[2023-03-16 06:12:34,966] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:12:34,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:12:34,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg5183821d-8756-43a0-a953-533db1241b44/dqc_reference
[2023-03-16 06:12:36,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:12:36,624] [INFO] Task started: Prodigal
[2023-03-16 06:12:36,625] [INFO] Running command: cat /var/lib/cwl/stgb8dd39a4-2aa8-40d8-acc4-cc62abe39c70/OceanDNA-b36174.fa | prodigal -d OceanDNA-b36174/cds.fna -a OceanDNA-b36174/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:12:42,325] [INFO] Task succeeded: Prodigal
[2023-03-16 06:12:42,325] [INFO] Task started: HMMsearch
[2023-03-16 06:12:42,325] [INFO] Running command: hmmsearch --tblout OceanDNA-b36174/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5183821d-8756-43a0-a953-533db1241b44/dqc_reference/reference_markers.hmm OceanDNA-b36174/protein.faa > /dev/null
[2023-03-16 06:12:42,484] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:12:42,484] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb8dd39a4-2aa8-40d8-acc4-cc62abe39c70/OceanDNA-b36174.fa]
[2023-03-16 06:12:42,498] [INFO] Query marker FASTA was written to OceanDNA-b36174/markers.fasta
[2023-03-16 06:12:42,498] [INFO] Task started: Blastn
[2023-03-16 06:12:42,498] [INFO] Running command: blastn -query OceanDNA-b36174/markers.fasta -db /var/lib/cwl/stg5183821d-8756-43a0-a953-533db1241b44/dqc_reference/reference_markers.fasta -out OceanDNA-b36174/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:12:43,002] [INFO] Task succeeded: Blastn
[2023-03-16 06:12:43,005] [INFO] Selected 19 target genomes.
[2023-03-16 06:12:43,006] [INFO] Target genome list was writen to OceanDNA-b36174/target_genomes.txt
[2023-03-16 06:12:43,017] [INFO] Task started: fastANI
[2023-03-16 06:12:43,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8dd39a4-2aa8-40d8-acc4-cc62abe39c70/OceanDNA-b36174.fa --refList OceanDNA-b36174/target_genomes.txt --output OceanDNA-b36174/fastani_result.tsv --threads 1
[2023-03-16 06:12:54,981] [INFO] Task succeeded: fastANI
[2023-03-16 06:12:54,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5183821d-8756-43a0-a953-533db1241b44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:12:54,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5183821d-8756-43a0-a953-533db1241b44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:12:54,982] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:12:54,982] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:12:54,982] [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 06:12:54,984] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36174/tc_result.tsv
[2023-03-16 06:12:54,985] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:12:54,985] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:12:54,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5183821d-8756-43a0-a953-533db1241b44/dqc_reference/checkm_data
[2023-03-16 06:12:54,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:12:54,991] [INFO] Task started: CheckM
[2023-03-16 06:12:54,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36174/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36174/checkm_input OceanDNA-b36174/checkm_result
[2023-03-16 06:13:14,724] [INFO] Task succeeded: CheckM
[2023-03-16 06:13:14,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:13:14,775] [INFO] ===== Completeness check finished =====
[2023-03-16 06:13:14,775] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:13:14,775] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36174/markers.fasta)
[2023-03-16 06:13:14,776] [INFO] Task started: Blastn
[2023-03-16 06:13:14,776] [INFO] Running command: blastn -query OceanDNA-b36174/markers.fasta -db /var/lib/cwl/stg5183821d-8756-43a0-a953-533db1241b44/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36174/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:15,469] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:15,473] [INFO] Selected 18 target genomes.
[2023-03-16 06:13:15,473] [INFO] Target genome list was writen to OceanDNA-b36174/target_genomes_gtdb.txt
[2023-03-16 06:13:15,514] [INFO] Task started: fastANI
[2023-03-16 06:13:15,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8dd39a4-2aa8-40d8-acc4-cc62abe39c70/OceanDNA-b36174.fa --refList OceanDNA-b36174/target_genomes_gtdb.txt --output OceanDNA-b36174/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:13:23,660] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:23,662] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:13:23,662] [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_013215805.1	s__41-12-T18 sp013215805	83.2329	284	361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:13:23,664] [INFO] GTDB search result was written to OceanDNA-b36174/result_gtdb.tsv
[2023-03-16 06:13:23,665] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:13:23,666] [INFO] DFAST_QC result json was written to OceanDNA-b36174/dqc_result.json
[2023-03-16 06:13:23,666] [INFO] DFAST_QC completed!
[2023-03-16 06:13:23,666] [INFO] Total running time: 0h0m49s