[2023-03-18 00:53:42,411] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,411] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,411] [INFO] DQC Reference Directory: /var/lib/cwl/stga28c9b00-0250-4689-80ff-e27258c010a4/dqc_reference
[2023-03-18 00:53:43,583] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:43,584] [INFO] Task started: Prodigal
[2023-03-18 00:53:43,584] [INFO] Running command: cat /var/lib/cwl/stg9c46eb37-120a-41f7-9566-1b6713ba8403/OceanDNA-b25737.fa | prodigal -d OceanDNA-b25737/cds.fna -a OceanDNA-b25737/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:46,214] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:46,214] [INFO] Task started: HMMsearch
[2023-03-18 00:53:46,214] [INFO] Running command: hmmsearch --tblout OceanDNA-b25737/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga28c9b00-0250-4689-80ff-e27258c010a4/dqc_reference/reference_markers.hmm OceanDNA-b25737/protein.faa > /dev/null
[2023-03-18 00:53:46,352] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:46,353] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9c46eb37-120a-41f7-9566-1b6713ba8403/OceanDNA-b25737.fa]
[2023-03-18 00:53:46,358] [INFO] Query marker FASTA was written to OceanDNA-b25737/markers.fasta
[2023-03-18 00:53:46,359] [INFO] Task started: Blastn
[2023-03-18 00:53:46,359] [INFO] Running command: blastn -query OceanDNA-b25737/markers.fasta -db /var/lib/cwl/stga28c9b00-0250-4689-80ff-e27258c010a4/dqc_reference/reference_markers.fasta -out OceanDNA-b25737/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:47,020] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:47,022] [INFO] Selected 5 target genomes.
[2023-03-18 00:53:47,022] [INFO] Target genome list was writen to OceanDNA-b25737/target_genomes.txt
[2023-03-18 00:53:47,028] [INFO] Task started: fastANI
[2023-03-18 00:53:47,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c46eb37-120a-41f7-9566-1b6713ba8403/OceanDNA-b25737.fa --refList OceanDNA-b25737/target_genomes.txt --output OceanDNA-b25737/fastani_result.tsv --threads 1
[2023-03-18 00:53:48,404] [INFO] Task succeeded: fastANI
[2023-03-18 00:53:48,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga28c9b00-0250-4689-80ff-e27258c010a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:53:48,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga28c9b00-0250-4689-80ff-e27258c010a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:53:48,405] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:53:48,406] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:53:48,406] [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 00:53:48,406] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25737/tc_result.tsv
[2023-03-18 00:53:48,406] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:53:48,406] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:53:48,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga28c9b00-0250-4689-80ff-e27258c010a4/dqc_reference/checkm_data
[2023-03-18 00:53:48,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:53:48,457] [INFO] Task started: CheckM
[2023-03-18 00:53:48,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25737/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25737/checkm_input OceanDNA-b25737/checkm_result
[2023-03-18 00:54:06,476] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:06,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.86%
Contamintation: 4.17%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-03-18 00:54:06,491] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:06,491] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:06,491] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25737/markers.fasta)
[2023-03-18 00:54:06,493] [INFO] Task started: Blastn
[2023-03-18 00:54:06,493] [INFO] Running command: blastn -query OceanDNA-b25737/markers.fasta -db /var/lib/cwl/stga28c9b00-0250-4689-80ff-e27258c010a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25737/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:07,485] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:07,486] [INFO] Selected 16 target genomes.
[2023-03-18 00:54:07,486] [INFO] Target genome list was writen to OceanDNA-b25737/target_genomes_gtdb.txt
[2023-03-18 00:54:07,495] [INFO] Task started: fastANI
[2023-03-18 00:54:07,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c46eb37-120a-41f7-9566-1b6713ba8403/OceanDNA-b25737.fa --refList OceanDNA-b25737/target_genomes_gtdb.txt --output OceanDNA-b25737/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:54:10,445] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:10,451] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:54:10,451] [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_003214525.1	s__Pelagibacter sp003214525	88.8764	122	146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902607115.1	s__Pelagibacter sp902607115	84.4197	92	146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902584915.1	s__Pelagibacter sp902584915	83.5421	71	146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574705.1	s__Pelagibacter sp902574705	80.4511	102	146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902612345.1	s__Pelagibacter sp902612345	80.0723	94	146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902631595.1	s__Pelagibacter sp902631595	79.3186	73	146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.95	98.95	0.60	0.60	2	-
GCA_003212415.1	s__Pelagibacter sp003212415	77.708	62	146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902604785.1	s__Pelagibacter sp902604785	76.7257	56	146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:54:10,458] [INFO] GTDB search result was written to OceanDNA-b25737/result_gtdb.tsv
[2023-03-18 00:54:10,463] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:54:10,464] [INFO] DFAST_QC result json was written to OceanDNA-b25737/dqc_result.json
[2023-03-18 00:54:10,464] [INFO] DFAST_QC completed!
[2023-03-18 00:54:10,464] [INFO] Total running time: 0h0m28s