[2023-03-16 04:54:07,082] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,082] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,082] [INFO] DQC Reference Directory: /var/lib/cwl/stga0584019-b09c-438d-87d3-051f103af3f1/dqc_reference
[2023-03-16 04:54:08,327] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,327] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,327] [INFO] Running command: cat /var/lib/cwl/stgc1234a19-bf2e-48fd-aa10-5845b3f734d0/OceanDNA-b33427.fa | prodigal -d OceanDNA-b33427/cds.fna -a OceanDNA-b33427/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:17,591] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:17,591] [INFO] Task started: HMMsearch
[2023-03-16 04:54:17,591] [INFO] Running command: hmmsearch --tblout OceanDNA-b33427/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0584019-b09c-438d-87d3-051f103af3f1/dqc_reference/reference_markers.hmm OceanDNA-b33427/protein.faa > /dev/null
[2023-03-16 04:54:17,828] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:17,828] [INFO] Found 6/6 markers.
[2023-03-16 04:54:17,844] [INFO] Query marker FASTA was written to OceanDNA-b33427/markers.fasta
[2023-03-16 04:54:17,845] [INFO] Task started: Blastn
[2023-03-16 04:54:17,845] [INFO] Running command: blastn -query OceanDNA-b33427/markers.fasta -db /var/lib/cwl/stga0584019-b09c-438d-87d3-051f103af3f1/dqc_reference/reference_markers.fasta -out OceanDNA-b33427/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:18,451] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:18,452] [INFO] Selected 31 target genomes.
[2023-03-16 04:54:18,452] [INFO] Target genome list was writen to OceanDNA-b33427/target_genomes.txt
[2023-03-16 04:54:18,466] [INFO] Task started: fastANI
[2023-03-16 04:54:18,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1234a19-bf2e-48fd-aa10-5845b3f734d0/OceanDNA-b33427.fa --refList OceanDNA-b33427/target_genomes.txt --output OceanDNA-b33427/fastani_result.tsv --threads 1
[2023-03-16 04:54:41,367] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:41,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0584019-b09c-438d-87d3-051f103af3f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:41,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0584019-b09c-438d-87d3-051f103af3f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:41,368] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:41,368] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:41,368] [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
--------------------------------------------------------------------------------
[2023-03-16 04:54:41,369] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33427/tc_result.tsv
[2023-03-16 04:54:41,369] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:41,369] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:41,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0584019-b09c-438d-87d3-051f103af3f1/dqc_reference/checkm_data
[2023-03-16 04:54:41,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:41,410] [INFO] Task started: CheckM
[2023-03-16 04:54:41,410] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33427/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33427/checkm_input OceanDNA-b33427/checkm_result
[2023-03-16 04:55:10,346] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:10,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 2.43%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:10,349] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:10,349] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:10,349] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33427/markers.fasta)
[2023-03-16 04:55:10,350] [INFO] Task started: Blastn
[2023-03-16 04:55:10,350] [INFO] Running command: blastn -query OceanDNA-b33427/markers.fasta -db /var/lib/cwl/stga0584019-b09c-438d-87d3-051f103af3f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33427/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:11,409] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:11,410] [INFO] Selected 25 target genomes.
[2023-03-16 04:55:11,410] [INFO] Target genome list was writen to OceanDNA-b33427/target_genomes_gtdb.txt
[2023-03-16 04:55:11,469] [INFO] Task started: fastANI
[2023-03-16 04:55:11,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1234a19-bf2e-48fd-aa10-5845b3f734d0/OceanDNA-b33427.fa --refList OceanDNA-b33427/target_genomes_gtdb.txt --output OceanDNA-b33427/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:25,411] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:25,414] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:55:25,414] [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_000496475.1	s__RS62 sp000496475	94.6643	347	358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	98.53	98.53	0.95	0.95	2	-
GCA_018607835.1	s__RS62 sp002340675	76.8578	55	358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	99.19	98.96	0.91	0.88	5	-
GCA_003241965.1	s__Hydrogenophaga sp003241965	76.0672	50	358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:25,415] [INFO] GTDB search result was written to OceanDNA-b33427/result_gtdb.tsv
[2023-03-16 04:55:25,415] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:25,415] [INFO] DFAST_QC result json was written to OceanDNA-b33427/dqc_result.json
[2023-03-16 04:55:25,415] [INFO] DFAST_QC completed!
[2023-03-16 04:55:25,415] [INFO] Total running time: 0h1m18s