[2023-03-16 08:22:21,884] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:22:21,884] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:22:21,884] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ddeb7cc-5296-4cee-b544-d99c289cf421/dqc_reference
[2023-03-16 08:22:23,023] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:22:23,024] [INFO] Task started: Prodigal
[2023-03-16 08:22:23,024] [INFO] Running command: cat /var/lib/cwl/stg8be5deb1-07a7-4131-b37e-98fee6eafec8/OceanDNA-b15892.fa | prodigal -d OceanDNA-b15892/cds.fna -a OceanDNA-b15892/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:22:28,431] [INFO] Task succeeded: Prodigal
[2023-03-16 08:22:28,431] [INFO] Task started: HMMsearch
[2023-03-16 08:22:28,431] [INFO] Running command: hmmsearch --tblout OceanDNA-b15892/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ddeb7cc-5296-4cee-b544-d99c289cf421/dqc_reference/reference_markers.hmm OceanDNA-b15892/protein.faa > /dev/null
[2023-03-16 08:22:28,591] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:22:28,591] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8be5deb1-07a7-4131-b37e-98fee6eafec8/OceanDNA-b15892.fa]
[2023-03-16 08:22:28,603] [INFO] Query marker FASTA was written to OceanDNA-b15892/markers.fasta
[2023-03-16 08:22:28,604] [INFO] Task started: Blastn
[2023-03-16 08:22:28,604] [INFO] Running command: blastn -query OceanDNA-b15892/markers.fasta -db /var/lib/cwl/stg9ddeb7cc-5296-4cee-b544-d99c289cf421/dqc_reference/reference_markers.fasta -out OceanDNA-b15892/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:29,158] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:29,161] [INFO] Selected 11 target genomes.
[2023-03-16 08:22:29,161] [INFO] Target genome list was writen to OceanDNA-b15892/target_genomes.txt
[2023-03-16 08:22:29,168] [INFO] Task started: fastANI
[2023-03-16 08:22:29,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg8be5deb1-07a7-4131-b37e-98fee6eafec8/OceanDNA-b15892.fa --refList OceanDNA-b15892/target_genomes.txt --output OceanDNA-b15892/fastani_result.tsv --threads 1
[2023-03-16 08:22:34,414] [INFO] Task succeeded: fastANI
[2023-03-16 08:22:34,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ddeb7cc-5296-4cee-b544-d99c289cf421/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:22:34,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ddeb7cc-5296-4cee-b544-d99c289cf421/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:22:34,415] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:22:34,415] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:22:34,415] [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
--------------------------------------------------------------------------------
[2023-03-16 08:22:34,416] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15892/tc_result.tsv
[2023-03-16 08:22:34,419] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:22:34,419] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:22:34,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ddeb7cc-5296-4cee-b544-d99c289cf421/dqc_reference/checkm_data
[2023-03-16 08:22:34,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:22:34,426] [INFO] Task started: CheckM
[2023-03-16 08:22:34,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15892/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15892/checkm_input OceanDNA-b15892/checkm_result
[2023-03-16 08:22:53,715] [INFO] Task succeeded: CheckM
[2023-03-16 08:22:53,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.36%
Contamintation: 2.43%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:22:53,724] [INFO] ===== Completeness check finished =====
[2023-03-16 08:22:53,724] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:22:53,725] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15892/markers.fasta)
[2023-03-16 08:22:53,726] [INFO] Task started: Blastn
[2023-03-16 08:22:53,726] [INFO] Running command: blastn -query OceanDNA-b15892/markers.fasta -db /var/lib/cwl/stg9ddeb7cc-5296-4cee-b544-d99c289cf421/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15892/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:54,444] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:54,448] [INFO] Selected 14 target genomes.
[2023-03-16 08:22:54,448] [INFO] Target genome list was writen to OceanDNA-b15892/target_genomes_gtdb.txt
[2023-03-16 08:22:54,491] [INFO] Task started: fastANI
[2023-03-16 08:22:54,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg8be5deb1-07a7-4131-b37e-98fee6eafec8/OceanDNA-b15892.fa --refList OceanDNA-b15892/target_genomes_gtdb.txt --output OceanDNA-b15892/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:23:01,121] [INFO] Task succeeded: fastANI
[2023-03-16 08:23:01,123] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:23:01,123] [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_002450835.1	s__UBA6926 sp002450835	82.4722	203	336	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA6926;f__UBA6926;g__UBA6926	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:23:01,123] [INFO] GTDB search result was written to OceanDNA-b15892/result_gtdb.tsv
[2023-03-16 08:23:01,124] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:23:01,124] [INFO] DFAST_QC result json was written to OceanDNA-b15892/dqc_result.json
[2023-03-16 08:23:01,125] [INFO] DFAST_QC completed!
[2023-03-16 08:23:01,125] [INFO] Total running time: 0h0m39s