[2023-03-15 13:20:51,549] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,549] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e2fb0cf-61be-4882-9344-3ec3abe1765f/dqc_reference
[2023-03-15 13:20:52,679] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,679] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,679] [INFO] Running command: cat /var/lib/cwl/stg9275017f-4a90-4442-ac21-9d9248cb945d/OceanDNA-b26066.fa | prodigal -d OceanDNA-b26066/cds.fna -a OceanDNA-b26066/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:20:56,489] [INFO] Task succeeded: Prodigal
[2023-03-15 13:20:56,489] [INFO] Task started: HMMsearch
[2023-03-15 13:20:56,489] [INFO] Running command: hmmsearch --tblout OceanDNA-b26066/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e2fb0cf-61be-4882-9344-3ec3abe1765f/dqc_reference/reference_markers.hmm OceanDNA-b26066/protein.faa > /dev/null
[2023-03-15 13:20:56,725] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:20:56,726] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9275017f-4a90-4442-ac21-9d9248cb945d/OceanDNA-b26066.fa]
[2023-03-15 13:20:56,739] [INFO] Query marker FASTA was written to OceanDNA-b26066/markers.fasta
[2023-03-15 13:20:56,741] [INFO] Task started: Blastn
[2023-03-15 13:20:56,742] [INFO] Running command: blastn -query OceanDNA-b26066/markers.fasta -db /var/lib/cwl/stg6e2fb0cf-61be-4882-9344-3ec3abe1765f/dqc_reference/reference_markers.fasta -out OceanDNA-b26066/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:20:57,402] [INFO] Task succeeded: Blastn
[2023-03-15 13:20:57,403] [INFO] Selected 20 target genomes.
[2023-03-15 13:20:57,404] [INFO] Target genome list was writen to OceanDNA-b26066/target_genomes.txt
[2023-03-15 13:20:57,419] [INFO] Task started: fastANI
[2023-03-15 13:20:57,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg9275017f-4a90-4442-ac21-9d9248cb945d/OceanDNA-b26066.fa --refList OceanDNA-b26066/target_genomes.txt --output OceanDNA-b26066/fastani_result.tsv --threads 1
[2023-03-15 13:21:06,599] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:06,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e2fb0cf-61be-4882-9344-3ec3abe1765f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:06,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e2fb0cf-61be-4882-9344-3ec3abe1765f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:06,599] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:06,599] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:21:06,600] [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 13:21:06,600] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26066/tc_result.tsv
[2023-03-15 13:21:06,601] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:06,601] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:06,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e2fb0cf-61be-4882-9344-3ec3abe1765f/dqc_reference/checkm_data
[2023-03-15 13:21:06,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:06,607] [INFO] Task started: CheckM
[2023-03-15 13:21:06,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26066/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26066/checkm_input OceanDNA-b26066/checkm_result
[2023-03-15 13:21:24,570] [INFO] Task succeeded: CheckM
[2023-03-15 13:21:24,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.88%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:21:24,573] [INFO] ===== Completeness check finished =====
[2023-03-15 13:21:24,573] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:21:24,573] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26066/markers.fasta)
[2023-03-15 13:21:24,574] [INFO] Task started: Blastn
[2023-03-15 13:21:24,575] [INFO] Running command: blastn -query OceanDNA-b26066/markers.fasta -db /var/lib/cwl/stg6e2fb0cf-61be-4882-9344-3ec3abe1765f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26066/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:25,646] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:25,648] [INFO] Selected 30 target genomes.
[2023-03-15 13:21:25,648] [INFO] Target genome list was writen to OceanDNA-b26066/target_genomes_gtdb.txt
[2023-03-15 13:21:25,687] [INFO] Task started: fastANI
[2023-03-15 13:21:25,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg9275017f-4a90-4442-ac21-9d9248cb945d/OceanDNA-b26066.fa --refList OceanDNA-b26066/target_genomes_gtdb.txt --output OceanDNA-b26066/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:21:32,622] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:32,622] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:21:32,622] [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 13:21:32,623] [INFO] GTDB search result was written to OceanDNA-b26066/result_gtdb.tsv
[2023-03-15 13:21:32,623] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:21:32,624] [INFO] DFAST_QC result json was written to OceanDNA-b26066/dqc_result.json
[2023-03-15 13:21:32,624] [INFO] DFAST_QC completed!
[2023-03-15 13:21:32,624] [INFO] Total running time: 0h0m41s