[2023-03-15 12:33:51,724] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,724] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,724] [INFO] DQC Reference Directory: /var/lib/cwl/stgda9b303b-9c06-4f6c-b895-f0a233768ae1/dqc_reference
[2023-03-15 12:33:52,861] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,861] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,861] [INFO] Running command: cat /var/lib/cwl/stgee5c9b6b-faa5-4ab8-8115-7f4bc004d49a/OceanDNA-b37449.fa | prodigal -d OceanDNA-b37449/cds.fna -a OceanDNA-b37449/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:10,408] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:10,409] [INFO] Task started: HMMsearch
[2023-03-15 12:34:10,409] [INFO] Running command: hmmsearch --tblout OceanDNA-b37449/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda9b303b-9c06-4f6c-b895-f0a233768ae1/dqc_reference/reference_markers.hmm OceanDNA-b37449/protein.faa > /dev/null
[2023-03-15 12:34:10,616] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:10,617] [INFO] Found 6/6 markers.
[2023-03-15 12:34:10,638] [INFO] Query marker FASTA was written to OceanDNA-b37449/markers.fasta
[2023-03-15 12:34:10,639] [INFO] Task started: Blastn
[2023-03-15 12:34:10,639] [INFO] Running command: blastn -query OceanDNA-b37449/markers.fasta -db /var/lib/cwl/stgda9b303b-9c06-4f6c-b895-f0a233768ae1/dqc_reference/reference_markers.fasta -out OceanDNA-b37449/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:11,214] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:11,216] [INFO] Selected 24 target genomes.
[2023-03-15 12:34:11,216] [INFO] Target genome list was writen to OceanDNA-b37449/target_genomes.txt
[2023-03-15 12:34:11,230] [INFO] Task started: fastANI
[2023-03-15 12:34:11,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5c9b6b-faa5-4ab8-8115-7f4bc004d49a/OceanDNA-b37449.fa --refList OceanDNA-b37449/target_genomes.txt --output OceanDNA-b37449/fastani_result.tsv --threads 1
[2023-03-15 12:34:25,644] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:25,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda9b303b-9c06-4f6c-b895-f0a233768ae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:25,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda9b303b-9c06-4f6c-b895-f0a233768ae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:25,645] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:25,645] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:34:25,645] [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 12:34:25,646] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37449/tc_result.tsv
[2023-03-15 12:34:25,646] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:25,646] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:25,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda9b303b-9c06-4f6c-b895-f0a233768ae1/dqc_reference/checkm_data
[2023-03-15 12:34:25,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:25,655] [INFO] Task started: CheckM
[2023-03-15 12:34:25,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37449/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37449/checkm_input OceanDNA-b37449/checkm_result
[2023-03-15 12:35:11,926] [INFO] Task succeeded: CheckM
[2023-03-15 12:35:11,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:35:11,937] [INFO] ===== Completeness check finished =====
[2023-03-15 12:35:11,938] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:35:11,938] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37449/markers.fasta)
[2023-03-15 12:35:11,939] [INFO] Task started: Blastn
[2023-03-15 12:35:11,939] [INFO] Running command: blastn -query OceanDNA-b37449/markers.fasta -db /var/lib/cwl/stgda9b303b-9c06-4f6c-b895-f0a233768ae1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37449/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:35:12,903] [INFO] Task succeeded: Blastn
[2023-03-15 12:35:12,909] [INFO] Selected 27 target genomes.
[2023-03-15 12:35:12,909] [INFO] Target genome list was writen to OceanDNA-b37449/target_genomes_gtdb.txt
[2023-03-15 12:35:13,101] [INFO] Task started: fastANI
[2023-03-15 12:35:13,101] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5c9b6b-faa5-4ab8-8115-7f4bc004d49a/OceanDNA-b37449.fa --refList OceanDNA-b37449/target_genomes_gtdb.txt --output OceanDNA-b37449/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:35:26,850] [INFO] Task succeeded: fastANI
[2023-03-15 12:35:26,853] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:35:26,854] [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_002689445.1	s__UBA9926 sp002689445	99.7204	878	971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016779565.1	s__UBA9926 sp016779565	77.6564	73	971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647445.1	s__UBA9926 sp018647445	76.1907	67	971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.28	99.28	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-15 12:35:26,856] [INFO] GTDB search result was written to OceanDNA-b37449/result_gtdb.tsv
[2023-03-15 12:35:26,859] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:35:26,862] [INFO] DFAST_QC result json was written to OceanDNA-b37449/dqc_result.json
[2023-03-15 12:35:26,862] [INFO] DFAST_QC completed!
[2023-03-15 12:35:26,862] [INFO] Total running time: 0h1m35s