[2023-03-19 00:19:08,848] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:19:08,848] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:19:08,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e58fdb1-7636-4761-a3d8-5bf10ede7223/dqc_reference
[2023-03-19 00:19:10,373] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:19:10,373] [INFO] Task started: Prodigal
[2023-03-19 00:19:10,373] [INFO] Running command: cat /var/lib/cwl/stg29132104-4358-45ea-af90-ca113f960ccb/OceanDNA-b39468.fa | prodigal -d OceanDNA-b39468/cds.fna -a OceanDNA-b39468/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:19:22,219] [INFO] Task succeeded: Prodigal
[2023-03-19 00:19:22,220] [INFO] Task started: HMMsearch
[2023-03-19 00:19:22,220] [INFO] Running command: hmmsearch --tblout OceanDNA-b39468/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e58fdb1-7636-4761-a3d8-5bf10ede7223/dqc_reference/reference_markers.hmm OceanDNA-b39468/protein.faa > /dev/null
[2023-03-19 00:19:22,410] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:19:22,411] [INFO] Found 6/6 markers.
[2023-03-19 00:19:22,426] [INFO] Query marker FASTA was written to OceanDNA-b39468/markers.fasta
[2023-03-19 00:19:22,427] [INFO] Task started: Blastn
[2023-03-19 00:19:22,427] [INFO] Running command: blastn -query OceanDNA-b39468/markers.fasta -db /var/lib/cwl/stg0e58fdb1-7636-4761-a3d8-5bf10ede7223/dqc_reference/reference_markers.fasta -out OceanDNA-b39468/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:19:23,039] [INFO] Task succeeded: Blastn
[2023-03-19 00:19:23,040] [INFO] Selected 29 target genomes.
[2023-03-19 00:19:23,041] [INFO] Target genome list was writen to OceanDNA-b39468/target_genomes.txt
[2023-03-19 00:19:23,060] [INFO] Task started: fastANI
[2023-03-19 00:19:23,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg29132104-4358-45ea-af90-ca113f960ccb/OceanDNA-b39468.fa --refList OceanDNA-b39468/target_genomes.txt --output OceanDNA-b39468/fastani_result.tsv --threads 1
[2023-03-19 00:19:40,992] [INFO] Task succeeded: fastANI
[2023-03-19 00:19:40,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e58fdb1-7636-4761-a3d8-5bf10ede7223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:19:40,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e58fdb1-7636-4761-a3d8-5bf10ede7223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:19:40,992] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:19:40,992] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:19:40,992] [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
--------------------------------------------------------------------------------
[2023-03-19 00:19:40,993] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39468/tc_result.tsv
[2023-03-19 00:19:40,993] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:19:40,993] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:19:40,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e58fdb1-7636-4761-a3d8-5bf10ede7223/dqc_reference/checkm_data
[2023-03-19 00:19:40,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:19:40,999] [INFO] Task started: CheckM
[2023-03-19 00:19:40,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39468/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39468/checkm_input OceanDNA-b39468/checkm_result
[2023-03-19 00:20:14,499] [INFO] Task succeeded: CheckM
[2023-03-19 00:20:14,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:20:14,501] [INFO] ===== Completeness check finished =====
[2023-03-19 00:20:14,502] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:20:14,502] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39468/markers.fasta)
[2023-03-19 00:20:14,503] [INFO] Task started: Blastn
[2023-03-19 00:20:14,503] [INFO] Running command: blastn -query OceanDNA-b39468/markers.fasta -db /var/lib/cwl/stg0e58fdb1-7636-4761-a3d8-5bf10ede7223/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39468/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:20:15,468] [INFO] Task succeeded: Blastn
[2023-03-19 00:20:15,469] [INFO] Selected 12 target genomes.
[2023-03-19 00:20:15,469] [INFO] Target genome list was writen to OceanDNA-b39468/target_genomes_gtdb.txt
[2023-03-19 00:20:15,486] [INFO] Task started: fastANI
[2023-03-19 00:20:15,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg29132104-4358-45ea-af90-ca113f960ccb/OceanDNA-b39468.fa --refList OceanDNA-b39468/target_genomes_gtdb.txt --output OceanDNA-b39468/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:20:20,162] [INFO] Task succeeded: fastANI
[2023-03-19 00:20:20,168] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:20:20,169] [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_018663035.1	s__HTCC2207 sp018663035	81.2105	442	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_002334915.1	s__HTCC2207 sp002334915	79.9903	305	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_018664075.1	s__HTCC2207 sp018664075	79.727	283	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_002378645.1	s__HTCC2207 sp002378645	79.1341	295	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_905182265.1	s__HTCC2207 sp905182265	77.9353	240	688	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	77.6209	94	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_002335945.1	s__HTCC2207 sp002335945	77.4386	194	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_002685715.1	s__HTCC2207 sp002685715	77.2043	126	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182245.1	s__HTCC2207 sp905182245	76.913	114	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182855.1	s__HTCC2207 sp905182855	76.7371	81	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:20:20,169] [INFO] GTDB search result was written to OceanDNA-b39468/result_gtdb.tsv
[2023-03-19 00:20:20,169] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:20:20,170] [INFO] DFAST_QC result json was written to OceanDNA-b39468/dqc_result.json
[2023-03-19 00:20:20,170] [INFO] DFAST_QC completed!
[2023-03-19 00:20:20,170] [INFO] Total running time: 0h1m11s