[2023-03-16 05:41:22,579] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:41:22,579] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:41:22,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg889e9fc6-88a8-42c0-9122-e1fce5cc8042/dqc_reference
[2023-03-16 05:41:23,690] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:41:23,691] [INFO] Task started: Prodigal
[2023-03-16 05:41:23,691] [INFO] Running command: cat /var/lib/cwl/stge015bb9a-ee52-4e93-b49d-838b29c70069/OceanDNA-a4117.fa | prodigal -d OceanDNA-a4117/cds.fna -a OceanDNA-a4117/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:41:27,148] [INFO] Task succeeded: Prodigal
[2023-03-16 05:41:27,148] [INFO] Task started: HMMsearch
[2023-03-16 05:41:27,148] [INFO] Running command: hmmsearch --tblout OceanDNA-a4117/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg889e9fc6-88a8-42c0-9122-e1fce5cc8042/dqc_reference/reference_markers.hmm OceanDNA-a4117/protein.faa > /dev/null
[2023-03-16 05:41:27,292] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:41:27,293] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge015bb9a-ee52-4e93-b49d-838b29c70069/OceanDNA-a4117.fa]
[2023-03-16 05:41:27,300] [INFO] Query marker FASTA was written to OceanDNA-a4117/markers.fasta
[2023-03-16 05:41:27,301] [INFO] Task started: Blastn
[2023-03-16 05:41:27,301] [INFO] Running command: blastn -query OceanDNA-a4117/markers.fasta -db /var/lib/cwl/stg889e9fc6-88a8-42c0-9122-e1fce5cc8042/dqc_reference/reference_markers.fasta -out OceanDNA-a4117/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:41:27,756] [INFO] Task succeeded: Blastn
[2023-03-16 05:41:27,756] [INFO] Selected 1 target genomes.
[2023-03-16 05:41:27,757] [INFO] Target genome list was writen to OceanDNA-a4117/target_genomes.txt
[2023-03-16 05:41:27,758] [INFO] Task started: fastANI
[2023-03-16 05:41:27,758] [INFO] Running command: fastANI --query /var/lib/cwl/stge015bb9a-ee52-4e93-b49d-838b29c70069/OceanDNA-a4117.fa --refList OceanDNA-a4117/target_genomes.txt --output OceanDNA-a4117/fastani_result.tsv --threads 1
[2023-03-16 05:41:28,439] [INFO] Task succeeded: fastANI
[2023-03-16 05:41:28,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg889e9fc6-88a8-42c0-9122-e1fce5cc8042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:41:28,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg889e9fc6-88a8-42c0-9122-e1fce5cc8042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:41:28,440] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:41:28,440] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:41:28,440] [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 05:41:28,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4117/tc_result.tsv
[2023-03-16 05:41:28,440] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:41:28,440] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:41:28,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg889e9fc6-88a8-42c0-9122-e1fce5cc8042/dqc_reference/checkm_data
[2023-03-16 05:41:28,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:41:28,495] [INFO] Task started: CheckM
[2023-03-16 05:41:28,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4117/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4117/checkm_input OceanDNA-a4117/checkm_result
[2023-03-16 05:41:45,760] [INFO] Task succeeded: CheckM
[2023-03-16 05:41:45,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.30%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:41:45,762] [INFO] ===== Completeness check finished =====
[2023-03-16 05:41:45,762] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:41:45,762] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4117/markers.fasta)
[2023-03-16 05:41:45,764] [INFO] Task started: Blastn
[2023-03-16 05:41:45,764] [INFO] Running command: blastn -query OceanDNA-a4117/markers.fasta -db /var/lib/cwl/stg889e9fc6-88a8-42c0-9122-e1fce5cc8042/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4117/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:41:46,588] [INFO] Task succeeded: Blastn
[2023-03-16 05:41:46,589] [INFO] Selected 6 target genomes.
[2023-03-16 05:41:46,589] [INFO] Target genome list was writen to OceanDNA-a4117/target_genomes_gtdb.txt
[2023-03-16 05:41:46,594] [INFO] Task started: fastANI
[2023-03-16 05:41:46,594] [INFO] Running command: fastANI --query /var/lib/cwl/stge015bb9a-ee52-4e93-b49d-838b29c70069/OceanDNA-a4117.fa --refList OceanDNA-a4117/target_genomes_gtdb.txt --output OceanDNA-a4117/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:41:48,551] [INFO] Task succeeded: fastANI
[2023-03-16 05:41:48,551] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:41:48,551] [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
--------------------------------------------------------------------------------
[2023-03-16 05:41:48,551] [INFO] GTDB search result was written to OceanDNA-a4117/result_gtdb.tsv
[2023-03-16 05:41:48,551] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:41:48,552] [INFO] DFAST_QC result json was written to OceanDNA-a4117/dqc_result.json
[2023-03-16 05:41:48,552] [INFO] DFAST_QC completed!
[2023-03-16 05:41:48,552] [INFO] Total running time: 0h0m26s