[2023-03-16 23:35:12,976] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:12,976] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:12,976] [INFO] DQC Reference Directory: /var/lib/cwl/stg2231a115-c396-4ce7-a1c1-d78962adc595/dqc_reference
[2023-03-16 23:35:14,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,100] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,100] [INFO] Running command: cat /var/lib/cwl/stga73b454a-c8cc-4096-a950-940c15e80fdc/OceanDNA-b42246.fa | prodigal -d OceanDNA-b42246/cds.fna -a OceanDNA-b42246/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:19,440] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:19,440] [INFO] Task started: HMMsearch
[2023-03-16 23:35:19,440] [INFO] Running command: hmmsearch --tblout OceanDNA-b42246/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2231a115-c396-4ce7-a1c1-d78962adc595/dqc_reference/reference_markers.hmm OceanDNA-b42246/protein.faa > /dev/null
[2023-03-16 23:35:19,591] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:19,591] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga73b454a-c8cc-4096-a950-940c15e80fdc/OceanDNA-b42246.fa]
[2023-03-16 23:35:19,601] [INFO] Query marker FASTA was written to OceanDNA-b42246/markers.fasta
[2023-03-16 23:35:19,601] [INFO] Task started: Blastn
[2023-03-16 23:35:19,601] [INFO] Running command: blastn -query OceanDNA-b42246/markers.fasta -db /var/lib/cwl/stg2231a115-c396-4ce7-a1c1-d78962adc595/dqc_reference/reference_markers.fasta -out OceanDNA-b42246/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:20,336] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:20,337] [INFO] Selected 10 target genomes.
[2023-03-16 23:35:20,337] [INFO] Target genome list was writen to OceanDNA-b42246/target_genomes.txt
[2023-03-16 23:35:20,343] [INFO] Task started: fastANI
[2023-03-16 23:35:20,343] [INFO] Running command: fastANI --query /var/lib/cwl/stga73b454a-c8cc-4096-a950-940c15e80fdc/OceanDNA-b42246.fa --refList OceanDNA-b42246/target_genomes.txt --output OceanDNA-b42246/fastani_result.tsv --threads 1
[2023-03-16 23:35:26,860] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:26,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2231a115-c396-4ce7-a1c1-d78962adc595/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:26,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2231a115-c396-4ce7-a1c1-d78962adc595/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:26,861] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:26,861] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:35:26,861] [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
--------------------------------------------------------------------------------
[2023-03-16 23:35:26,861] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42246/tc_result.tsv
[2023-03-16 23:35:26,861] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:26,862] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:26,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2231a115-c396-4ce7-a1c1-d78962adc595/dqc_reference/checkm_data
[2023-03-16 23:35:26,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:26,867] [INFO] Task started: CheckM
[2023-03-16 23:35:26,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42246/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42246/checkm_input OceanDNA-b42246/checkm_result
[2023-03-16 23:35:46,651] [INFO] Task succeeded: CheckM
[2023-03-16 23:35:46,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:35:46,653] [INFO] ===== Completeness check finished =====
[2023-03-16 23:35:46,653] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:35:46,653] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42246/markers.fasta)
[2023-03-16 23:35:46,655] [INFO] Task started: Blastn
[2023-03-16 23:35:46,655] [INFO] Running command: blastn -query OceanDNA-b42246/markers.fasta -db /var/lib/cwl/stg2231a115-c396-4ce7-a1c1-d78962adc595/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42246/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:47,753] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:47,754] [INFO] Selected 17 target genomes.
[2023-03-16 23:35:47,754] [INFO] Target genome list was writen to OceanDNA-b42246/target_genomes_gtdb.txt
[2023-03-16 23:35:48,121] [INFO] Task started: fastANI
[2023-03-16 23:35:48,121] [INFO] Running command: fastANI --query /var/lib/cwl/stga73b454a-c8cc-4096-a950-940c15e80fdc/OceanDNA-b42246.fa --refList OceanDNA-b42246/target_genomes_gtdb.txt --output OceanDNA-b42246/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:35:51,821] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:51,828] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:35:51,828] [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_002469975.1	s__D2472 sp002469975	99.3831	266	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.56	99.38	0.87	0.81	4	conclusive
GCA_002358345.1	s__D2472 sp002358345	81.9653	243	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.61	97.74	0.92	0.85	27	-
GCA_905181595.1	s__D2472 sp905181595	79.9124	179	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602595.1	s__D2472 sp902602595	77.2562	81	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511575.1	s__D2472 sp902511575	77.2169	88	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515775.1	s__D2472 sp902515775	77.1571	59	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596165.1	s__D2472 sp902596165	77.1527	97	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623685.1	s__D2472 sp902623685	76.8747	65	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
GCA_902608115.1	s__D2472 sp902608115	76.8339	72	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528215.1	s__D2472 sp902528215	76.3902	74	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:35:51,828] [INFO] GTDB search result was written to OceanDNA-b42246/result_gtdb.tsv
[2023-03-16 23:35:51,828] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:35:51,829] [INFO] DFAST_QC result json was written to OceanDNA-b42246/dqc_result.json
[2023-03-16 23:35:51,829] [INFO] DFAST_QC completed!
[2023-03-16 23:35:51,829] [INFO] Total running time: 0h0m39s