[2023-03-18 20:13:32,250] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,250] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,250] [INFO] DQC Reference Directory: /var/lib/cwl/stgd60e35f1-414d-4abf-98ff-961df4d822d1/dqc_reference
[2023-03-18 20:13:33,442] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,442] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,442] [INFO] Running command: cat /var/lib/cwl/stg0c79d165-7827-44f9-98a6-7fa444d6568d/OceanDNA-b40098.fa | prodigal -d OceanDNA-b40098/cds.fna -a OceanDNA-b40098/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:49,773] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:49,774] [INFO] Task started: HMMsearch
[2023-03-18 20:13:49,774] [INFO] Running command: hmmsearch --tblout OceanDNA-b40098/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd60e35f1-414d-4abf-98ff-961df4d822d1/dqc_reference/reference_markers.hmm OceanDNA-b40098/protein.faa > /dev/null
[2023-03-18 20:13:50,005] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:50,005] [INFO] Found 6/6 markers.
[2023-03-18 20:13:50,022] [INFO] Query marker FASTA was written to OceanDNA-b40098/markers.fasta
[2023-03-18 20:13:50,022] [INFO] Task started: Blastn
[2023-03-18 20:13:50,022] [INFO] Running command: blastn -query OceanDNA-b40098/markers.fasta -db /var/lib/cwl/stgd60e35f1-414d-4abf-98ff-961df4d822d1/dqc_reference/reference_markers.fasta -out OceanDNA-b40098/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:50,646] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:50,646] [INFO] Selected 30 target genomes.
[2023-03-18 20:13:50,647] [INFO] Target genome list was writen to OceanDNA-b40098/target_genomes.txt
[2023-03-18 20:13:50,669] [INFO] Task started: fastANI
[2023-03-18 20:13:50,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c79d165-7827-44f9-98a6-7fa444d6568d/OceanDNA-b40098.fa --refList OceanDNA-b40098/target_genomes.txt --output OceanDNA-b40098/fastani_result.tsv --threads 1
[2023-03-18 20:14:09,926] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:09,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd60e35f1-414d-4abf-98ff-961df4d822d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:09,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd60e35f1-414d-4abf-98ff-961df4d822d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:09,930] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 20:14:09,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 20:14:09,930] [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
Porticoccus hydrocarbonoclasticus	strain=MCTG13d	GCA_000744735.1	1073414	1073414	type	True	98.7222	783	878	95	conclusive
Exilibacterium tricleocarpae	strain=R142	GCA_007004655.1	2591008	2591008	type	True	75.9228	54	878	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:14:09,930] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40098/tc_result.tsv
[2023-03-18 20:14:09,931] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:09,931] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:09,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd60e35f1-414d-4abf-98ff-961df4d822d1/dqc_reference/checkm_data
[2023-03-18 20:14:09,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:09,936] [INFO] Task started: CheckM
[2023-03-18 20:14:09,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40098/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40098/checkm_input OceanDNA-b40098/checkm_result
[2023-03-18 20:14:53,070] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:53,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:53,073] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:53,073] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:53,073] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40098/markers.fasta)
[2023-03-18 20:14:53,073] [INFO] Task started: Blastn
[2023-03-18 20:14:53,073] [INFO] Running command: blastn -query OceanDNA-b40098/markers.fasta -db /var/lib/cwl/stgd60e35f1-414d-4abf-98ff-961df4d822d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40098/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:54,089] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:54,089] [INFO] Selected 10 target genomes.
[2023-03-18 20:14:54,089] [INFO] Target genome list was writen to OceanDNA-b40098/target_genomes_gtdb.txt
[2023-03-18 20:14:54,316] [INFO] Task started: fastANI
[2023-03-18 20:14:54,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c79d165-7827-44f9-98a6-7fa444d6568d/OceanDNA-b40098.fa --refList OceanDNA-b40098/target_genomes_gtdb.txt --output OceanDNA-b40098/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:00,817] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:00,822] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:15:00,822] [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
GCF_000744735.1	s__Porticoccus hydrocarbonoclasticus	98.7222	783	878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.20	98.73	0.89	0.78	4	conclusive
GCA_002707685.1	s__Porticoccus sp002707685	94.9255	767	878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.58	99.58	0.96	0.96	2	-
GCA_002341315.1	s__Porticoccus sp002341315	94.6437	716	878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733125.1	s__Porticoccus sp002733125	93.8649	638	878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227015.1	s__Porticoccus sp006227015	76.676	72	878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746985.1	s__Porticoccus sp002746985	76.5287	83	878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	97.07	97.07	0.91	0.91	2	-
GCA_011049795.1	s__Porticoccus sp011049795	76.1595	71	878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:15:00,823] [INFO] GTDB search result was written to OceanDNA-b40098/result_gtdb.tsv
[2023-03-18 20:15:00,823] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:00,823] [INFO] DFAST_QC result json was written to OceanDNA-b40098/dqc_result.json
[2023-03-18 20:15:00,824] [INFO] DFAST_QC completed!
[2023-03-18 20:15:00,824] [INFO] Total running time: 0h1m29s