[2023-03-18 07:58:06,152] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:58:06,153] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:58:06,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d22353a-e635-437e-a796-0f889520810a/dqc_reference
[2023-03-18 07:58:07,253] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:58:07,253] [INFO] Task started: Prodigal
[2023-03-18 07:58:07,253] [INFO] Running command: cat /var/lib/cwl/stgb9bc2cc7-5943-4d7d-a1e0-30297e675e91/OceanDNA-b15188.fa | prodigal -d OceanDNA-b15188/cds.fna -a OceanDNA-b15188/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:58:12,713] [INFO] Task succeeded: Prodigal
[2023-03-18 07:58:12,713] [INFO] Task started: HMMsearch
[2023-03-18 07:58:12,714] [INFO] Running command: hmmsearch --tblout OceanDNA-b15188/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d22353a-e635-437e-a796-0f889520810a/dqc_reference/reference_markers.hmm OceanDNA-b15188/protein.faa > /dev/null
[2023-03-18 07:58:12,850] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:58:12,850] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9bc2cc7-5943-4d7d-a1e0-30297e675e91/OceanDNA-b15188.fa]
[2023-03-18 07:58:12,858] [INFO] Query marker FASTA was written to OceanDNA-b15188/markers.fasta
[2023-03-18 07:58:12,858] [INFO] Task started: Blastn
[2023-03-18 07:58:12,858] [INFO] Running command: blastn -query OceanDNA-b15188/markers.fasta -db /var/lib/cwl/stg1d22353a-e635-437e-a796-0f889520810a/dqc_reference/reference_markers.fasta -out OceanDNA-b15188/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:58:13,352] [INFO] Task succeeded: Blastn
[2023-03-18 07:58:13,353] [INFO] Selected 13 target genomes.
[2023-03-18 07:58:13,353] [INFO] Target genome list was writen to OceanDNA-b15188/target_genomes.txt
[2023-03-18 07:58:13,359] [INFO] Task started: fastANI
[2023-03-18 07:58:13,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9bc2cc7-5943-4d7d-a1e0-30297e675e91/OceanDNA-b15188.fa --refList OceanDNA-b15188/target_genomes.txt --output OceanDNA-b15188/fastani_result.tsv --threads 1
[2023-03-18 07:58:18,711] [INFO] Task succeeded: fastANI
[2023-03-18 07:58:18,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d22353a-e635-437e-a796-0f889520810a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:58:18,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d22353a-e635-437e-a796-0f889520810a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:58:18,711] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:58:18,711] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:58:18,711] [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
--------------------------------------------------------------------------------
[2023-03-18 07:58:18,712] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15188/tc_result.tsv
[2023-03-18 07:58:18,712] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:58:18,712] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:58:18,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d22353a-e635-437e-a796-0f889520810a/dqc_reference/checkm_data
[2023-03-18 07:58:18,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:58:18,717] [INFO] Task started: CheckM
[2023-03-18 07:58:18,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15188/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15188/checkm_input OceanDNA-b15188/checkm_result
[2023-03-18 07:58:37,626] [INFO] Task succeeded: CheckM
[2023-03-18 07:58:37,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:58:37,628] [INFO] ===== Completeness check finished =====
[2023-03-18 07:58:37,628] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:58:37,628] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15188/markers.fasta)
[2023-03-18 07:58:37,628] [INFO] Task started: Blastn
[2023-03-18 07:58:37,628] [INFO] Running command: blastn -query OceanDNA-b15188/markers.fasta -db /var/lib/cwl/stg1d22353a-e635-437e-a796-0f889520810a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15188/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:58:38,269] [INFO] Task succeeded: Blastn
[2023-03-18 07:58:38,269] [INFO] Selected 13 target genomes.
[2023-03-18 07:58:38,270] [INFO] Target genome list was writen to OceanDNA-b15188/target_genomes_gtdb.txt
[2023-03-18 07:58:38,285] [INFO] Task started: fastANI
[2023-03-18 07:58:38,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9bc2cc7-5943-4d7d-a1e0-30297e675e91/OceanDNA-b15188.fa --refList OceanDNA-b15188/target_genomes_gtdb.txt --output OceanDNA-b15188/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:58:41,369] [INFO] Task succeeded: fastANI
[2023-03-18 07:58:41,371] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:58:41,371] [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_003228125.1	s__GCA-002718395 sp003228125	99.84	309	355	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__GCA-002718395	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 07:58:41,371] [INFO] GTDB search result was written to OceanDNA-b15188/result_gtdb.tsv
[2023-03-18 07:58:41,371] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:58:41,371] [INFO] DFAST_QC result json was written to OceanDNA-b15188/dqc_result.json
[2023-03-18 07:58:41,371] [INFO] DFAST_QC completed!
[2023-03-18 07:58:41,371] [INFO] Total running time: 0h0m35s