[2023-03-19 03:00:35,764] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:00:35,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:00:35,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg2710da61-963f-40bd-8410-345c06d6a486/dqc_reference
[2023-03-19 03:00:36,877] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:00:36,877] [INFO] Task started: Prodigal
[2023-03-19 03:00:36,877] [INFO] Running command: cat /var/lib/cwl/stg323d7f7e-8cbd-4a97-aa8e-31dce47d7ed6/OceanDNA-b45263.fa | prodigal -d OceanDNA-b45263/cds.fna -a OceanDNA-b45263/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:00:50,809] [INFO] Task succeeded: Prodigal
[2023-03-19 03:00:50,810] [INFO] Task started: HMMsearch
[2023-03-19 03:00:50,810] [INFO] Running command: hmmsearch --tblout OceanDNA-b45263/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2710da61-963f-40bd-8410-345c06d6a486/dqc_reference/reference_markers.hmm OceanDNA-b45263/protein.faa > /dev/null
[2023-03-19 03:00:50,979] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:00:50,979] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg323d7f7e-8cbd-4a97-aa8e-31dce47d7ed6/OceanDNA-b45263.fa]
[2023-03-19 03:00:51,005] [INFO] Query marker FASTA was written to OceanDNA-b45263/markers.fasta
[2023-03-19 03:00:51,006] [INFO] Task started: Blastn
[2023-03-19 03:00:51,006] [INFO] Running command: blastn -query OceanDNA-b45263/markers.fasta -db /var/lib/cwl/stg2710da61-963f-40bd-8410-345c06d6a486/dqc_reference/reference_markers.fasta -out OceanDNA-b45263/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:00:54,988] [INFO] Task succeeded: Blastn
[2023-03-19 03:00:54,990] [INFO] Selected 27 target genomes.
[2023-03-19 03:00:54,990] [INFO] Target genome list was writen to OceanDNA-b45263/target_genomes.txt
[2023-03-19 03:00:55,013] [INFO] Task started: fastANI
[2023-03-19 03:00:55,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg323d7f7e-8cbd-4a97-aa8e-31dce47d7ed6/OceanDNA-b45263.fa --refList OceanDNA-b45263/target_genomes.txt --output OceanDNA-b45263/fastani_result.tsv --threads 1
[2023-03-19 03:01:12,100] [INFO] Task succeeded: fastANI
[2023-03-19 03:01:12,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2710da61-963f-40bd-8410-345c06d6a486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:01:12,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2710da61-963f-40bd-8410-345c06d6a486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:01:12,100] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:01:12,100] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:01:12,101] [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
--------------------------------------------------------------------------------
[2023-03-19 03:01:12,102] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45263/tc_result.tsv
[2023-03-19 03:01:12,102] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:01:12,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:01:12,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2710da61-963f-40bd-8410-345c06d6a486/dqc_reference/checkm_data
[2023-03-19 03:01:12,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:01:12,110] [INFO] Task started: CheckM
[2023-03-19 03:01:12,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45263/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45263/checkm_input OceanDNA-b45263/checkm_result
[2023-03-19 03:01:49,942] [INFO] Task succeeded: CheckM
[2023-03-19 03:01:49,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:01:49,947] [INFO] ===== Completeness check finished =====
[2023-03-19 03:01:49,947] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:01:49,948] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45263/markers.fasta)
[2023-03-19 03:01:49,948] [INFO] Task started: Blastn
[2023-03-19 03:01:49,948] [INFO] Running command: blastn -query OceanDNA-b45263/markers.fasta -db /var/lib/cwl/stg2710da61-963f-40bd-8410-345c06d6a486/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45263/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:01:50,720] [INFO] Task succeeded: Blastn
[2023-03-19 03:01:50,721] [INFO] Selected 30 target genomes.
[2023-03-19 03:01:50,721] [INFO] Target genome list was writen to OceanDNA-b45263/target_genomes_gtdb.txt
[2023-03-19 03:01:50,747] [INFO] Task started: fastANI
[2023-03-19 03:01:50,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg323d7f7e-8cbd-4a97-aa8e-31dce47d7ed6/OceanDNA-b45263.fa --refList OceanDNA-b45263/target_genomes_gtdb.txt --output OceanDNA-b45263/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:02:08,517] [INFO] Task succeeded: fastANI
[2023-03-19 03:02:08,519] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:02:08,519] [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_016190025.1	s__JACPRG01 sp016190025	77.888	174	730	d__Bacteria;p__UBA8248;c__UBA8248;o__JACPRG01;f__JACPRG01;g__JACPRG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:02:08,521] [INFO] GTDB search result was written to OceanDNA-b45263/result_gtdb.tsv
[2023-03-19 03:02:08,521] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:02:08,523] [INFO] DFAST_QC result json was written to OceanDNA-b45263/dqc_result.json
[2023-03-19 03:02:08,523] [INFO] DFAST_QC completed!
[2023-03-19 03:02:08,523] [INFO] Total running time: 0h1m33s