[2023-03-18 10:10:14,116] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:10:14,116] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:10:14,116] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa23fde0-0eb4-41a0-a004-2376b3c76504/dqc_reference
[2023-03-18 10:10:15,255] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:10:15,273] [INFO] Task started: Prodigal
[2023-03-18 10:10:15,273] [INFO] Running command: cat /var/lib/cwl/stge491d7e9-3ff9-4071-8a70-9f9eb766b3df/OceanDNA-b31353.fa | prodigal -d OceanDNA-b31353/cds.fna -a OceanDNA-b31353/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:10:22,568] [INFO] Task succeeded: Prodigal
[2023-03-18 10:10:22,568] [INFO] Task started: HMMsearch
[2023-03-18 10:10:22,568] [INFO] Running command: hmmsearch --tblout OceanDNA-b31353/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa23fde0-0eb4-41a0-a004-2376b3c76504/dqc_reference/reference_markers.hmm OceanDNA-b31353/protein.faa > /dev/null
[2023-03-18 10:10:22,758] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:10:22,759] [INFO] Found 6/6 markers.
[2023-03-18 10:10:22,770] [INFO] Query marker FASTA was written to OceanDNA-b31353/markers.fasta
[2023-03-18 10:10:22,772] [INFO] Task started: Blastn
[2023-03-18 10:10:22,772] [INFO] Running command: blastn -query OceanDNA-b31353/markers.fasta -db /var/lib/cwl/stgfa23fde0-0eb4-41a0-a004-2376b3c76504/dqc_reference/reference_markers.fasta -out OceanDNA-b31353/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:10:23,487] [INFO] Task succeeded: Blastn
[2023-03-18 10:10:23,489] [INFO] Selected 21 target genomes.
[2023-03-18 10:10:23,489] [INFO] Target genome list was writen to OceanDNA-b31353/target_genomes.txt
[2023-03-18 10:10:23,566] [INFO] Task started: fastANI
[2023-03-18 10:10:23,566] [INFO] Running command: fastANI --query /var/lib/cwl/stge491d7e9-3ff9-4071-8a70-9f9eb766b3df/OceanDNA-b31353.fa --refList OceanDNA-b31353/target_genomes.txt --output OceanDNA-b31353/fastani_result.tsv --threads 1
[2023-03-18 10:10:32,044] [INFO] Task succeeded: fastANI
[2023-03-18 10:10:32,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa23fde0-0eb4-41a0-a004-2376b3c76504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:10:32,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa23fde0-0eb4-41a0-a004-2376b3c76504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:10:32,045] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:10:32,045] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:10:32,045] [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 10:10:32,046] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31353/tc_result.tsv
[2023-03-18 10:10:32,047] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:10:32,047] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:10:32,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa23fde0-0eb4-41a0-a004-2376b3c76504/dqc_reference/checkm_data
[2023-03-18 10:10:32,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:10:32,149] [INFO] Task started: CheckM
[2023-03-18 10:10:32,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31353/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31353/checkm_input OceanDNA-b31353/checkm_result
[2023-03-18 10:10:58,872] [INFO] Task succeeded: CheckM
[2023-03-18 10:10:58,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:10:58,875] [INFO] ===== Completeness check finished =====
[2023-03-18 10:10:58,875] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:10:58,875] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31353/markers.fasta)
[2023-03-18 10:10:58,877] [INFO] Task started: Blastn
[2023-03-18 10:10:58,877] [INFO] Running command: blastn -query OceanDNA-b31353/markers.fasta -db /var/lib/cwl/stgfa23fde0-0eb4-41a0-a004-2376b3c76504/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31353/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:11:00,050] [INFO] Task succeeded: Blastn
[2023-03-18 10:11:00,053] [INFO] Selected 19 target genomes.
[2023-03-18 10:11:00,053] [INFO] Target genome list was writen to OceanDNA-b31353/target_genomes_gtdb.txt
[2023-03-18 10:11:00,068] [INFO] Task started: fastANI
[2023-03-18 10:11:00,068] [INFO] Running command: fastANI --query /var/lib/cwl/stge491d7e9-3ff9-4071-8a70-9f9eb766b3df/OceanDNA-b31353.fa --refList OceanDNA-b31353/target_genomes_gtdb.txt --output OceanDNA-b31353/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:11:04,640] [INFO] Task succeeded: fastANI
[2023-03-18 10:11:04,642] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:11:04,642] [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_905478165.1	s__CAJQHK01 sp905478165	99.7656	356	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__UBA1997;g__CAJQHK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 10:11:04,643] [INFO] GTDB search result was written to OceanDNA-b31353/result_gtdb.tsv
[2023-03-18 10:11:04,643] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:11:04,644] [INFO] DFAST_QC result json was written to OceanDNA-b31353/dqc_result.json
[2023-03-18 10:11:04,644] [INFO] DFAST_QC completed!
[2023-03-18 10:11:04,645] [INFO] Total running time: 0h0m51s