[2023-03-19 01:12:13,943] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:12:13,944] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:12:13,944] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d62ee2e-4299-4176-af38-4f406b2415f5/dqc_reference
[2023-03-19 01:12:15,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:12:15,733] [INFO] Task started: Prodigal
[2023-03-19 01:12:15,733] [INFO] Running command: cat /var/lib/cwl/stgce70879f-f498-48ee-acd2-e71962ef02a6/OceanDNA-b39552.fa | prodigal -d OceanDNA-b39552/cds.fna -a OceanDNA-b39552/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:12:24,576] [INFO] Task succeeded: Prodigal
[2023-03-19 01:12:24,576] [INFO] Task started: HMMsearch
[2023-03-19 01:12:24,576] [INFO] Running command: hmmsearch --tblout OceanDNA-b39552/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d62ee2e-4299-4176-af38-4f406b2415f5/dqc_reference/reference_markers.hmm OceanDNA-b39552/protein.faa > /dev/null
[2023-03-19 01:12:24,743] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:12:24,743] [INFO] Found 6/6 markers.
[2023-03-19 01:12:24,757] [INFO] Query marker FASTA was written to OceanDNA-b39552/markers.fasta
[2023-03-19 01:12:24,757] [INFO] Task started: Blastn
[2023-03-19 01:12:24,757] [INFO] Running command: blastn -query OceanDNA-b39552/markers.fasta -db /var/lib/cwl/stg5d62ee2e-4299-4176-af38-4f406b2415f5/dqc_reference/reference_markers.fasta -out OceanDNA-b39552/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:25,339] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:25,340] [INFO] Selected 32 target genomes.
[2023-03-19 01:12:25,340] [INFO] Target genome list was writen to OceanDNA-b39552/target_genomes.txt
[2023-03-19 01:12:25,363] [INFO] Task started: fastANI
[2023-03-19 01:12:25,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgce70879f-f498-48ee-acd2-e71962ef02a6/OceanDNA-b39552.fa --refList OceanDNA-b39552/target_genomes.txt --output OceanDNA-b39552/fastani_result.tsv --threads 1
[2023-03-19 01:12:47,205] [INFO] Task succeeded: fastANI
[2023-03-19 01:12:47,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d62ee2e-4299-4176-af38-4f406b2415f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:12:47,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d62ee2e-4299-4176-af38-4f406b2415f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:12:47,206] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:12:47,206] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:12:47,206] [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 01:12:47,207] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39552/tc_result.tsv
[2023-03-19 01:12:47,207] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:12:47,207] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:12:47,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d62ee2e-4299-4176-af38-4f406b2415f5/dqc_reference/checkm_data
[2023-03-19 01:12:47,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:12:47,214] [INFO] Task started: CheckM
[2023-03-19 01:12:47,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39552/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39552/checkm_input OceanDNA-b39552/checkm_result
[2023-03-19 01:13:13,952] [INFO] Task succeeded: CheckM
[2023-03-19 01:13:13,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:13:13,955] [INFO] ===== Completeness check finished =====
[2023-03-19 01:13:13,955] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:13:13,955] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39552/markers.fasta)
[2023-03-19 01:13:13,956] [INFO] Task started: Blastn
[2023-03-19 01:13:13,956] [INFO] Running command: blastn -query OceanDNA-b39552/markers.fasta -db /var/lib/cwl/stg5d62ee2e-4299-4176-af38-4f406b2415f5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39552/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:14,793] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:14,795] [INFO] Selected 13 target genomes.
[2023-03-19 01:13:14,795] [INFO] Target genome list was writen to OceanDNA-b39552/target_genomes_gtdb.txt
[2023-03-19 01:13:14,807] [INFO] Task started: fastANI
[2023-03-19 01:13:14,807] [INFO] Running command: fastANI --query /var/lib/cwl/stgce70879f-f498-48ee-acd2-e71962ef02a6/OceanDNA-b39552.fa --refList OceanDNA-b39552/target_genomes_gtdb.txt --output OceanDNA-b39552/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:13:19,536] [INFO] Task succeeded: fastANI
[2023-03-19 01:13:19,542] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:13:19,542] [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_002378645.1	s__HTCC2207 sp002378645	83.4422	399	509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_002334915.1	s__HTCC2207 sp002334915	83.0285	387	509	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	80.2527	245	509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_018663035.1	s__HTCC2207 sp018663035	78.3898	204	509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_905182265.1	s__HTCC2207 sp905182265	78.1847	229	509	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	77.8152	144	509	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	77.5219	94	509	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	77.3082	91	509	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	77.0371	126	509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:13:19,542] [INFO] GTDB search result was written to OceanDNA-b39552/result_gtdb.tsv
[2023-03-19 01:13:19,543] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:13:19,544] [INFO] DFAST_QC result json was written to OceanDNA-b39552/dqc_result.json
[2023-03-19 01:13:19,544] [INFO] DFAST_QC completed!
[2023-03-19 01:13:19,544] [INFO] Total running time: 0h1m6s