[2023-03-16 01:21:12,713] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:21:12,715] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:21:12,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f62d091-057d-4f43-aa27-e9fa34a8d89f/dqc_reference
[2023-03-16 01:21:13,828] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:21:13,828] [INFO] Task started: Prodigal
[2023-03-16 01:21:13,828] [INFO] Running command: cat /var/lib/cwl/stg92e7d9fd-241e-4aa4-9cac-cbf62f9520d9/OceanDNA-b31313.fa | prodigal -d OceanDNA-b31313/cds.fna -a OceanDNA-b31313/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:21:32,421] [INFO] Task succeeded: Prodigal
[2023-03-16 01:21:32,422] [INFO] Task started: HMMsearch
[2023-03-16 01:21:32,422] [INFO] Running command: hmmsearch --tblout OceanDNA-b31313/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f62d091-057d-4f43-aa27-e9fa34a8d89f/dqc_reference/reference_markers.hmm OceanDNA-b31313/protein.faa > /dev/null
[2023-03-16 01:21:32,626] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:21:32,626] [INFO] Found 6/6 markers.
[2023-03-16 01:21:32,670] [INFO] Query marker FASTA was written to OceanDNA-b31313/markers.fasta
[2023-03-16 01:21:32,671] [INFO] Task started: Blastn
[2023-03-16 01:21:32,672] [INFO] Running command: blastn -query OceanDNA-b31313/markers.fasta -db /var/lib/cwl/stg6f62d091-057d-4f43-aa27-e9fa34a8d89f/dqc_reference/reference_markers.fasta -out OceanDNA-b31313/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:21:33,235] [INFO] Task succeeded: Blastn
[2023-03-16 01:21:33,245] [INFO] Selected 30 target genomes.
[2023-03-16 01:21:33,245] [INFO] Target genome list was writen to OceanDNA-b31313/target_genomes.txt
[2023-03-16 01:21:33,292] [INFO] Task started: fastANI
[2023-03-16 01:21:33,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg92e7d9fd-241e-4aa4-9cac-cbf62f9520d9/OceanDNA-b31313.fa --refList OceanDNA-b31313/target_genomes.txt --output OceanDNA-b31313/fastani_result.tsv --threads 1
[2023-03-16 01:21:53,014] [INFO] Task succeeded: fastANI
[2023-03-16 01:21:53,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f62d091-057d-4f43-aa27-e9fa34a8d89f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:21:53,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f62d091-057d-4f43-aa27-e9fa34a8d89f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:21:53,015] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:21:53,015] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:21:53,015] [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 01:21:53,019] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31313/tc_result.tsv
[2023-03-16 01:21:53,026] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:21:53,026] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:21:53,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f62d091-057d-4f43-aa27-e9fa34a8d89f/dqc_reference/checkm_data
[2023-03-16 01:21:53,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:21:53,041] [INFO] Task started: CheckM
[2023-03-16 01:21:53,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31313/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31313/checkm_input OceanDNA-b31313/checkm_result
[2023-03-16 01:22:40,882] [INFO] Task succeeded: CheckM
[2023-03-16 01:22:40,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:22:40,932] [INFO] ===== Completeness check finished =====
[2023-03-16 01:22:40,932] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:22:40,932] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31313/markers.fasta)
[2023-03-16 01:22:40,933] [INFO] Task started: Blastn
[2023-03-16 01:22:40,933] [INFO] Running command: blastn -query OceanDNA-b31313/markers.fasta -db /var/lib/cwl/stg6f62d091-057d-4f43-aa27-e9fa34a8d89f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31313/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:22:41,749] [INFO] Task succeeded: Blastn
[2023-03-16 01:22:41,763] [INFO] Selected 26 target genomes.
[2023-03-16 01:22:41,763] [INFO] Target genome list was writen to OceanDNA-b31313/target_genomes_gtdb.txt
[2023-03-16 01:22:42,167] [INFO] Task started: fastANI
[2023-03-16 01:22:42,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg92e7d9fd-241e-4aa4-9cac-cbf62f9520d9/OceanDNA-b31313.fa --refList OceanDNA-b31313/target_genomes_gtdb.txt --output OceanDNA-b31313/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:23:00,431] [INFO] Task succeeded: fastANI
[2023-03-16 01:23:00,435] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:23:00,435] [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_002712165.1	s__UBA11612 sp002712165	76.811	142	1005	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__UBA11612	95.0	99.52	99.52	0.89	0.89	2	-
GCA_903896775.1	s__SHVO01 sp903896775	76.3665	60	1005	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SHVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888485.1	s__SHVO01 sp903888485	76.0272	103	1005	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SHVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297485.1	s__SCTM01 sp004297485	75.9735	82	1005	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SCTM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793085.1	s__GCA-2737725 sp016793085	75.8424	62	1005	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:23:00,440] [INFO] GTDB search result was written to OceanDNA-b31313/result_gtdb.tsv
[2023-03-16 01:23:00,450] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:23:00,457] [INFO] DFAST_QC result json was written to OceanDNA-b31313/dqc_result.json
[2023-03-16 01:23:00,457] [INFO] DFAST_QC completed!
[2023-03-16 01:23:00,457] [INFO] Total running time: 0h1m48s