[2023-03-17 11:08:00,274] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,275] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg495dac6c-0484-42ad-bef4-5ea2bac79b1a/dqc_reference
[2023-03-17 11:08:01,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,419] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,419] [INFO] Running command: cat /var/lib/cwl/stg0e81bacf-98de-4f99-a27c-223406eba88f/OceanDNA-a4837.fa | prodigal -d OceanDNA-a4837/cds.fna -a OceanDNA-a4837/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:09,969] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:09,970] [INFO] Task started: HMMsearch
[2023-03-17 11:08:09,970] [INFO] Running command: hmmsearch --tblout OceanDNA-a4837/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg495dac6c-0484-42ad-bef4-5ea2bac79b1a/dqc_reference/reference_markers.hmm OceanDNA-a4837/protein.faa > /dev/null
[2023-03-17 11:08:10,137] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:10,137] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0e81bacf-98de-4f99-a27c-223406eba88f/OceanDNA-a4837.fa]
[2023-03-17 11:08:10,190] [INFO] Query marker FASTA was written to OceanDNA-a4837/markers.fasta
[2023-03-17 11:08:10,190] [INFO] Task started: Blastn
[2023-03-17 11:08:10,190] [INFO] Running command: blastn -query OceanDNA-a4837/markers.fasta -db /var/lib/cwl/stg495dac6c-0484-42ad-bef4-5ea2bac79b1a/dqc_reference/reference_markers.fasta -out OceanDNA-a4837/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:10,610] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:10,629] [INFO] Selected 2 target genomes.
[2023-03-17 11:08:10,630] [INFO] Target genome list was writen to OceanDNA-a4837/target_genomes.txt
[2023-03-17 11:08:10,631] [INFO] Task started: fastANI
[2023-03-17 11:08:10,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e81bacf-98de-4f99-a27c-223406eba88f/OceanDNA-a4837.fa --refList OceanDNA-a4837/target_genomes.txt --output OceanDNA-a4837/fastani_result.tsv --threads 1
[2023-03-17 11:08:11,385] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:11,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg495dac6c-0484-42ad-bef4-5ea2bac79b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:11,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg495dac6c-0484-42ad-bef4-5ea2bac79b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:11,386] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:11,386] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:08:11,386] [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
--------------------------------------------------------------------------------
[2023-03-17 11:08:11,391] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4837/tc_result.tsv
[2023-03-17 11:08:11,402] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:11,402] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:11,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg495dac6c-0484-42ad-bef4-5ea2bac79b1a/dqc_reference/checkm_data
[2023-03-17 11:08:11,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:11,418] [INFO] Task started: CheckM
[2023-03-17 11:08:11,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4837/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4837/checkm_input OceanDNA-a4837/checkm_result
[2023-03-17 11:08:37,339] [INFO] Task succeeded: CheckM
[2023-03-17 11:08:37,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.42%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:08:37,384] [INFO] ===== Completeness check finished =====
[2023-03-17 11:08:37,385] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:08:37,385] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4837/markers.fasta)
[2023-03-17 11:08:37,386] [INFO] Task started: Blastn
[2023-03-17 11:08:37,386] [INFO] Running command: blastn -query OceanDNA-a4837/markers.fasta -db /var/lib/cwl/stg495dac6c-0484-42ad-bef4-5ea2bac79b1a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4837/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:37,790] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:37,803] [INFO] Selected 9 target genomes.
[2023-03-17 11:08:37,803] [INFO] Target genome list was writen to OceanDNA-a4837/target_genomes_gtdb.txt
[2023-03-17 11:08:37,947] [INFO] Task started: fastANI
[2023-03-17 11:08:37,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e81bacf-98de-4f99-a27c-223406eba88f/OceanDNA-a4837.fa --refList OceanDNA-a4837/target_genomes_gtdb.txt --output OceanDNA-a4837/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:08:40,525] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:40,526] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:08:40,527] [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_002725475.1	s__MGIIb-Q1 sp002725475	99.8005	375	491	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-17 11:08:40,534] [INFO] GTDB search result was written to OceanDNA-a4837/result_gtdb.tsv
[2023-03-17 11:08:40,545] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:08:40,551] [INFO] DFAST_QC result json was written to OceanDNA-a4837/dqc_result.json
[2023-03-17 11:08:40,551] [INFO] DFAST_QC completed!
[2023-03-17 11:08:40,551] [INFO] Total running time: 0h0m40s