[2023-03-19 05:19:33,810] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,810] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,810] [INFO] DQC Reference Directory: /var/lib/cwl/stga9efeaa9-a06e-4a60-8501-0d1027f9be43/dqc_reference
[2023-03-19 05:19:35,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,401] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,401] [INFO] Running command: cat /var/lib/cwl/stg9c486256-8e7f-4051-b3c7-57d88766884b/OceanDNA-b13273.fa | prodigal -d OceanDNA-b13273/cds.fna -a OceanDNA-b13273/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:20:00,684] [INFO] Task succeeded: Prodigal
[2023-03-19 05:20:00,685] [INFO] Task started: HMMsearch
[2023-03-19 05:20:00,685] [INFO] Running command: hmmsearch --tblout OceanDNA-b13273/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9efeaa9-a06e-4a60-8501-0d1027f9be43/dqc_reference/reference_markers.hmm OceanDNA-b13273/protein.faa > /dev/null
[2023-03-19 05:20:00,990] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:20:00,991] [INFO] Found 6/6 markers.
[2023-03-19 05:20:01,024] [INFO] Query marker FASTA was written to OceanDNA-b13273/markers.fasta
[2023-03-19 05:20:01,024] [INFO] Task started: Blastn
[2023-03-19 05:20:01,024] [INFO] Running command: blastn -query OceanDNA-b13273/markers.fasta -db /var/lib/cwl/stga9efeaa9-a06e-4a60-8501-0d1027f9be43/dqc_reference/reference_markers.fasta -out OceanDNA-b13273/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:01,547] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:01,548] [INFO] Selected 27 target genomes.
[2023-03-19 05:20:01,548] [INFO] Target genome list was writen to OceanDNA-b13273/target_genomes.txt
[2023-03-19 05:20:01,564] [INFO] Task started: fastANI
[2023-03-19 05:20:01,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c486256-8e7f-4051-b3c7-57d88766884b/OceanDNA-b13273.fa --refList OceanDNA-b13273/target_genomes.txt --output OceanDNA-b13273/fastani_result.tsv --threads 1
[2023-03-19 05:20:16,042] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:16,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9efeaa9-a06e-4a60-8501-0d1027f9be43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:20:16,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9efeaa9-a06e-4a60-8501-0d1027f9be43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:16,043] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:16,043] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:20:16,043] [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 05:20:16,044] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13273/tc_result.tsv
[2023-03-19 05:20:16,044] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:16,044] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:16,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9efeaa9-a06e-4a60-8501-0d1027f9be43/dqc_reference/checkm_data
[2023-03-19 05:20:16,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:16,053] [INFO] Task started: CheckM
[2023-03-19 05:20:16,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13273/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13273/checkm_input OceanDNA-b13273/checkm_result
[2023-03-19 05:21:18,298] [INFO] Task succeeded: CheckM
[2023-03-19 05:21:18,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 05:21:18,302] [INFO] ===== Completeness check finished =====
[2023-03-19 05:21:18,302] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:21:18,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13273/markers.fasta)
[2023-03-19 05:21:18,304] [INFO] Task started: Blastn
[2023-03-19 05:21:18,304] [INFO] Running command: blastn -query OceanDNA-b13273/markers.fasta -db /var/lib/cwl/stga9efeaa9-a06e-4a60-8501-0d1027f9be43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13273/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:21:19,021] [INFO] Task succeeded: Blastn
[2023-03-19 05:21:19,022] [INFO] Selected 37 target genomes.
[2023-03-19 05:21:19,022] [INFO] Target genome list was writen to OceanDNA-b13273/target_genomes_gtdb.txt
[2023-03-19 05:21:19,186] [INFO] Task started: fastANI
[2023-03-19 05:21:19,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c486256-8e7f-4051-b3c7-57d88766884b/OceanDNA-b13273.fa --refList OceanDNA-b13273/target_genomes_gtdb.txt --output OceanDNA-b13273/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:21:36,367] [INFO] Task succeeded: fastANI
[2023-03-19 05:21:36,368] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:21:36,368] [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
--------------------------------------------------------------------------------
[2023-03-19 05:21:36,368] [INFO] GTDB search result was written to OceanDNA-b13273/result_gtdb.tsv
[2023-03-19 05:21:36,368] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:21:36,368] [INFO] DFAST_QC result json was written to OceanDNA-b13273/dqc_result.json
[2023-03-19 05:21:36,369] [INFO] DFAST_QC completed!
[2023-03-19 05:21:36,369] [INFO] Total running time: 0h2m3s