[2023-03-17 08:39:27,395] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:27,395] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:27,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg06fd4977-e33c-4604-ab18-2f6c5060d766/dqc_reference
[2023-03-17 08:39:28,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:28,534] [INFO] Task started: Prodigal
[2023-03-17 08:39:28,534] [INFO] Running command: cat /var/lib/cwl/stg98a316ac-6edb-41e4-9a0a-d94803361290/OceanDNA-b39556.fa | prodigal -d OceanDNA-b39556/cds.fna -a OceanDNA-b39556/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:39:40,203] [INFO] Task succeeded: Prodigal
[2023-03-17 08:39:40,203] [INFO] Task started: HMMsearch
[2023-03-17 08:39:40,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b39556/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06fd4977-e33c-4604-ab18-2f6c5060d766/dqc_reference/reference_markers.hmm OceanDNA-b39556/protein.faa > /dev/null
[2023-03-17 08:39:40,412] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:39:40,413] [INFO] Found 6/6 markers.
[2023-03-17 08:39:40,427] [INFO] Query marker FASTA was written to OceanDNA-b39556/markers.fasta
[2023-03-17 08:39:40,428] [INFO] Task started: Blastn
[2023-03-17 08:39:40,428] [INFO] Running command: blastn -query OceanDNA-b39556/markers.fasta -db /var/lib/cwl/stg06fd4977-e33c-4604-ab18-2f6c5060d766/dqc_reference/reference_markers.fasta -out OceanDNA-b39556/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:40,985] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:40,985] [INFO] Selected 34 target genomes.
[2023-03-17 08:39:40,986] [INFO] Target genome list was writen to OceanDNA-b39556/target_genomes.txt
[2023-03-17 08:39:41,299] [INFO] Task started: fastANI
[2023-03-17 08:39:41,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg98a316ac-6edb-41e4-9a0a-d94803361290/OceanDNA-b39556.fa --refList OceanDNA-b39556/target_genomes.txt --output OceanDNA-b39556/fastani_result.tsv --threads 1
[2023-03-17 08:40:00,346] [INFO] Task succeeded: fastANI
[2023-03-17 08:40:00,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06fd4977-e33c-4604-ab18-2f6c5060d766/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:40:00,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06fd4977-e33c-4604-ab18-2f6c5060d766/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:40:00,346] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:40:00,347] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:40:00,347] [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 08:40:00,347] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39556/tc_result.tsv
[2023-03-17 08:40:00,347] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:40:00,347] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:40:00,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06fd4977-e33c-4604-ab18-2f6c5060d766/dqc_reference/checkm_data
[2023-03-17 08:40:00,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:40:00,354] [INFO] Task started: CheckM
[2023-03-17 08:40:00,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39556/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39556/checkm_input OceanDNA-b39556/checkm_result
[2023-03-17 08:40:33,365] [INFO] Task succeeded: CheckM
[2023-03-17 08:40:33,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:40:33,367] [INFO] ===== Completeness check finished =====
[2023-03-17 08:40:33,367] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:40:33,367] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39556/markers.fasta)
[2023-03-17 08:40:33,368] [INFO] Task started: Blastn
[2023-03-17 08:40:33,369] [INFO] Running command: blastn -query OceanDNA-b39556/markers.fasta -db /var/lib/cwl/stg06fd4977-e33c-4604-ab18-2f6c5060d766/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39556/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:40:34,166] [INFO] Task succeeded: Blastn
[2023-03-17 08:40:34,166] [INFO] Selected 24 target genomes.
[2023-03-17 08:40:34,167] [INFO] Target genome list was writen to OceanDNA-b39556/target_genomes_gtdb.txt
[2023-03-17 08:40:34,425] [INFO] Task started: fastANI
[2023-03-17 08:40:34,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg98a316ac-6edb-41e4-9a0a-d94803361290/OceanDNA-b39556.fa --refList OceanDNA-b39556/target_genomes_gtdb.txt --output OceanDNA-b39556/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:40:43,181] [INFO] Task succeeded: fastANI
[2023-03-17 08:40:43,191] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:40:43,191] [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_905182245.1	s__HTCC2207 sp905182245	79.1614	178	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335945.1	s__HTCC2207 sp002335945	79.1246	286	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_018664075.1	s__HTCC2207 sp018664075	78.0037	174	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_905478975.1	s__HTCC2207 sp905478975	77.8727	100	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153445.1	s__HTCC2207 sp000153445	77.8665	128	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_002378645.1	s__HTCC2207 sp002378645	77.432	157	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_905182855.1	s__HTCC2207 sp905182855	77.3954	135	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002334915.1	s__HTCC2207 sp002334915	77.3881	172	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_017858135.1	s__HTCC2207 sp017858135	77.223	105	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_018663035.1	s__HTCC2207 sp018663035	77.1419	140	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_000511875.1	s__HTCC2207 sp000511875	76.9114	130	671	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	76.882	71	671	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	76.7985	66	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.34	98.71	0.91	0.87	10	-
GCA_905182275.1	s__HTCC2207 sp905182275	76.7639	57	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002382445.1	s__HTCC2207 sp002382445	76.7511	60	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.82	99.82	0.95	0.95	2	-
GCA_017858295.1	s__HTCC2207 sp017858295	76.6298	89	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-03-17 08:40:43,191] [INFO] GTDB search result was written to OceanDNA-b39556/result_gtdb.tsv
[2023-03-17 08:40:43,191] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:40:43,192] [INFO] DFAST_QC result json was written to OceanDNA-b39556/dqc_result.json
[2023-03-17 08:40:43,192] [INFO] DFAST_QC completed!
[2023-03-17 08:40:43,192] [INFO] Total running time: 0h1m16s