 01:54:29,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg32402957-30cc-4b77-b052-cf15aff1ab9b/OceanDNA-b21554.fa --refList OceanDNA-b21554/target_genomes.txt --output OceanDNA-b21554/fastani_result.tsv --threads 1
[2023-03-18 01:54:33,763] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:33,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1bdc88b-9272-4b71-8f99-ead1f2521281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:54:33,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1bdc88b-9272-4b71-8f99-ead1f2521281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:54:33,764] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:54:33,764] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:54:33,764] [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
--------------------------------------------------------------------------------
[2023-03-18 01:54:33,772] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21554/tc_result.tsv
[2023-03-18 01:54:33,773] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:54:33,773] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:54:33,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1bdc88b-9272-4b71-8f99-ead1f2521281/dqc_reference/checkm_data
[2023-03-18 01:54:33,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:54:33,780] [INFO] Task started: CheckM
[2023-03-18 01:54:33,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21554/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21554/checkm_input OceanDNA-b21554/checkm_result
[2023-03-18 01:54:59,181] [INFO] Task succeeded: CheckM
[2023-03-18 01:54:59,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:54:59,193] [INFO] ===== Completeness check finished =====
[2023-03-18 01:54:59,193] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:54:59,193] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21554/markers.fasta)
[2023-03-18 01:54:59,194] [INFO] Task started: Blastn
[2023-03-18 01:54:59,194] [INFO] Running command: blastn -query OceanDNA-b21554/markers.fasta -db /var/lib/cwl/stga1bdc88b-9272-4b71-8f99-ead1f2521281/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21554/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:59,876] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:59,946] [INFO] Selected 18 target genomes.
[2023-03-18 01:54:59,946] [INFO] Target genome list was writen to OceanDNA-b21554/target_genomes_gtdb.txt
[2023-03-18 01:54:59,982] [INFO] Task started: fastANI
[2023-03-18 01:54:59,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg32402957-30cc-4b77-b052-cf15aff1ab9b/OceanDNA-b21554.fa --refList OceanDNA-b21554/target_genomes_gtdb.txt --output OceanDNA-b21554/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:55:05,232] [INFO] Task succeeded: fastANI
[2023-03-18 01:55:05,234] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:55:05,234] [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_002328295.1	s__UBA2144 sp002328295	99.5698	282	349	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Peribacterales;f__Peribacteraceae;g__UBA2144	95.0	99.33	99.31	0.79	0.78	3	conclusive
--------------------------------------------------------------------------------
[2023-03-18 01:55:05,262] [INFO] GTDB search result was written to OceanDNA-b21554/result_gtdb.tsv
[2023-03-18 01:55:05,299] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:55:05,307] [INFO] DFAST_QC result json was written to OceanDNA-b21554/dqc_result.json
[2023-03-18 01:55:05,307] [INFO] DFAST_QC completed!
[2023-03-18 01:55:05,307] [INFO] Total running time: 0h0m46s