[2023-03-15 23:42:29,663] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,663] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,663] [INFO] DQC Reference Directory: /var/lib/cwl/stgb28d9609-9af1-4564-b7cc-a170108c8e4f/dqc_reference
[2023-03-15 23:42:31,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,275] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,276] [INFO] Running command: cat /var/lib/cwl/stgac03e32c-919a-4eca-a5bb-80cf25da1ade/OceanDNA-b36266.fa | prodigal -d OceanDNA-b36266/cds.fna -a OceanDNA-b36266/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:39,315] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:39,315] [INFO] Task started: HMMsearch
[2023-03-15 23:42:39,315] [INFO] Running command: hmmsearch --tblout OceanDNA-b36266/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb28d9609-9af1-4564-b7cc-a170108c8e4f/dqc_reference/reference_markers.hmm OceanDNA-b36266/protein.faa > /dev/null
[2023-03-15 23:42:39,482] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:39,483] [INFO] Found 6/6 markers.
[2023-03-15 23:42:39,495] [INFO] Query marker FASTA was written to OceanDNA-b36266/markers.fasta
[2023-03-15 23:42:39,496] [INFO] Task started: Blastn
[2023-03-15 23:42:39,496] [INFO] Running command: blastn -query OceanDNA-b36266/markers.fasta -db /var/lib/cwl/stgb28d9609-9af1-4564-b7cc-a170108c8e4f/dqc_reference/reference_markers.fasta -out OceanDNA-b36266/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:40,067] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:40,067] [INFO] Selected 27 target genomes.
[2023-03-15 23:42:40,068] [INFO] Target genome list was writen to OceanDNA-b36266/target_genomes.txt
[2023-03-15 23:42:40,085] [INFO] Task started: fastANI
[2023-03-15 23:42:40,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgac03e32c-919a-4eca-a5bb-80cf25da1ade/OceanDNA-b36266.fa --refList OceanDNA-b36266/target_genomes.txt --output OceanDNA-b36266/fastani_result.tsv --threads 1
[2023-03-15 23:42:53,449] [INFO] Task succeeded: fastANI
[2023-03-15 23:42:53,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb28d9609-9af1-4564-b7cc-a170108c8e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:42:53,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb28d9609-9af1-4564-b7cc-a170108c8e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:42:53,452] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:42:53,453] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:42:53,453] [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
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	76.2235	52	486	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:42:53,453] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36266/tc_result.tsv
[2023-03-15 23:42:53,453] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:42:53,453] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:42:53,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb28d9609-9af1-4564-b7cc-a170108c8e4f/dqc_reference/checkm_data
[2023-03-15 23:42:53,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:42:53,457] [INFO] Task started: CheckM
[2023-03-15 23:42:53,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36266/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36266/checkm_input OceanDNA-b36266/checkm_result
[2023-03-15 23:43:18,623] [INFO] Task succeeded: CheckM
[2023-03-15 23:43:18,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.46%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:43:18,626] [INFO] ===== Completeness check finished =====
[2023-03-15 23:43:18,626] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:43:18,626] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36266/markers.fasta)
[2023-03-15 23:43:18,626] [INFO] Task started: Blastn
[2023-03-15 23:43:18,626] [INFO] Running command: blastn -query OceanDNA-b36266/markers.fasta -db /var/lib/cwl/stgb28d9609-9af1-4564-b7cc-a170108c8e4f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36266/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:43:19,579] [INFO] Task succeeded: Blastn
[2023-03-15 23:43:19,579] [INFO] Selected 14 target genomes.
[2023-03-15 23:43:19,580] [INFO] Target genome list was writen to OceanDNA-b36266/target_genomes_gtdb.txt
[2023-03-15 23:43:19,591] [INFO] Task started: fastANI
[2023-03-15 23:43:19,591] [INFO] Running command: fastANI --query /var/lib/cwl/stgac03e32c-919a-4eca-a5bb-80cf25da1ade/OceanDNA-b36266.fa --refList OceanDNA-b36266/target_genomes_gtdb.txt --output OceanDNA-b36266/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:43:24,860] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:24,867] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:43:24,867] [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_905479985.1	s__GCA-002733105 sp905479985	79.2887	271	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018646825.1	s__GCA-002733105 sp018646825	79.0249	226	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479075.1	s__GCA-002733105 sp905479075	77.9277	108	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181885.1	s__GCA-002733105 sp905181885	76.9415	84	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215775.1	s__GCA-002733105 sp013215775	76.7868	71	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163115.1	s__41-12-T18 sp002163115	76.7477	78	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215825.1	s__GCA-002733105 sp013215825	76.5053	69	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859375.1	s__GCA-002733105 sp014859375	76.4792	72	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003645385.1	s__GCA-002733105 sp003645385	76.4206	55	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	98.88	98.88	0.61	0.61	2	-
GCA_002733105.1	s__GCA-002733105 sp002733105	76.3293	63	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163085.1	s__41-12-T18 sp002163085	76.2187	72	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002402245.1	s__GCA-002733105 sp002402245	76.1355	73	486	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:43:24,868] [INFO] GTDB search result was written to OceanDNA-b36266/result_gtdb.tsv
[2023-03-15 23:43:24,868] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:43:24,869] [INFO] DFAST_QC result json was written to OceanDNA-b36266/dqc_result.json
[2023-03-15 23:43:24,869] [INFO] DFAST_QC completed!
[2023-03-15 23:43:24,869] [INFO] Total running time: 0h0m55s