[2023-03-19 01:50:01,573] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,573] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgebb10eb1-eb12-4d0a-b854-0e453552db44/dqc_reference
[2023-03-19 01:50:02,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:02,675] [INFO] Task started: Prodigal
[2023-03-19 01:50:02,675] [INFO] Running command: cat /var/lib/cwl/stg34929a85-b3b5-404e-9f5e-978fa0037897/OceanDNA-b37356.fa | prodigal -d OceanDNA-b37356/cds.fna -a OceanDNA-b37356/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:21,827] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:21,827] [INFO] Task started: HMMsearch
[2023-03-19 01:50:21,827] [INFO] Running command: hmmsearch --tblout OceanDNA-b37356/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebb10eb1-eb12-4d0a-b854-0e453552db44/dqc_reference/reference_markers.hmm OceanDNA-b37356/protein.faa > /dev/null
[2023-03-19 01:50:22,041] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:22,042] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg34929a85-b3b5-404e-9f5e-978fa0037897/OceanDNA-b37356.fa]
[2023-03-19 01:50:22,062] [INFO] Query marker FASTA was written to OceanDNA-b37356/markers.fasta
[2023-03-19 01:50:22,063] [INFO] Task started: Blastn
[2023-03-19 01:50:22,063] [INFO] Running command: blastn -query OceanDNA-b37356/markers.fasta -db /var/lib/cwl/stgebb10eb1-eb12-4d0a-b854-0e453552db44/dqc_reference/reference_markers.fasta -out OceanDNA-b37356/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:22,611] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:22,612] [INFO] Selected 30 target genomes.
[2023-03-19 01:50:22,613] [INFO] Target genome list was writen to OceanDNA-b37356/target_genomes.txt
[2023-03-19 01:50:22,633] [INFO] Task started: fastANI
[2023-03-19 01:50:22,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg34929a85-b3b5-404e-9f5e-978fa0037897/OceanDNA-b37356.fa --refList OceanDNA-b37356/target_genomes.txt --output OceanDNA-b37356/fastani_result.tsv --threads 1
[2023-03-19 01:50:42,419] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:42,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebb10eb1-eb12-4d0a-b854-0e453552db44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:42,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebb10eb1-eb12-4d0a-b854-0e453552db44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:42,420] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:42,420] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:50:42,420] [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
--------------------------------------------------------------------------------
[2023-03-19 01:50:42,420] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37356/tc_result.tsv
[2023-03-19 01:50:42,420] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:42,420] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:42,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebb10eb1-eb12-4d0a-b854-0e453552db44/dqc_reference/checkm_data
[2023-03-19 01:50:42,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:42,429] [INFO] Task started: CheckM
[2023-03-19 01:50:42,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37356/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37356/checkm_input OceanDNA-b37356/checkm_result
[2023-03-19 01:51:32,723] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:32,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:32,726] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:32,726] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:32,727] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37356/markers.fasta)
[2023-03-19 01:51:32,727] [INFO] Task started: Blastn
[2023-03-19 01:51:32,727] [INFO] Running command: blastn -query OceanDNA-b37356/markers.fasta -db /var/lib/cwl/stgebb10eb1-eb12-4d0a-b854-0e453552db44/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37356/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:33,513] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:33,514] [INFO] Selected 20 target genomes.
[2023-03-19 01:51:33,514] [INFO] Target genome list was writen to OceanDNA-b37356/target_genomes_gtdb.txt
[2023-03-19 01:51:33,529] [INFO] Task started: fastANI
[2023-03-19 01:51:33,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg34929a85-b3b5-404e-9f5e-978fa0037897/OceanDNA-b37356.fa --refList OceanDNA-b37356/target_genomes_gtdb.txt --output OceanDNA-b37356/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:47,760] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:47,763] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:51:47,764] [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_016779585.1	s__UBA9659 sp016779585	89.5975	908	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642855.1	s__UBA9659 sp017642855	78.5511	451	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.28	99.09	0.95	0.93	7	-
GCA_018665025.1	s__UBA9659 sp018665025	76.3483	68	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.67	99.61	0.89	0.86	14	-
GCA_012961165.1	s__UBA9659 sp012961165	76.2802	104	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.55	99.55	0.89	0.89	2	-
GCA_018645845.1	s__UBA9659 sp018645845	75.908	54	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	98.73	98.60	0.77	0.73	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:51:47,764] [INFO] GTDB search result was written to OceanDNA-b37356/result_gtdb.tsv
[2023-03-19 01:51:47,764] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:47,764] [INFO] DFAST_QC result json was written to OceanDNA-b37356/dqc_result.json
[2023-03-19 01:51:47,765] [INFO] DFAST_QC completed!
[2023-03-19 01:51:47,765] [INFO] Total running time: 0h1m46s