[2023-03-18 09:41:09,190] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:09,190] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:09,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c198d2e-12da-4e80-a93d-7fc029be2057/dqc_reference
[2023-03-18 09:41:10,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:10,359] [INFO] Task started: Prodigal
[2023-03-18 09:41:10,359] [INFO] Running command: cat /var/lib/cwl/stg65c4589b-f44a-427c-9005-e2cf270a7a63/OceanDNA-b13299.fa | prodigal -d OceanDNA-b13299/cds.fna -a OceanDNA-b13299/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:21,625] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:21,626] [INFO] Task started: HMMsearch
[2023-03-18 09:41:21,626] [INFO] Running command: hmmsearch --tblout OceanDNA-b13299/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c198d2e-12da-4e80-a93d-7fc029be2057/dqc_reference/reference_markers.hmm OceanDNA-b13299/protein.faa > /dev/null
[2023-03-18 09:41:21,790] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:21,791] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg65c4589b-f44a-427c-9005-e2cf270a7a63/OceanDNA-b13299.fa]
[2023-03-18 09:41:21,806] [INFO] Query marker FASTA was written to OceanDNA-b13299/markers.fasta
[2023-03-18 09:41:21,806] [INFO] Task started: Blastn
[2023-03-18 09:41:21,806] [INFO] Running command: blastn -query OceanDNA-b13299/markers.fasta -db /var/lib/cwl/stg9c198d2e-12da-4e80-a93d-7fc029be2057/dqc_reference/reference_markers.fasta -out OceanDNA-b13299/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:22,360] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:22,361] [INFO] Selected 20 target genomes.
[2023-03-18 09:41:22,361] [INFO] Target genome list was writen to OceanDNA-b13299/target_genomes.txt
[2023-03-18 09:41:22,378] [INFO] Task started: fastANI
[2023-03-18 09:41:22,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c4589b-f44a-427c-9005-e2cf270a7a63/OceanDNA-b13299.fa --refList OceanDNA-b13299/target_genomes.txt --output OceanDNA-b13299/fastani_result.tsv --threads 1
[2023-03-18 09:41:34,342] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:34,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c198d2e-12da-4e80-a93d-7fc029be2057/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:34,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c198d2e-12da-4e80-a93d-7fc029be2057/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:34,343] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:34,343] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:34,343] [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 09:41:34,343] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13299/tc_result.tsv
[2023-03-18 09:41:34,344] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:34,344] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:34,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c198d2e-12da-4e80-a93d-7fc029be2057/dqc_reference/checkm_data
[2023-03-18 09:41:34,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:34,355] [INFO] Task started: CheckM
[2023-03-18 09:41:34,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13299/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13299/checkm_input OceanDNA-b13299/checkm_result
[2023-03-18 09:42:06,370] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:06,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:06,373] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:06,374] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:06,374] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13299/markers.fasta)
[2023-03-18 09:42:06,374] [INFO] Task started: Blastn
[2023-03-18 09:42:06,374] [INFO] Running command: blastn -query OceanDNA-b13299/markers.fasta -db /var/lib/cwl/stg9c198d2e-12da-4e80-a93d-7fc029be2057/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13299/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:07,134] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:07,135] [INFO] Selected 25 target genomes.
[2023-03-18 09:42:07,135] [INFO] Target genome list was writen to OceanDNA-b13299/target_genomes_gtdb.txt
[2023-03-18 09:42:07,185] [INFO] Task started: fastANI
[2023-03-18 09:42:07,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c4589b-f44a-427c-9005-e2cf270a7a63/OceanDNA-b13299.fa --refList OceanDNA-b13299/target_genomes_gtdb.txt --output OceanDNA-b13299/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:21,161] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:21,162] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:42:21,162] [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 09:42:21,162] [INFO] GTDB search result was written to OceanDNA-b13299/result_gtdb.tsv
[2023-03-18 09:42:21,162] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:21,162] [INFO] DFAST_QC result json was written to OceanDNA-b13299/dqc_result.json
[2023-03-18 09:42:21,163] [INFO] DFAST_QC completed!
[2023-03-18 09:42:21,163] [INFO] Total running time: 0h1m12s