[2023-03-15 20:34:26,716] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,716] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,716] [INFO] DQC Reference Directory: /var/lib/cwl/stgb74bb124-61b1-4477-a090-6804310f2c86/dqc_reference
[2023-03-15 20:34:28,458] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,458] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,458] [INFO] Running command: cat /var/lib/cwl/stgae3294ec-ea8b-46fb-b635-b0ab1ffcf2f0/OceanDNA-b35980.fa | prodigal -d OceanDNA-b35980/cds.fna -a OceanDNA-b35980/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:39,612] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:39,612] [INFO] Task started: HMMsearch
[2023-03-15 20:34:39,612] [INFO] Running command: hmmsearch --tblout OceanDNA-b35980/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb74bb124-61b1-4477-a090-6804310f2c86/dqc_reference/reference_markers.hmm OceanDNA-b35980/protein.faa > /dev/null
[2023-03-15 20:34:39,790] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:39,791] [INFO] Found 6/6 markers.
[2023-03-15 20:34:39,805] [INFO] Query marker FASTA was written to OceanDNA-b35980/markers.fasta
[2023-03-15 20:34:39,805] [INFO] Task started: Blastn
[2023-03-15 20:34:39,805] [INFO] Running command: blastn -query OceanDNA-b35980/markers.fasta -db /var/lib/cwl/stgb74bb124-61b1-4477-a090-6804310f2c86/dqc_reference/reference_markers.fasta -out OceanDNA-b35980/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:40,325] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:40,326] [INFO] Selected 26 target genomes.
[2023-03-15 20:34:40,326] [INFO] Target genome list was writen to OceanDNA-b35980/target_genomes.txt
[2023-03-15 20:34:40,341] [INFO] Task started: fastANI
[2023-03-15 20:34:40,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgae3294ec-ea8b-46fb-b635-b0ab1ffcf2f0/OceanDNA-b35980.fa --refList OceanDNA-b35980/target_genomes.txt --output OceanDNA-b35980/fastani_result.tsv --threads 1
[2023-03-15 20:34:55,650] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:55,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb74bb124-61b1-4477-a090-6804310f2c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:55,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb74bb124-61b1-4477-a090-6804310f2c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:55,654] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:55,654] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 20:34:55,654] [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
Cycloclasticus pugetii	strain=PS-1	GCA_000384415.1	34068	34068	type	True	77.0103	127	659	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:34:55,654] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35980/tc_result.tsv
[2023-03-15 20:34:55,654] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:55,654] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:55,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb74bb124-61b1-4477-a090-6804310f2c86/dqc_reference/checkm_data
[2023-03-15 20:34:55,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:55,659] [INFO] Task started: CheckM
[2023-03-15 20:34:55,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35980/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35980/checkm_input OceanDNA-b35980/checkm_result
[2023-03-15 20:35:27,030] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:27,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:27,032] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:27,032] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:27,032] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35980/markers.fasta)
[2023-03-15 20:35:27,034] [INFO] Task started: Blastn
[2023-03-15 20:35:27,034] [INFO] Running command: blastn -query OceanDNA-b35980/markers.fasta -db /var/lib/cwl/stgb74bb124-61b1-4477-a090-6804310f2c86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35980/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:27,768] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:27,769] [INFO] Selected 19 target genomes.
[2023-03-15 20:35:27,769] [INFO] Target genome list was writen to OceanDNA-b35980/target_genomes_gtdb.txt
[2023-03-15 20:35:28,419] [INFO] Task started: fastANI
[2023-03-15 20:35:28,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgae3294ec-ea8b-46fb-b635-b0ab1ffcf2f0/OceanDNA-b35980.fa --refList OceanDNA-b35980/target_genomes_gtdb.txt --output OceanDNA-b35980/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:35,828] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:35,835] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:35:35,835] [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_002292375.1	s__Cycloclasticus sp002292375	98.9995	613	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018066825.1	s__Cycloclasticus sp018066825	89.1436	433	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	99.96	99.96	0.89	0.89	2	-
GCA_002101235.1	s__Cycloclasticus sp002101235	77.5074	114	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001566825.1	s__Cycloclasticus sp001566825	77.4837	77	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	98.53	98.53	0.59	0.59	2	-
GCA_002162695.1	s__Cycloclasticus sp002162695	77.2568	120	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	97.08	97.08	0.97	0.97	2	-
GCF_000384415.1	s__Cycloclasticus pugetii	77.0103	127	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	98.68	98.33	0.92	0.87	8	-
GCA_012959695.1	s__Cycloclasticus sp012959695	76.9969	107	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	99.70	99.70	0.87	0.87	2	-
GCA_002162705.1	s__Cycloclasticus sp002162705	76.9456	108	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733135.1	s__Cycloclasticus sp002733135	76.848	106	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700385.1	s__Cycloclasticus sp002700385	76.7545	104	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	99.97	99.95	0.99	0.97	4	-
GCA_012960055.1	s__Cycloclasticus sp012960055	76.6627	79	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:35,835] [INFO] GTDB search result was written to OceanDNA-b35980/result_gtdb.tsv
[2023-03-15 20:35:35,835] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:35,836] [INFO] DFAST_QC result json was written to OceanDNA-b35980/dqc_result.json
[2023-03-15 20:35:35,836] [INFO] DFAST_QC completed!
[2023-03-15 20:35:35,836] [INFO] Total running time: 0h1m9s