[2023-03-15 23:15:05,778] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:15:05,779] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:15:05,779] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4aaeef4-031f-493c-b83e-5067a2e83467/dqc_reference
[2023-03-15 23:15:07,541] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:15:07,541] [INFO] Task started: Prodigal
[2023-03-15 23:15:07,541] [INFO] Running command: cat /var/lib/cwl/stg279e4526-2d84-4afc-a171-5ceb902812de/OceanDNA-b13794.fa | prodigal -d OceanDNA-b13794/cds.fna -a OceanDNA-b13794/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:15:14,195] [INFO] Task succeeded: Prodigal
[2023-03-15 23:15:14,195] [INFO] Task started: HMMsearch
[2023-03-15 23:15:14,195] [INFO] Running command: hmmsearch --tblout OceanDNA-b13794/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4aaeef4-031f-493c-b83e-5067a2e83467/dqc_reference/reference_markers.hmm OceanDNA-b13794/protein.faa > /dev/null
[2023-03-15 23:15:14,346] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:15:14,346] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg279e4526-2d84-4afc-a171-5ceb902812de/OceanDNA-b13794.fa]
[2023-03-15 23:15:14,360] [INFO] Query marker FASTA was written to OceanDNA-b13794/markers.fasta
[2023-03-15 23:15:14,360] [INFO] Task started: Blastn
[2023-03-15 23:15:14,360] [INFO] Running command: blastn -query OceanDNA-b13794/markers.fasta -db /var/lib/cwl/stgb4aaeef4-031f-493c-b83e-5067a2e83467/dqc_reference/reference_markers.fasta -out OceanDNA-b13794/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:15,732] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:15,733] [INFO] Selected 8 target genomes.
[2023-03-15 23:15:15,733] [INFO] Target genome list was writen to OceanDNA-b13794/target_genomes.txt
[2023-03-15 23:15:15,740] [INFO] Task started: fastANI
[2023-03-15 23:15:15,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg279e4526-2d84-4afc-a171-5ceb902812de/OceanDNA-b13794.fa --refList OceanDNA-b13794/target_genomes.txt --output OceanDNA-b13794/fastani_result.tsv --threads 1
[2023-03-15 23:15:20,222] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:20,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4aaeef4-031f-493c-b83e-5067a2e83467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:15:20,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4aaeef4-031f-493c-b83e-5067a2e83467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:15:20,223] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:15:20,223] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:15:20,223] [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 23:15:20,223] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13794/tc_result.tsv
[2023-03-15 23:15:20,223] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:15:20,223] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:15:20,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4aaeef4-031f-493c-b83e-5067a2e83467/dqc_reference/checkm_data
[2023-03-15 23:15:20,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:15:20,232] [INFO] Task started: CheckM
[2023-03-15 23:15:20,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13794/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13794/checkm_input OceanDNA-b13794/checkm_result
[2023-03-15 23:15:42,368] [INFO] Task succeeded: CheckM
[2023-03-15 23:15:42,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.61%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:15:42,405] [INFO] ===== Completeness check finished =====
[2023-03-15 23:15:42,406] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:15:42,406] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13794/markers.fasta)
[2023-03-15 23:15:42,407] [INFO] Task started: Blastn
[2023-03-15 23:15:42,407] [INFO] Running command: blastn -query OceanDNA-b13794/markers.fasta -db /var/lib/cwl/stgb4aaeef4-031f-493c-b83e-5067a2e83467/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13794/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:42,833] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:42,836] [INFO] Selected 13 target genomes.
[2023-03-15 23:15:42,836] [INFO] Target genome list was writen to OceanDNA-b13794/target_genomes_gtdb.txt
[2023-03-15 23:15:42,923] [INFO] Task started: fastANI
[2023-03-15 23:15:42,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg279e4526-2d84-4afc-a171-5ceb902812de/OceanDNA-b13794.fa --refList OceanDNA-b13794/target_genomes_gtdb.txt --output OceanDNA-b13794/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:15:48,225] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:48,227] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:15:48,228] [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_009392195.1	s__OSU-TB39 sp009392195	83.9221	384	421	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__OSU-TB39;g__OSU-TB39	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:15:48,228] [INFO] GTDB search result was written to OceanDNA-b13794/result_gtdb.tsv
[2023-03-15 23:15:48,230] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:15:48,231] [INFO] DFAST_QC result json was written to OceanDNA-b13794/dqc_result.json
[2023-03-15 23:15:48,232] [INFO] DFAST_QC completed!
[2023-03-15 23:15:48,232] [INFO] Total running time: 0h0m42s