[2023-03-18 02:27:37,217] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,218] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,218] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8fa5245-f258-4986-894c-d87d3234d3fb/dqc_reference
[2023-03-18 02:27:38,462] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,463] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,463] [INFO] Running command: cat /var/lib/cwl/stgb166d220-1b9a-40fb-b36d-73049de9bcba/OceanDNA-b27416.fa | prodigal -d OceanDNA-b27416/cds.fna -a OceanDNA-b27416/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:27:44,257] [INFO] Task succeeded: Prodigal
[2023-03-18 02:27:44,257] [INFO] Task started: HMMsearch
[2023-03-18 02:27:44,257] [INFO] Running command: hmmsearch --tblout OceanDNA-b27416/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8fa5245-f258-4986-894c-d87d3234d3fb/dqc_reference/reference_markers.hmm OceanDNA-b27416/protein.faa > /dev/null
[2023-03-18 02:27:44,418] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:27:44,418] [INFO] Found 6/6 markers.
[2023-03-18 02:27:44,427] [INFO] Query marker FASTA was written to OceanDNA-b27416/markers.fasta
[2023-03-18 02:27:44,427] [INFO] Task started: Blastn
[2023-03-18 02:27:44,427] [INFO] Running command: blastn -query OceanDNA-b27416/markers.fasta -db /var/lib/cwl/stgb8fa5245-f258-4986-894c-d87d3234d3fb/dqc_reference/reference_markers.fasta -out OceanDNA-b27416/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:27:44,983] [INFO] Task succeeded: Blastn
[2023-03-18 02:27:44,984] [INFO] Selected 18 target genomes.
[2023-03-18 02:27:44,984] [INFO] Target genome list was writen to OceanDNA-b27416/target_genomes.txt
[2023-03-18 02:27:44,992] [INFO] Task started: fastANI
[2023-03-18 02:27:44,993] [INFO] Running command: fastANI --query /var/lib/cwl/stgb166d220-1b9a-40fb-b36d-73049de9bcba/OceanDNA-b27416.fa --refList OceanDNA-b27416/target_genomes.txt --output OceanDNA-b27416/fastani_result.tsv --threads 1
[2023-03-18 02:27:57,032] [INFO] Task succeeded: fastANI
[2023-03-18 02:27:57,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8fa5245-f258-4986-894c-d87d3234d3fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:27:57,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8fa5245-f258-4986-894c-d87d3234d3fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:27:57,033] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:27:57,033] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:27:57,033] [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 02:27:57,033] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27416/tc_result.tsv
[2023-03-18 02:27:57,033] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:27:57,033] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:27:57,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8fa5245-f258-4986-894c-d87d3234d3fb/dqc_reference/checkm_data
[2023-03-18 02:27:57,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:27:57,038] [INFO] Task started: CheckM
[2023-03-18 02:27:57,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27416/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27416/checkm_input OceanDNA-b27416/checkm_result
[2023-03-18 02:28:17,316] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:17,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:17,318] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:17,318] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:17,318] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27416/markers.fasta)
[2023-03-18 02:28:17,319] [INFO] Task started: Blastn
[2023-03-18 02:28:17,319] [INFO] Running command: blastn -query OceanDNA-b27416/markers.fasta -db /var/lib/cwl/stgb8fa5245-f258-4986-894c-d87d3234d3fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27416/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:18,255] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:18,256] [INFO] Selected 11 target genomes.
[2023-03-18 02:28:18,256] [INFO] Target genome list was writen to OceanDNA-b27416/target_genomes_gtdb.txt
[2023-03-18 02:28:18,271] [INFO] Task started: fastANI
[2023-03-18 02:28:18,271] [INFO] Running command: fastANI --query /var/lib/cwl/stgb166d220-1b9a-40fb-b36d-73049de9bcba/OceanDNA-b27416.fa --refList OceanDNA-b27416/target_genomes_gtdb.txt --output OceanDNA-b27416/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:20,915] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:20,921] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:28:20,921] [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_902633855.1	s__TMED25 sp902633855	89.8838	282	356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	99.57	99.57	0.84	0.84	2	-
GCA_002694595.1	s__TMED25 sp002694595	89.6831	126	356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	98.56	98.18	0.76	0.67	3	-
GCA_902613795.1	s__TMED25 sp902613795	89.5664	322	356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	99.47	99.34	0.93	0.93	3	-
GCA_902538185.1	s__TMED25 sp902538185	89.494	188	356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902632055.1	s__TMED25 sp902632055	84.2522	232	356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699615.1	s__TMED25 sp002699615	83.4342	279	356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	97.16	95.98	0.85	0.81	4	-
GCA_016780665.1	s__TMED25 sp016780665	77.0726	53	356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	99.95	99.95	0.98	0.98	2	-
GCA_002168075.1	s__TMED25 sp002168075	77.0436	72	356	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	98.97	97.02	0.94	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-18 02:28:20,921] [INFO] GTDB search result was written to OceanDNA-b27416/result_gtdb.tsv
[2023-03-18 02:28:20,921] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:20,922] [INFO] DFAST_QC result json was written to OceanDNA-b27416/dqc_result.json
[2023-03-18 02:28:20,922] [INFO] DFAST_QC completed!
[2023-03-18 02:28:20,922] [INFO] Total running time: 0h0m44s