[2023-03-18 09:41:07,205] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,205] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,205] [INFO] DQC Reference Directory: /var/lib/cwl/stge20ceb68-dcf5-4743-a078-7e65477fe7e4/dqc_reference
[2023-03-18 09:41:08,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,308] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,308] [INFO] Running command: cat /var/lib/cwl/stga88b36f0-a864-4e46-885c-2cab39918295/OceanDNA-b40624.fa | prodigal -d OceanDNA-b40624/cds.fna -a OceanDNA-b40624/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:29,478] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:29,479] [INFO] Task started: HMMsearch
[2023-03-18 09:41:29,479] [INFO] Running command: hmmsearch --tblout OceanDNA-b40624/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge20ceb68-dcf5-4743-a078-7e65477fe7e4/dqc_reference/reference_markers.hmm OceanDNA-b40624/protein.faa > /dev/null
[2023-03-18 09:41:29,713] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:29,714] [INFO] Found 6/6 markers.
[2023-03-18 09:41:29,737] [INFO] Query marker FASTA was written to OceanDNA-b40624/markers.fasta
[2023-03-18 09:41:29,737] [INFO] Task started: Blastn
[2023-03-18 09:41:29,737] [INFO] Running command: blastn -query OceanDNA-b40624/markers.fasta -db /var/lib/cwl/stge20ceb68-dcf5-4743-a078-7e65477fe7e4/dqc_reference/reference_markers.fasta -out OceanDNA-b40624/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:30,345] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:30,346] [INFO] Selected 20 target genomes.
[2023-03-18 09:41:30,346] [INFO] Target genome list was writen to OceanDNA-b40624/target_genomes.txt
[2023-03-18 09:41:30,354] [INFO] Task started: fastANI
[2023-03-18 09:41:30,354] [INFO] Running command: fastANI --query /var/lib/cwl/stga88b36f0-a864-4e46-885c-2cab39918295/OceanDNA-b40624.fa --refList OceanDNA-b40624/target_genomes.txt --output OceanDNA-b40624/fastani_result.tsv --threads 1
[2023-03-18 09:41:42,635] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:42,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge20ceb68-dcf5-4743-a078-7e65477fe7e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:42,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge20ceb68-dcf5-4743-a078-7e65477fe7e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:42,636] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:42,636] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:42,636] [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 09:41:42,636] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40624/tc_result.tsv
[2023-03-18 09:41:42,636] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:42,636] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:42,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge20ceb68-dcf5-4743-a078-7e65477fe7e4/dqc_reference/checkm_data
[2023-03-18 09:41:42,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:42,644] [INFO] Task started: CheckM
[2023-03-18 09:41:42,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40624/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40624/checkm_input OceanDNA-b40624/checkm_result
[2023-03-18 09:42:35,845] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:35,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:35,848] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:35,848] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:35,848] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40624/markers.fasta)
[2023-03-18 09:42:35,849] [INFO] Task started: Blastn
[2023-03-18 09:42:35,849] [INFO] Running command: blastn -query OceanDNA-b40624/markers.fasta -db /var/lib/cwl/stge20ceb68-dcf5-4743-a078-7e65477fe7e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40624/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:36,833] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:36,833] [INFO] Selected 14 target genomes.
[2023-03-18 09:42:36,833] [INFO] Target genome list was writen to OceanDNA-b40624/target_genomes_gtdb.txt
[2023-03-18 09:42:36,848] [INFO] Task started: fastANI
[2023-03-18 09:42:36,848] [INFO] Running command: fastANI --query /var/lib/cwl/stga88b36f0-a864-4e46-885c-2cab39918295/OceanDNA-b40624.fa --refList OceanDNA-b40624/target_genomes_gtdb.txt --output OceanDNA-b40624/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:44,499] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:44,504] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:42:44,504] [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_002401885.1	s__UBA9145 sp002401885	84.9716	766	1234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762975.1	s__UBA9145 sp016762975	82.7934	588	1234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762995.1	s__UBA9145 sp016762995	82.616	644	1234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	96.79	96.79	0.78	0.78	2	-
GCA_905478195.1	s__UBA9145 sp003483155	78.4032	353	1234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.23	98.96	0.87	0.81	6	-
GCA_012960305.1	s__UBA9145 sp012960305	77.6761	114	1234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.98	99.98	0.97	0.97	2	-
GCA_002402175.1	s__UBA9145 sp002402175	76.977	96	1234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:44,504] [INFO] GTDB search result was written to OceanDNA-b40624/result_gtdb.tsv
[2023-03-18 09:42:44,504] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:44,505] [INFO] DFAST_QC result json was written to OceanDNA-b40624/dqc_result.json
[2023-03-18 09:42:44,505] [INFO] DFAST_QC completed!
[2023-03-18 09:42:44,505] [INFO] Total running time: 0h1m37s