[2023-03-17 22:37:12,600] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:37:12,600] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:37:12,600] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8af2d49-32fa-41d0-b4fe-b37bd48ab98b/dqc_reference
[2023-03-17 22:37:14,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:37:14,346] [INFO] Task started: Prodigal
[2023-03-17 22:37:14,346] [INFO] Running command: cat /var/lib/cwl/stg40837273-5daa-403a-9297-c7a7bc59b080/OceanDNA-b40083.fa | prodigal -d OceanDNA-b40083/cds.fna -a OceanDNA-b40083/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:37:20,225] [INFO] Task succeeded: Prodigal
[2023-03-17 22:37:20,225] [INFO] Task started: HMMsearch
[2023-03-17 22:37:20,225] [INFO] Running command: hmmsearch --tblout OceanDNA-b40083/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8af2d49-32fa-41d0-b4fe-b37bd48ab98b/dqc_reference/reference_markers.hmm OceanDNA-b40083/protein.faa > /dev/null
[2023-03-17 22:37:20,416] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:37:20,417] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg40837273-5daa-403a-9297-c7a7bc59b080/OceanDNA-b40083.fa]
[2023-03-17 22:37:20,426] [INFO] Query marker FASTA was written to OceanDNA-b40083/markers.fasta
[2023-03-17 22:37:20,426] [INFO] Task started: Blastn
[2023-03-17 22:37:20,426] [INFO] Running command: blastn -query OceanDNA-b40083/markers.fasta -db /var/lib/cwl/stgf8af2d49-32fa-41d0-b4fe-b37bd48ab98b/dqc_reference/reference_markers.fasta -out OceanDNA-b40083/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:21,459] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:21,460] [INFO] Selected 28 target genomes.
[2023-03-17 22:37:21,460] [INFO] Target genome list was writen to OceanDNA-b40083/target_genomes.txt
[2023-03-17 22:37:21,477] [INFO] Task started: fastANI
[2023-03-17 22:37:21,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg40837273-5daa-403a-9297-c7a7bc59b080/OceanDNA-b40083.fa --refList OceanDNA-b40083/target_genomes.txt --output OceanDNA-b40083/fastani_result.tsv --threads 1
[2023-03-17 22:37:35,769] [INFO] Task succeeded: fastANI
[2023-03-17 22:37:35,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8af2d49-32fa-41d0-b4fe-b37bd48ab98b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:37:35,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8af2d49-32fa-41d0-b4fe-b37bd48ab98b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:37:35,770] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:37:35,770] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:37:35,770] [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 22:37:35,770] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40083/tc_result.tsv
[2023-03-17 22:37:35,770] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:37:35,771] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:37:35,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8af2d49-32fa-41d0-b4fe-b37bd48ab98b/dqc_reference/checkm_data
[2023-03-17 22:37:35,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:37:35,833] [INFO] Task started: CheckM
[2023-03-17 22:37:35,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40083/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40083/checkm_input OceanDNA-b40083/checkm_result
[2023-03-17 22:37:55,777] [INFO] Task succeeded: CheckM
[2023-03-17 22:37:55,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:37:55,779] [INFO] ===== Completeness check finished =====
[2023-03-17 22:37:55,779] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:37:55,779] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40083/markers.fasta)
[2023-03-17 22:37:55,780] [INFO] Task started: Blastn
[2023-03-17 22:37:55,780] [INFO] Running command: blastn -query OceanDNA-b40083/markers.fasta -db /var/lib/cwl/stgf8af2d49-32fa-41d0-b4fe-b37bd48ab98b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40083/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:56,606] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:56,607] [INFO] Selected 24 target genomes.
[2023-03-17 22:37:56,607] [INFO] Target genome list was writen to OceanDNA-b40083/target_genomes_gtdb.txt
[2023-03-17 22:37:56,729] [INFO] Task started: fastANI
[2023-03-17 22:37:56,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg40837273-5daa-403a-9297-c7a7bc59b080/OceanDNA-b40083.fa --refList OceanDNA-b40083/target_genomes_gtdb.txt --output OceanDNA-b40083/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:38:06,381] [INFO] Task succeeded: fastANI
[2023-03-17 22:38:06,384] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:38:06,384] [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_002390525.1	s__Porticoccus sp002390525	87.5919	317	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.28	98.80	0.84	0.81	4	-
GCA_002685455.1	s__Porticoccus sp002685455	80.3426	232	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181945.1	s__Porticoccus sp905181945	77.1806	93	375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	98.63	98.63	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-17 22:38:06,384] [INFO] GTDB search result was written to OceanDNA-b40083/result_gtdb.tsv
[2023-03-17 22:38:06,384] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:38:06,385] [INFO] DFAST_QC result json was written to OceanDNA-b40083/dqc_result.json
[2023-03-17 22:38:06,385] [INFO] DFAST_QC completed!
[2023-03-17 22:38:06,385] [INFO] Total running time: 0h0m54s