[2023-03-19 01:38:53,854] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:38:53,855] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:38:53,855] [INFO] DQC Reference Directory: /var/lib/cwl/stgae539168-5668-4d63-88ea-573c85e699f0/dqc_reference
[2023-03-19 01:38:54,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:38:54,945] [INFO] Task started: Prodigal
[2023-03-19 01:38:54,945] [INFO] Running command: cat /var/lib/cwl/stg45287ac2-cb06-4d52-b6e4-94db60d4249e/OceanDNA-b15143.fa | prodigal -d OceanDNA-b15143/cds.fna -a OceanDNA-b15143/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:39:00,632] [INFO] Task succeeded: Prodigal
[2023-03-19 01:39:00,632] [INFO] Task started: HMMsearch
[2023-03-19 01:39:00,632] [INFO] Running command: hmmsearch --tblout OceanDNA-b15143/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae539168-5668-4d63-88ea-573c85e699f0/dqc_reference/reference_markers.hmm OceanDNA-b15143/protein.faa > /dev/null
[2023-03-19 01:39:00,770] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:39:00,771] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg45287ac2-cb06-4d52-b6e4-94db60d4249e/OceanDNA-b15143.fa]
[2023-03-19 01:39:00,784] [INFO] Query marker FASTA was written to OceanDNA-b15143/markers.fasta
[2023-03-19 01:39:00,784] [INFO] Task started: Blastn
[2023-03-19 01:39:00,785] [INFO] Running command: blastn -query OceanDNA-b15143/markers.fasta -db /var/lib/cwl/stgae539168-5668-4d63-88ea-573c85e699f0/dqc_reference/reference_markers.fasta -out OceanDNA-b15143/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:01,213] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:01,214] [INFO] Selected 16 target genomes.
[2023-03-19 01:39:01,214] [INFO] Target genome list was writen to OceanDNA-b15143/target_genomes.txt
[2023-03-19 01:39:01,224] [INFO] Task started: fastANI
[2023-03-19 01:39:01,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg45287ac2-cb06-4d52-b6e4-94db60d4249e/OceanDNA-b15143.fa --refList OceanDNA-b15143/target_genomes.txt --output OceanDNA-b15143/fastani_result.tsv --threads 1
[2023-03-19 01:39:14,044] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:14,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae539168-5668-4d63-88ea-573c85e699f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:39:14,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae539168-5668-4d63-88ea-573c85e699f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:39:14,044] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:39:14,045] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:39:14,045] [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 01:39:14,045] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15143/tc_result.tsv
[2023-03-19 01:39:14,045] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:39:14,045] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:39:14,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae539168-5668-4d63-88ea-573c85e699f0/dqc_reference/checkm_data
[2023-03-19 01:39:14,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:39:14,059] [INFO] Task started: CheckM
[2023-03-19 01:39:14,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15143/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15143/checkm_input OceanDNA-b15143/checkm_result
[2023-03-19 01:39:34,192] [INFO] Task succeeded: CheckM
[2023-03-19 01:39:34,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.03%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:39:34,285] [INFO] ===== Completeness check finished =====
[2023-03-19 01:39:34,286] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:39:34,286] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15143/markers.fasta)
[2023-03-19 01:39:34,286] [INFO] Task started: Blastn
[2023-03-19 01:39:34,287] [INFO] Running command: blastn -query OceanDNA-b15143/markers.fasta -db /var/lib/cwl/stgae539168-5668-4d63-88ea-573c85e699f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15143/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:34,733] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:34,735] [INFO] Selected 20 target genomes.
[2023-03-19 01:39:34,735] [INFO] Target genome list was writen to OceanDNA-b15143/target_genomes_gtdb.txt
[2023-03-19 01:39:34,807] [INFO] Task started: fastANI
[2023-03-19 01:39:34,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg45287ac2-cb06-4d52-b6e4-94db60d4249e/OceanDNA-b15143.fa --refList OceanDNA-b15143/target_genomes_gtdb.txt --output OceanDNA-b15143/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:39:46,386] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:46,386] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:39:46,386] [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 01:39:46,387] [INFO] GTDB search result was written to OceanDNA-b15143/result_gtdb.tsv
[2023-03-19 01:39:46,388] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:39:46,390] [INFO] DFAST_QC result json was written to OceanDNA-b15143/dqc_result.json
[2023-03-19 01:39:46,390] [INFO] DFAST_QC completed!
[2023-03-19 01:39:46,390] [INFO] Total running time: 0h0m53s