[2023-03-15 15:18:22,077] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,077] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f1d1845-0052-4237-a26c-351857afa6ff/dqc_reference
[2023-03-15 15:18:23,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,190] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,190] [INFO] Running command: cat /var/lib/cwl/stg2f3700cc-2f13-4908-acfd-8eac720fe33d/OceanDNA-b17049.fa | prodigal -d OceanDNA-b17049/cds.fna -a OceanDNA-b17049/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:29,213] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:29,214] [INFO] Task started: HMMsearch
[2023-03-15 15:18:29,214] [INFO] Running command: hmmsearch --tblout OceanDNA-b17049/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f1d1845-0052-4237-a26c-351857afa6ff/dqc_reference/reference_markers.hmm OceanDNA-b17049/protein.faa > /dev/null
[2023-03-15 15:18:29,399] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:29,400] [INFO] Found 6/6 markers.
[2023-03-15 15:18:29,421] [INFO] Query marker FASTA was written to OceanDNA-b17049/markers.fasta
[2023-03-15 15:18:29,422] [INFO] Task started: Blastn
[2023-03-15 15:18:29,422] [INFO] Running command: blastn -query OceanDNA-b17049/markers.fasta -db /var/lib/cwl/stg3f1d1845-0052-4237-a26c-351857afa6ff/dqc_reference/reference_markers.fasta -out OceanDNA-b17049/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:29,920] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:29,924] [INFO] Selected 8 target genomes.
[2023-03-15 15:18:29,924] [INFO] Target genome list was writen to OceanDNA-b17049/target_genomes.txt
[2023-03-15 15:18:29,931] [INFO] Task started: fastANI
[2023-03-15 15:18:29,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f3700cc-2f13-4908-acfd-8eac720fe33d/OceanDNA-b17049.fa --refList OceanDNA-b17049/target_genomes.txt --output OceanDNA-b17049/fastani_result.tsv --threads 1
[2023-03-15 15:18:32,750] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:32,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f1d1845-0052-4237-a26c-351857afa6ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:32,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f1d1845-0052-4237-a26c-351857afa6ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:32,751] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:18:32,751] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:18:32,751] [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 15:18:32,752] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17049/tc_result.tsv
[2023-03-15 15:18:32,756] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:32,756] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:32,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f1d1845-0052-4237-a26c-351857afa6ff/dqc_reference/checkm_data
[2023-03-15 15:18:32,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:32,787] [INFO] Task started: CheckM
[2023-03-15 15:18:32,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17049/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17049/checkm_input OceanDNA-b17049/checkm_result
[2023-03-15 15:18:53,546] [INFO] Task succeeded: CheckM
[2023-03-15 15:18:53,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:18:53,573] [INFO] ===== Completeness check finished =====
[2023-03-15 15:18:53,573] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:18:53,573] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17049/markers.fasta)
[2023-03-15 15:18:53,574] [INFO] Task started: Blastn
[2023-03-15 15:18:53,574] [INFO] Running command: blastn -query OceanDNA-b17049/markers.fasta -db /var/lib/cwl/stg3f1d1845-0052-4237-a26c-351857afa6ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17049/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:54,367] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:54,369] [INFO] Selected 17 target genomes.
[2023-03-15 15:18:54,369] [INFO] Target genome list was writen to OceanDNA-b17049/target_genomes_gtdb.txt
[2023-03-15 15:18:54,387] [INFO] Task started: fastANI
[2023-03-15 15:18:54,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f3700cc-2f13-4908-acfd-8eac720fe33d/OceanDNA-b17049.fa --refList OceanDNA-b17049/target_genomes_gtdb.txt --output OceanDNA-b17049/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:19:00,949] [INFO] Task succeeded: fastANI
[2023-03-15 15:19:00,951] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:19:00,951] [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
GCA_018647505.1	s__JABGSX01 sp018647505	99.8858	318	365	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__JABGSX01;g__JABGSX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-15 15:19:00,952] [INFO] GTDB search result was written to OceanDNA-b17049/result_gtdb.tsv
[2023-03-15 15:19:00,953] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:19:00,955] [INFO] DFAST_QC result json was written to OceanDNA-b17049/dqc_result.json
[2023-03-15 15:19:00,955] [INFO] DFAST_QC completed!
[2023-03-15 15:19:00,955] [INFO] Total running time: 0h0m39s