[2023-03-15 03:48:48,712] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:48:48,712] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:48:48,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg96068e2c-ff0a-432b-9277-dadce095e91e/dqc_reference
[2023-03-15 03:48:49,803] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:48:49,804] [INFO] Task started: Prodigal
[2023-03-15 03:48:49,804] [INFO] Running command: cat /var/lib/cwl/stgcd07595d-dc6e-4c7a-a32a-32605d506ef7/OceanDNA-b36040.fa | prodigal -d OceanDNA-b36040/cds.fna -a OceanDNA-b36040/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:48:59,196] [INFO] Task succeeded: Prodigal
[2023-03-15 03:48:59,196] [INFO] Task started: HMMsearch
[2023-03-15 03:48:59,196] [INFO] Running command: hmmsearch --tblout OceanDNA-b36040/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96068e2c-ff0a-432b-9277-dadce095e91e/dqc_reference/reference_markers.hmm OceanDNA-b36040/protein.faa > /dev/null
[2023-03-15 03:48:59,359] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:48:59,360] [INFO] Found 6/6 markers.
[2023-03-15 03:48:59,375] [INFO] Query marker FASTA was written to OceanDNA-b36040/markers.fasta
[2023-03-15 03:48:59,376] [INFO] Task started: Blastn
[2023-03-15 03:48:59,376] [INFO] Running command: blastn -query OceanDNA-b36040/markers.fasta -db /var/lib/cwl/stg96068e2c-ff0a-432b-9277-dadce095e91e/dqc_reference/reference_markers.fasta -out OceanDNA-b36040/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:48:59,961] [INFO] Task succeeded: Blastn
[2023-03-15 03:48:59,962] [INFO] Selected 24 target genomes.
[2023-03-15 03:48:59,962] [INFO] Target genome list was writen to OceanDNA-b36040/target_genomes.txt
[2023-03-15 03:48:59,975] [INFO] Task started: fastANI
[2023-03-15 03:48:59,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd07595d-dc6e-4c7a-a32a-32605d506ef7/OceanDNA-b36040.fa --refList OceanDNA-b36040/target_genomes.txt --output OceanDNA-b36040/fastani_result.tsv --threads 1
[2023-03-15 03:49:13,985] [INFO] Task succeeded: fastANI
[2023-03-15 03:49:13,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96068e2c-ff0a-432b-9277-dadce095e91e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:49:13,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96068e2c-ff0a-432b-9277-dadce095e91e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:49:13,986] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:49:13,986] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:49:13,986] [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 03:49:13,986] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36040/tc_result.tsv
[2023-03-15 03:49:13,986] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:49:13,986] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:49:13,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96068e2c-ff0a-432b-9277-dadce095e91e/dqc_reference/checkm_data
[2023-03-15 03:49:13,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:49:13,995] [INFO] Task started: CheckM
[2023-03-15 03:49:13,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36040/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36040/checkm_input OceanDNA-b36040/checkm_result
[2023-03-15 03:49:41,823] [INFO] Task succeeded: CheckM
[2023-03-15 03:49:41,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 03:49:41,827] [INFO] ===== Completeness check finished =====
[2023-03-15 03:49:41,827] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:49:41,827] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36040/markers.fasta)
[2023-03-15 03:49:41,829] [INFO] Task started: Blastn
[2023-03-15 03:49:41,829] [INFO] Running command: blastn -query OceanDNA-b36040/markers.fasta -db /var/lib/cwl/stg96068e2c-ff0a-432b-9277-dadce095e91e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36040/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:49:42,787] [INFO] Task succeeded: Blastn
[2023-03-15 03:49:42,788] [INFO] Selected 16 target genomes.
[2023-03-15 03:49:42,788] [INFO] Target genome list was writen to OceanDNA-b36040/target_genomes_gtdb.txt
[2023-03-15 03:49:42,801] [INFO] Task started: fastANI
[2023-03-15 03:49:42,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd07595d-dc6e-4c7a-a32a-32605d506ef7/OceanDNA-b36040.fa --refList OceanDNA-b36040/target_genomes_gtdb.txt --output OceanDNA-b36040/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:49:50,736] [INFO] Task succeeded: fastANI
[2023-03-15 03:49:50,739] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:49:50,739] [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_001901525.1	s__OPU3-GD-OMZ sp001901525	99.0327	449	563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__OPU3-GD-OMZ	95.0	98.79	96.80	0.86	0.78	19	conclusive
GCA_012965425.1	s__OPU3-GD-OMZ sp012965425	91.0018	510	563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__OPU3-GD-OMZ	95.0	99.81	99.76	0.91	0.86	6	-
GCA_012959905.1	s__OPU3-GD-OMZ sp012959905	83.7427	335	563	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__OPU3-GD-OMZ	95.0	99.80	99.80	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:49:50,739] [INFO] GTDB search result was written to OceanDNA-b36040/result_gtdb.tsv
[2023-03-15 03:49:50,739] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:49:50,740] [INFO] DFAST_QC result json was written to OceanDNA-b36040/dqc_result.json
[2023-03-15 03:49:50,740] [INFO] DFAST_QC completed!
[2023-03-15 03:49:50,740] [INFO] Total running time: 0h1m2s