[2023-03-19 01:13:44,401] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,401] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b8aec74-f0a7-4bba-8682-b9bc5f23126d/dqc_reference
[2023-03-19 01:13:45,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,589] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,589] [INFO] Running command: cat /var/lib/cwl/stg96013dc5-3190-41e4-9aa5-26ec24a1ec86/OceanDNA-a1371.fa | prodigal -d OceanDNA-a1371/cds.fna -a OceanDNA-a1371/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:52,493] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:52,494] [INFO] Task started: HMMsearch
[2023-03-19 01:13:52,494] [INFO] Running command: hmmsearch --tblout OceanDNA-a1371/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b8aec74-f0a7-4bba-8682-b9bc5f23126d/dqc_reference/reference_markers.hmm OceanDNA-a1371/protein.faa > /dev/null
[2023-03-19 01:13:52,639] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:52,639] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg96013dc5-3190-41e4-9aa5-26ec24a1ec86/OceanDNA-a1371.fa]
[2023-03-19 01:13:52,649] [INFO] Query marker FASTA was written to OceanDNA-a1371/markers.fasta
[2023-03-19 01:13:52,650] [INFO] Task started: Blastn
[2023-03-19 01:13:52,650] [INFO] Running command: blastn -query OceanDNA-a1371/markers.fasta -db /var/lib/cwl/stg8b8aec74-f0a7-4bba-8682-b9bc5f23126d/dqc_reference/reference_markers.fasta -out OceanDNA-a1371/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:53,115] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:53,116] [INFO] Selected 7 target genomes.
[2023-03-19 01:13:53,116] [INFO] Target genome list was writen to OceanDNA-a1371/target_genomes.txt
[2023-03-19 01:13:53,120] [INFO] Task started: fastANI
[2023-03-19 01:13:53,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg96013dc5-3190-41e4-9aa5-26ec24a1ec86/OceanDNA-a1371.fa --refList OceanDNA-a1371/target_genomes.txt --output OceanDNA-a1371/fastani_result.tsv --threads 1
[2023-03-19 01:13:56,999] [INFO] Task succeeded: fastANI
[2023-03-19 01:13:56,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b8aec74-f0a7-4bba-8682-b9bc5f23126d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:13:56,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b8aec74-f0a7-4bba-8682-b9bc5f23126d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:13:56,999] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:13:57,000] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:13:57,000] [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
--------------------------------------------------------------------------------
[2023-03-19 01:13:57,000] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1371/tc_result.tsv
[2023-03-19 01:13:57,000] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:13:57,000] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:13:57,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b8aec74-f0a7-4bba-8682-b9bc5f23126d/dqc_reference/checkm_data
[2023-03-19 01:13:57,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:13:57,133] [INFO] Task started: CheckM
[2023-03-19 01:13:57,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1371/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1371/checkm_input OceanDNA-a1371/checkm_result
[2023-03-19 01:14:20,015] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:20,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:20,018] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:20,018] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:20,018] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1371/markers.fasta)
[2023-03-19 01:14:20,018] [INFO] Task started: Blastn
[2023-03-19 01:14:20,018] [INFO] Running command: blastn -query OceanDNA-a1371/markers.fasta -db /var/lib/cwl/stg8b8aec74-f0a7-4bba-8682-b9bc5f23126d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1371/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:20,603] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:20,604] [INFO] Selected 9 target genomes.
[2023-03-19 01:14:20,604] [INFO] Target genome list was writen to OceanDNA-a1371/target_genomes_gtdb.txt
[2023-03-19 01:14:20,613] [INFO] Task started: fastANI
[2023-03-19 01:14:20,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg96013dc5-3190-41e4-9aa5-26ec24a1ec86/OceanDNA-a1371.fa --refList OceanDNA-a1371/target_genomes_gtdb.txt --output OceanDNA-a1371/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:22,374] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:22,376] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:14:22,376] [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_018657065.1	s__GW2011-AR15 sp018657065	99.9624	441	457	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GW2011-AR15;g__GW2011-AR15	95.0	99.94	99.88	0.94	0.90	8	conclusive
--------------------------------------------------------------------------------
[2023-03-19 01:14:22,376] [INFO] GTDB search result was written to OceanDNA-a1371/result_gtdb.tsv
[2023-03-19 01:14:22,376] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:22,377] [INFO] DFAST_QC result json was written to OceanDNA-a1371/dqc_result.json
[2023-03-19 01:14:22,377] [INFO] DFAST_QC completed!
[2023-03-19 01:14:22,377] [INFO] Total running time: 0h0m38s