[2023-03-18 08:36:16,018] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,018] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,018] [INFO] DQC Reference Directory: /var/lib/cwl/stg3edbb5dd-90b5-4230-81cd-f999a5be05a6/dqc_reference
[2023-03-18 08:36:17,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,827] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,827] [INFO] Running command: cat /var/lib/cwl/stgaa95e31e-02c4-40a9-a1f9-69eebe3ac2e5/OceanDNA-b12694.fa | prodigal -d OceanDNA-b12694/cds.fna -a OceanDNA-b12694/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:29,673] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:29,673] [INFO] Task started: HMMsearch
[2023-03-18 08:36:29,673] [INFO] Running command: hmmsearch --tblout OceanDNA-b12694/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3edbb5dd-90b5-4230-81cd-f999a5be05a6/dqc_reference/reference_markers.hmm OceanDNA-b12694/protein.faa > /dev/null
[2023-03-18 08:36:29,877] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:29,877] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaa95e31e-02c4-40a9-a1f9-69eebe3ac2e5/OceanDNA-b12694.fa]
[2023-03-18 08:36:29,898] [INFO] Query marker FASTA was written to OceanDNA-b12694/markers.fasta
[2023-03-18 08:36:29,899] [INFO] Task started: Blastn
[2023-03-18 08:36:29,899] [INFO] Running command: blastn -query OceanDNA-b12694/markers.fasta -db /var/lib/cwl/stg3edbb5dd-90b5-4230-81cd-f999a5be05a6/dqc_reference/reference_markers.fasta -out OceanDNA-b12694/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:30,397] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:30,398] [INFO] Selected 20 target genomes.
[2023-03-18 08:36:30,398] [INFO] Target genome list was writen to OceanDNA-b12694/target_genomes.txt
[2023-03-18 08:36:30,452] [INFO] Task started: fastANI
[2023-03-18 08:36:30,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa95e31e-02c4-40a9-a1f9-69eebe3ac2e5/OceanDNA-b12694.fa --refList OceanDNA-b12694/target_genomes.txt --output OceanDNA-b12694/fastani_result.tsv --threads 1
[2023-03-18 08:36:42,806] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:42,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3edbb5dd-90b5-4230-81cd-f999a5be05a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:42,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3edbb5dd-90b5-4230-81cd-f999a5be05a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:42,806] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:42,807] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:36:42,807] [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
--------------------------------------------------------------------------------
[2023-03-18 08:36:42,807] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12694/tc_result.tsv
[2023-03-18 08:36:42,807] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:42,807] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:42,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3edbb5dd-90b5-4230-81cd-f999a5be05a6/dqc_reference/checkm_data
[2023-03-18 08:36:42,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:42,814] [INFO] Task started: CheckM
[2023-03-18 08:36:42,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12694/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12694/checkm_input OceanDNA-b12694/checkm_result
[2023-03-18 08:37:16,504] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:16,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.94%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:16,508] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:16,508] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:16,508] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12694/markers.fasta)
[2023-03-18 08:37:16,509] [INFO] Task started: Blastn
[2023-03-18 08:37:16,509] [INFO] Running command: blastn -query OceanDNA-b12694/markers.fasta -db /var/lib/cwl/stg3edbb5dd-90b5-4230-81cd-f999a5be05a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12694/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:17,179] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:17,186] [INFO] Selected 29 target genomes.
[2023-03-18 08:37:17,186] [INFO] Target genome list was writen to OceanDNA-b12694/target_genomes_gtdb.txt
[2023-03-18 08:37:17,207] [INFO] Task started: fastANI
[2023-03-18 08:37:17,207] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa95e31e-02c4-40a9-a1f9-69eebe3ac2e5/OceanDNA-b12694.fa --refList OceanDNA-b12694/target_genomes_gtdb.txt --output OceanDNA-b12694/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:30,702] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:30,702] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:37:30,702] [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
--------------------------------------------------------------------------------
[2023-03-18 08:37:30,703] [INFO] GTDB search result was written to OceanDNA-b12694/result_gtdb.tsv
[2023-03-18 08:37:30,704] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:30,705] [INFO] DFAST_QC result json was written to OceanDNA-b12694/dqc_result.json
[2023-03-18 08:37:30,705] [INFO] DFAST_QC completed!
[2023-03-18 08:37:30,705] [INFO] Total running time: 0h1m15s