[2023-03-15 06:28:21,435] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg284f330f-c56a-4a05-99c0-983cbf60159b/dqc_reference
[2023-03-15 06:28:22,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,535] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,535] [INFO] Running command: cat /var/lib/cwl/stg878c08d8-1c8f-484d-8fdc-ecff11b659d5/OceanDNA-b39371.fa | prodigal -d OceanDNA-b39371/cds.fna -a OceanDNA-b39371/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:35,433] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:35,434] [INFO] Task started: HMMsearch
[2023-03-15 06:28:35,434] [INFO] Running command: hmmsearch --tblout OceanDNA-b39371/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg284f330f-c56a-4a05-99c0-983cbf60159b/dqc_reference/reference_markers.hmm OceanDNA-b39371/protein.faa > /dev/null
[2023-03-15 06:28:35,610] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:35,611] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg878c08d8-1c8f-484d-8fdc-ecff11b659d5/OceanDNA-b39371.fa]
[2023-03-15 06:28:35,627] [INFO] Query marker FASTA was written to OceanDNA-b39371/markers.fasta
[2023-03-15 06:28:35,628] [INFO] Task started: Blastn
[2023-03-15 06:28:35,628] [INFO] Running command: blastn -query OceanDNA-b39371/markers.fasta -db /var/lib/cwl/stg284f330f-c56a-4a05-99c0-983cbf60159b/dqc_reference/reference_markers.fasta -out OceanDNA-b39371/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:36,186] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:36,187] [INFO] Selected 28 target genomes.
[2023-03-15 06:28:36,187] [INFO] Target genome list was writen to OceanDNA-b39371/target_genomes.txt
[2023-03-15 06:28:36,201] [INFO] Task started: fastANI
[2023-03-15 06:28:36,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg878c08d8-1c8f-484d-8fdc-ecff11b659d5/OceanDNA-b39371.fa --refList OceanDNA-b39371/target_genomes.txt --output OceanDNA-b39371/fastani_result.tsv --threads 1
[2023-03-15 06:28:53,958] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:53,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg284f330f-c56a-4a05-99c0-983cbf60159b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:53,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg284f330f-c56a-4a05-99c0-983cbf60159b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:53,959] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:53,959] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:28:53,959] [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 06:28:53,959] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39371/tc_result.tsv
[2023-03-15 06:28:53,959] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:53,959] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:53,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg284f330f-c56a-4a05-99c0-983cbf60159b/dqc_reference/checkm_data
[2023-03-15 06:28:53,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:53,966] [INFO] Task started: CheckM
[2023-03-15 06:28:53,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39371/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39371/checkm_input OceanDNA-b39371/checkm_result
[2023-03-15 06:29:29,343] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:29,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:29,376] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:29,377] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:29,377] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39371/markers.fasta)
[2023-03-15 06:29:29,377] [INFO] Task started: Blastn
[2023-03-15 06:29:29,377] [INFO] Running command: blastn -query OceanDNA-b39371/markers.fasta -db /var/lib/cwl/stg284f330f-c56a-4a05-99c0-983cbf60159b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39371/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:30,164] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:30,183] [INFO] Selected 8 target genomes.
[2023-03-15 06:29:30,183] [INFO] Target genome list was writen to OceanDNA-b39371/target_genomes_gtdb.txt
[2023-03-15 06:29:30,188] [INFO] Task started: fastANI
[2023-03-15 06:29:30,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg878c08d8-1c8f-484d-8fdc-ecff11b659d5/OceanDNA-b39371.fa --refList OceanDNA-b39371/target_genomes_gtdb.txt --output OceanDNA-b39371/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:33,714] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:33,719] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 06:29:33,719] [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_905478975.1	s__HTCC2207 sp905478975	99.3206	547	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905478725.1	s__HTCC2207 sp905478725	85.3717	389	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000511875.1	s__HTCC2207 sp000511875	84.0545	547	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858295.1	s__HTCC2207 sp017858295	84.0308	392	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_000153445.1	s__HTCC2207 sp000153445	83.4787	562	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_017858135.1	s__HTCC2207 sp017858135	79.8602	388	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_018607545.1	s__HTCC2207 sp018607545	77.6298	131	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664075.1	s__HTCC2207 sp018664075	77.4512	165	748	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:33,729] [INFO] GTDB search result was written to OceanDNA-b39371/result_gtdb.tsv
[2023-03-15 06:29:33,729] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:33,730] [INFO] DFAST_QC result json was written to OceanDNA-b39371/dqc_result.json
[2023-03-15 06:29:33,730] [INFO] DFAST_QC completed!
[2023-03-15 06:29:33,730] [INFO] Total running time: 0h1m12s