[2023-03-15 06:19:32,785] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:19:32,785] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:19:32,785] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe64ae72-4704-407a-9467-087ec8fd717b/dqc_reference
[2023-03-15 06:19:34,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:19:34,568] [INFO] Task started: Prodigal
[2023-03-15 06:19:34,568] [INFO] Running command: cat /var/lib/cwl/stg205013e4-aabf-4e1b-aa4f-d85c55f625b7/OceanDNA-b39379.fa | prodigal -d OceanDNA-b39379/cds.fna -a OceanDNA-b39379/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:19:44,538] [INFO] Task succeeded: Prodigal
[2023-03-15 06:19:44,539] [INFO] Task started: HMMsearch
[2023-03-15 06:19:44,539] [INFO] Running command: hmmsearch --tblout OceanDNA-b39379/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe64ae72-4704-407a-9467-087ec8fd717b/dqc_reference/reference_markers.hmm OceanDNA-b39379/protein.faa > /dev/null
[2023-03-15 06:19:44,722] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:19:44,722] [INFO] Found 6/6 markers.
[2023-03-15 06:19:44,737] [INFO] Query marker FASTA was written to OceanDNA-b39379/markers.fasta
[2023-03-15 06:19:44,739] [INFO] Task started: Blastn
[2023-03-15 06:19:44,739] [INFO] Running command: blastn -query OceanDNA-b39379/markers.fasta -db /var/lib/cwl/stgbe64ae72-4704-407a-9467-087ec8fd717b/dqc_reference/reference_markers.fasta -out OceanDNA-b39379/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:19:45,363] [INFO] Task succeeded: Blastn
[2023-03-15 06:19:45,364] [INFO] Selected 35 target genomes.
[2023-03-15 06:19:45,364] [INFO] Target genome list was writen to OceanDNA-b39379/target_genomes.txt
[2023-03-15 06:19:45,387] [INFO] Task started: fastANI
[2023-03-15 06:19:45,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg205013e4-aabf-4e1b-aa4f-d85c55f625b7/OceanDNA-b39379.fa --refList OceanDNA-b39379/target_genomes.txt --output OceanDNA-b39379/fastani_result.tsv --threads 1
[2023-03-15 06:20:08,896] [INFO] Task succeeded: fastANI
[2023-03-15 06:20:08,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe64ae72-4704-407a-9467-087ec8fd717b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:20:08,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe64ae72-4704-407a-9467-087ec8fd717b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:20:08,897] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:20:08,897] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:20:08,897] [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 06:20:08,897] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39379/tc_result.tsv
[2023-03-15 06:20:08,897] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:20:08,897] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:20:08,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe64ae72-4704-407a-9467-087ec8fd717b/dqc_reference/checkm_data
[2023-03-15 06:20:08,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:20:08,968] [INFO] Task started: CheckM
[2023-03-15 06:20:08,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39379/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39379/checkm_input OceanDNA-b39379/checkm_result
[2023-03-15 06:20:38,322] [INFO] Task succeeded: CheckM
[2023-03-15 06:20:38,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:20:38,338] [INFO] ===== Completeness check finished =====
[2023-03-15 06:20:38,339] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:20:38,339] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39379/markers.fasta)
[2023-03-15 06:20:38,340] [INFO] Task started: Blastn
[2023-03-15 06:20:38,340] [INFO] Running command: blastn -query OceanDNA-b39379/markers.fasta -db /var/lib/cwl/stgbe64ae72-4704-407a-9467-087ec8fd717b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39379/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:20:39,368] [INFO] Task succeeded: Blastn
[2023-03-15 06:20:39,378] [INFO] Selected 10 target genomes.
[2023-03-15 06:20:39,379] [INFO] Target genome list was writen to OceanDNA-b39379/target_genomes_gtdb.txt
[2023-03-15 06:20:39,390] [INFO] Task started: fastANI
[2023-03-15 06:20:39,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg205013e4-aabf-4e1b-aa4f-d85c55f625b7/OceanDNA-b39379.fa --refList OceanDNA-b39379/target_genomes_gtdb.txt --output OceanDNA-b39379/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:20:43,844] [INFO] Task succeeded: fastANI
[2023-03-15 06:20:43,851] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:20:43,851] [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_905478975.1	s__HTCC2207 sp905478975	85.1108	378	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478725.1	s__HTCC2207 sp905478725	84.9638	354	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000511875.1	s__HTCC2207 sp000511875	83.933	471	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858295.1	s__HTCC2207 sp017858295	83.8735	336	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_000153445.1	s__HTCC2207 sp000153445	83.7402	465	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_017858135.1	s__HTCC2207 sp017858135	80.5007	343	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_002335945.1	s__HTCC2207 sp002335945	77.7952	164	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_018607545.1	s__HTCC2207 sp018607545	77.6898	82	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001438605.1	s__HTCC2207 sp001438605	77.2127	118	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.34	98.71	0.91	0.87	10	-
GCA_018663035.1	s__HTCC2207 sp018663035	76.239	80	560	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-15 06:20:43,858] [INFO] GTDB search result was written to OceanDNA-b39379/result_gtdb.tsv
[2023-03-15 06:20:43,858] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:20:43,859] [INFO] DFAST_QC result json was written to OceanDNA-b39379/dqc_result.json
[2023-03-15 06:20:43,859] [INFO] DFAST_QC completed!
[2023-03-15 06:20:43,859] [INFO] Total running time: 0h1m11s