[2023-03-17 04:48:53,934] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:53,934] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:53,934] [INFO] DQC Reference Directory: /var/lib/cwl/stgee8fe119-3536-4938-976e-bd2edf71c117/dqc_reference
[2023-03-17 04:48:55,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,155] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,155] [INFO] Running command: cat /var/lib/cwl/stg64ca540a-057a-4ee2-8fa3-bc88287e2684/OceanDNA-b42286.fa | prodigal -d OceanDNA-b42286/cds.fna -a OceanDNA-b42286/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:48:58,131] [INFO] Task succeeded: Prodigal
[2023-03-17 04:48:58,131] [INFO] Task started: HMMsearch
[2023-03-17 04:48:58,131] [INFO] Running command: hmmsearch --tblout OceanDNA-b42286/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee8fe119-3536-4938-976e-bd2edf71c117/dqc_reference/reference_markers.hmm OceanDNA-b42286/protein.faa > /dev/null
[2023-03-17 04:48:58,291] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:48:58,291] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg64ca540a-057a-4ee2-8fa3-bc88287e2684/OceanDNA-b42286.fa]
[2023-03-17 04:48:58,299] [INFO] Query marker FASTA was written to OceanDNA-b42286/markers.fasta
[2023-03-17 04:48:58,300] [INFO] Task started: Blastn
[2023-03-17 04:48:58,300] [INFO] Running command: blastn -query OceanDNA-b42286/markers.fasta -db /var/lib/cwl/stgee8fe119-3536-4938-976e-bd2edf71c117/dqc_reference/reference_markers.fasta -out OceanDNA-b42286/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:48:59,127] [INFO] Task succeeded: Blastn
[2023-03-17 04:48:59,128] [INFO] Selected 30 target genomes.
[2023-03-17 04:48:59,128] [INFO] Target genome list was writen to OceanDNA-b42286/target_genomes.txt
[2023-03-17 04:48:59,142] [INFO] Task started: fastANI
[2023-03-17 04:48:59,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg64ca540a-057a-4ee2-8fa3-bc88287e2684/OceanDNA-b42286.fa --refList OceanDNA-b42286/target_genomes.txt --output OceanDNA-b42286/fastani_result.tsv --threads 1
[2023-03-17 04:49:09,757] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:09,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee8fe119-3536-4938-976e-bd2edf71c117/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:09,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee8fe119-3536-4938-976e-bd2edf71c117/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:09,758] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:09,758] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:09,758] [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
--------------------------------------------------------------------------------
[2023-03-17 04:49:09,758] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42286/tc_result.tsv
[2023-03-17 04:49:09,758] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:09,758] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:09,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee8fe119-3536-4938-976e-bd2edf71c117/dqc_reference/checkm_data
[2023-03-17 04:49:09,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:09,763] [INFO] Task started: CheckM
[2023-03-17 04:49:09,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42286/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42286/checkm_input OceanDNA-b42286/checkm_result
[2023-03-17 04:49:24,062] [INFO] Task succeeded: CheckM
[2023-03-17 04:49:24,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.28%
Contamintation: 3.01%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-17 04:49:24,064] [INFO] ===== Completeness check finished =====
[2023-03-17 04:49:24,064] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:49:24,064] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42286/markers.fasta)
[2023-03-17 04:49:24,065] [INFO] Task started: Blastn
[2023-03-17 04:49:24,065] [INFO] Running command: blastn -query OceanDNA-b42286/markers.fasta -db /var/lib/cwl/stgee8fe119-3536-4938-976e-bd2edf71c117/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42286/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:24,898] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:24,899] [INFO] Selected 27 target genomes.
[2023-03-17 04:49:24,899] [INFO] Target genome list was writen to OceanDNA-b42286/target_genomes_gtdb.txt
[2023-03-17 04:49:25,714] [INFO] Task started: fastANI
[2023-03-17 04:49:25,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg64ca540a-057a-4ee2-8fa3-bc88287e2684/OceanDNA-b42286.fa --refList OceanDNA-b42286/target_genomes_gtdb.txt --output OceanDNA-b42286/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:49:30,737] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:30,748] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:49:30,748] [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_902560315.1	s__SAR86A sp902560315	82.8014	132	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_902517505.1	s__SAR86A sp902517505	82.662	130	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_902630885.1	s__SAR86A sp902630885	79.128	92	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556105.1	s__SAR86A sp902556105	79.0946	94	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902631785.1	s__SAR86A sp902631785	78.8308	87	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_902551185.1	s__SAR86A sp902551185	78.4308	71	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.17	99.17	0.78	0.78	2	-
GCA_902617045.1	s__SAR86A sp902617045	78.3738	96	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902612915.1	s__SAR86A sp902612915	78.3261	76	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	-
GCA_902563835.1	s__SAR86A sp902563835	78.2539	75	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591925.1	s__SAR86A sp902591925	78.1503	94	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902520725.1	s__SAR86A sp902520725	78.05	70	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	-
GCA_902586925.1	s__SAR86A sp902586925	77.9409	76	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.82	96.82	0.89	0.89	2	-
GCA_902583575.1	s__SAR86A sp902583575	77.8671	83	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517425.1	s__SAR86A sp902517425	77.7484	63	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213495.1	s__SAR86A sp003213495	77.6432	75	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.20	96.41	0.97	0.94	3	-
GCA_902626385.1	s__SAR86A sp902626385	77.6333	50	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557965.1	s__SAR86A sp902557965	77.3928	64	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.42	97.04	0.73	0.71	3	-
GCA_902582355.1	s__SAR86A sp902582355	77.1123	66	169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	98.87	98.87	0.67	0.67	2	-
--------------------------------------------------------------------------------
[2023-03-17 04:49:30,748] [INFO] GTDB search result was written to OceanDNA-b42286/result_gtdb.tsv
[2023-03-17 04:49:30,748] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:49:30,749] [INFO] DFAST_QC result json was written to OceanDNA-b42286/dqc_result.json
[2023-03-17 04:49:30,750] [INFO] DFAST_QC completed!
[2023-03-17 04:49:30,750] [INFO] Total running time: 0h0m37s