[2023-03-15 13:39:34,883] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:39:34,890] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:39:34,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg7343020e-8e58-4d65-aa4b-2ce0cc7158f1/dqc_reference
[2023-03-15 13:39:37,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:39:37,047] [INFO] Task started: Prodigal
[2023-03-15 13:39:37,048] [INFO] Running command: cat /var/lib/cwl/stgd2a3111e-bd0c-4aca-8ffc-7d8b3421975e/OceanDNA-b21788.fa | prodigal -d OceanDNA-b21788/cds.fna -a OceanDNA-b21788/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:39:43,807] [INFO] Task succeeded: Prodigal
[2023-03-15 13:39:43,808] [INFO] Task started: HMMsearch
[2023-03-15 13:39:43,808] [INFO] Running command: hmmsearch --tblout OceanDNA-b21788/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7343020e-8e58-4d65-aa4b-2ce0cc7158f1/dqc_reference/reference_markers.hmm OceanDNA-b21788/protein.faa > /dev/null
[2023-03-15 13:39:43,960] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:39:43,961] [INFO] Found 6/6 markers.
[2023-03-15 13:39:44,030] [INFO] Query marker FASTA was written to OceanDNA-b21788/markers.fasta
[2023-03-15 13:39:44,030] [INFO] Task started: Blastn
[2023-03-15 13:39:44,030] [INFO] Running command: blastn -query OceanDNA-b21788/markers.fasta -db /var/lib/cwl/stg7343020e-8e58-4d65-aa4b-2ce0cc7158f1/dqc_reference/reference_markers.fasta -out OceanDNA-b21788/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:39:44,533] [INFO] Task succeeded: Blastn
[2023-03-15 13:39:44,557] [INFO] Selected 14 target genomes.
[2023-03-15 13:39:44,557] [INFO] Target genome list was writen to OceanDNA-b21788/target_genomes.txt
[2023-03-15 13:39:44,567] [INFO] Task started: fastANI
[2023-03-15 13:39:44,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2a3111e-bd0c-4aca-8ffc-7d8b3421975e/OceanDNA-b21788.fa --refList OceanDNA-b21788/target_genomes.txt --output OceanDNA-b21788/fastani_result.tsv --threads 1
[2023-03-15 13:39:54,723] [INFO] Task succeeded: fastANI
[2023-03-15 13:39:54,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7343020e-8e58-4d65-aa4b-2ce0cc7158f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:39:54,723] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7343020e-8e58-4d65-aa4b-2ce0cc7158f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:39:54,724] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:39:54,724] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:39:54,724] [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
--------------------------------------------------------------------------------
[2023-03-15 13:39:54,733] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21788/tc_result.tsv
[2023-03-15 13:39:54,749] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:39:54,750] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:39:54,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7343020e-8e58-4d65-aa4b-2ce0cc7158f1/dqc_reference/checkm_data
[2023-03-15 13:39:54,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:39:54,777] [INFO] Task started: CheckM
[2023-03-15 13:39:54,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21788/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21788/checkm_input OceanDNA-b21788/checkm_result
[2023-03-15 13:40:17,640] [INFO] Task succeeded: CheckM
[2023-03-15 13:40:17,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.44%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:40:17,813] [INFO] ===== Completeness check finished =====
[2023-03-15 13:40:17,813] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:40:17,813] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21788/markers.fasta)
[2023-03-15 13:40:17,814] [INFO] Task started: Blastn
[2023-03-15 13:40:17,815] [INFO] Running command: blastn -query OceanDNA-b21788/markers.fasta -db /var/lib/cwl/stg7343020e-8e58-4d65-aa4b-2ce0cc7158f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21788/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:40:18,503] [INFO] Task succeeded: Blastn
[2023-03-15 13:40:18,536] [INFO] Selected 25 target genomes.
[2023-03-15 13:40:18,536] [INFO] Target genome list was writen to OceanDNA-b21788/target_genomes_gtdb.txt
[2023-03-15 13:40:18,615] [INFO] Task started: fastANI
[2023-03-15 13:40:18,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2a3111e-bd0c-4aca-8ffc-7d8b3421975e/OceanDNA-b21788.fa --refList OceanDNA-b21788/target_genomes_gtdb.txt --output OceanDNA-b21788/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:40:25,184] [INFO] Task succeeded: fastANI
[2023-03-15 13:40:25,184] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:40:25,184] [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
--------------------------------------------------------------------------------
[2023-03-15 13:40:25,196] [INFO] GTDB search result was written to OceanDNA-b21788/result_gtdb.tsv
[2023-03-15 13:40:25,217] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:40:25,229] [INFO] DFAST_QC result json was written to OceanDNA-b21788/dqc_result.json
[2023-03-15 13:40:25,229] [INFO] DFAST_QC completed!
[2023-03-15 13:40:25,229] [INFO] Total running time: 0h0m50s