[2023-03-15 11:10:12,910] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:10:12,912] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:10:12,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a6858fb-b1ba-48d8-86f9-6304808d1902/dqc_reference
[2023-03-15 11:10:14,053] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:10:14,053] [INFO] Task started: Prodigal
[2023-03-15 11:10:14,053] [INFO] Running command: cat /var/lib/cwl/stga76b943c-41b2-4530-8fed-41fe19c0b47f/OceanDNA-b26147.fa | prodigal -d OceanDNA-b26147/cds.fna -a OceanDNA-b26147/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:10:20,385] [INFO] Task succeeded: Prodigal
[2023-03-15 11:10:20,385] [INFO] Task started: HMMsearch
[2023-03-15 11:10:20,385] [INFO] Running command: hmmsearch --tblout OceanDNA-b26147/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a6858fb-b1ba-48d8-86f9-6304808d1902/dqc_reference/reference_markers.hmm OceanDNA-b26147/protein.faa > /dev/null
[2023-03-15 11:10:20,530] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:10:20,530] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga76b943c-41b2-4530-8fed-41fe19c0b47f/OceanDNA-b26147.fa]
[2023-03-15 11:10:20,579] [INFO] Query marker FASTA was written to OceanDNA-b26147/markers.fasta
[2023-03-15 11:10:20,579] [INFO] Task started: Blastn
[2023-03-15 11:10:20,579] [INFO] Running command: blastn -query OceanDNA-b26147/markers.fasta -db /var/lib/cwl/stg0a6858fb-b1ba-48d8-86f9-6304808d1902/dqc_reference/reference_markers.fasta -out OceanDNA-b26147/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:21,101] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:21,107] [INFO] Selected 15 target genomes.
[2023-03-15 11:10:21,108] [INFO] Target genome list was writen to OceanDNA-b26147/target_genomes.txt
[2023-03-15 11:10:21,117] [INFO] Task started: fastANI
[2023-03-15 11:10:21,117] [INFO] Running command: fastANI --query /var/lib/cwl/stga76b943c-41b2-4530-8fed-41fe19c0b47f/OceanDNA-b26147.fa --refList OceanDNA-b26147/target_genomes.txt --output OceanDNA-b26147/fastani_result.tsv --threads 1
[2023-03-15 11:10:30,133] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:30,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a6858fb-b1ba-48d8-86f9-6304808d1902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:10:30,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a6858fb-b1ba-48d8-86f9-6304808d1902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:10:30,134] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:10:30,134] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:10:30,134] [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
--------------------------------------------------------------------------------
[2023-03-15 11:10:30,148] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26147/tc_result.tsv
[2023-03-15 11:10:30,160] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:10:30,160] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:10:30,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a6858fb-b1ba-48d8-86f9-6304808d1902/dqc_reference/checkm_data
[2023-03-15 11:10:30,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:10:30,169] [INFO] Task started: CheckM
[2023-03-15 11:10:30,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26147/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26147/checkm_input OceanDNA-b26147/checkm_result
[2023-03-15 11:10:52,674] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:52,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:52,726] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:52,726] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:52,726] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26147/markers.fasta)
[2023-03-15 11:10:52,728] [INFO] Task started: Blastn
[2023-03-15 11:10:52,728] [INFO] Running command: blastn -query OceanDNA-b26147/markers.fasta -db /var/lib/cwl/stg0a6858fb-b1ba-48d8-86f9-6304808d1902/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26147/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:53,451] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:53,455] [INFO] Selected 9 target genomes.
[2023-03-15 11:10:53,455] [INFO] Target genome list was writen to OceanDNA-b26147/target_genomes_gtdb.txt
[2023-03-15 11:10:53,466] [INFO] Task started: fastANI
[2023-03-15 11:10:53,466] [INFO] Running command: fastANI --query /var/lib/cwl/stga76b943c-41b2-4530-8fed-41fe19c0b47f/OceanDNA-b26147.fa --refList OceanDNA-b26147/target_genomes_gtdb.txt --output OceanDNA-b26147/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:56,804] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:56,809] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:56,809] [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_902596655.1	s__MED-G116 sp902596655	87.839	181	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	84.5435	243	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547925.1	s__MED-G116 sp902547925	84.1969	113	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623185.1	s__MED-G116 sp902623185	81.6044	101	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	77.5307	59	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_018624035.1	s__UBA8309 sp018624035	77.3766	64	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920665.1	s__UBA8309 sp009920665	77.2841	71	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:56,813] [INFO] GTDB search result was written to OceanDNA-b26147/result_gtdb.tsv
[2023-03-15 11:10:56,817] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:56,820] [INFO] DFAST_QC result json was written to OceanDNA-b26147/dqc_result.json
[2023-03-15 11:10:56,820] [INFO] DFAST_QC completed!
[2023-03-15 11:10:56,820] [INFO] Total running time: 0h0m44s