[2023-03-17 15:30:07,751] [INFO] DFAST_QC pipeline started.
[2023-03-17 15:30:07,751] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 15:30:07,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b4ee304-db96-40ec-b7ad-d95603a56f39/dqc_reference
[2023-03-17 15:30:08,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 15:30:08,890] [INFO] Task started: Prodigal
[2023-03-17 15:30:08,890] [INFO] Running command: cat /var/lib/cwl/stg74134650-503e-44fb-8f86-aba9162dc4df/OceanDNA-b36821.fa | prodigal -d OceanDNA-b36821/cds.fna -a OceanDNA-b36821/protein.faa -g 11 -q > /dev/null
[2023-03-17 15:30:22,791] [INFO] Task succeeded: Prodigal
[2023-03-17 15:30:22,791] [INFO] Task started: HMMsearch
[2023-03-17 15:30:22,791] [INFO] Running command: hmmsearch --tblout OceanDNA-b36821/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b4ee304-db96-40ec-b7ad-d95603a56f39/dqc_reference/reference_markers.hmm OceanDNA-b36821/protein.faa > /dev/null
[2023-03-17 15:30:23,246] [INFO] Task succeeded: HMMsearch
[2023-03-17 15:30:23,247] [INFO] Found 6/6 markers.
[2023-03-17 15:30:23,264] [INFO] Query marker FASTA was written to OceanDNA-b36821/markers.fasta
[2023-03-17 15:30:23,264] [INFO] Task started: Blastn
[2023-03-17 15:30:23,264] [INFO] Running command: blastn -query OceanDNA-b36821/markers.fasta -db /var/lib/cwl/stg0b4ee304-db96-40ec-b7ad-d95603a56f39/dqc_reference/reference_markers.fasta -out OceanDNA-b36821/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:30:24,763] [INFO] Task succeeded: Blastn
[2023-03-17 15:30:24,763] [INFO] Selected 24 target genomes.
[2023-03-17 15:30:24,764] [INFO] Target genome list was writen to OceanDNA-b36821/target_genomes.txt
[2023-03-17 15:30:24,778] [INFO] Task started: fastANI
[2023-03-17 15:30:24,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg74134650-503e-44fb-8f86-aba9162dc4df/OceanDNA-b36821.fa --refList OceanDNA-b36821/target_genomes.txt --output OceanDNA-b36821/fastani_result.tsv --threads 1
[2023-03-17 15:30:45,944] [INFO] Task succeeded: fastANI
[2023-03-17 15:30:45,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b4ee304-db96-40ec-b7ad-d95603a56f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 15:30:45,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b4ee304-db96-40ec-b7ad-d95603a56f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 15:30:45,945] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 15:30:45,945] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 15:30:45,945] [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 15:30:45,945] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36821/tc_result.tsv
[2023-03-17 15:30:45,946] [INFO] ===== Taxonomy check completed =====
[2023-03-17 15:30:45,946] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 15:30:45,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b4ee304-db96-40ec-b7ad-d95603a56f39/dqc_reference/checkm_data
[2023-03-17 15:30:45,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 15:30:45,952] [INFO] Task started: CheckM
[2023-03-17 15:30:45,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36821/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36821/checkm_input OceanDNA-b36821/checkm_result
[2023-03-17 15:31:31,282] [INFO] Task succeeded: CheckM
[2023-03-17 15:31:31,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 15:31:31,285] [INFO] ===== Completeness check finished =====
[2023-03-17 15:31:31,285] [INFO] ===== Start GTDB Search =====
[2023-03-17 15:31:31,285] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36821/markers.fasta)
[2023-03-17 15:31:31,287] [INFO] Task started: Blastn
[2023-03-17 15:31:31,287] [INFO] Running command: blastn -query OceanDNA-b36821/markers.fasta -db /var/lib/cwl/stg0b4ee304-db96-40ec-b7ad-d95603a56f39/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36821/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:31:32,329] [INFO] Task succeeded: Blastn
[2023-03-17 15:31:32,330] [INFO] Selected 21 target genomes.
[2023-03-17 15:31:32,331] [INFO] Target genome list was writen to OceanDNA-b36821/target_genomes_gtdb.txt
[2023-03-17 15:31:32,657] [INFO] Task started: fastANI
[2023-03-17 15:31:32,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg74134650-503e-44fb-8f86-aba9162dc4df/OceanDNA-b36821.fa --refList OceanDNA-b36821/target_genomes_gtdb.txt --output OceanDNA-b36821/fastani_result_gtdb.tsv --threads 1
[2023-03-17 15:31:43,702] [INFO] Task succeeded: fastANI
[2023-03-17 15:31:43,705] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 15:31:43,705] [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_002313255.1	s__UBA11889 sp002313255	79.4454	443	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.77	98.77	0.86	0.86	2	-
GCA_002719135.1	s__UBA11889 sp002719135	79.1499	341	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.11	97.65	0.74	0.72	3	-
GCA_002715785.1	s__UBA11889 sp002715785	78.6387	299	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	99.18	99.12	0.79	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-17 15:31:43,706] [INFO] GTDB search result was written to OceanDNA-b36821/result_gtdb.tsv
[2023-03-17 15:31:43,706] [INFO] ===== GTDB Search completed =====
[2023-03-17 15:31:43,706] [INFO] DFAST_QC result json was written to OceanDNA-b36821/dqc_result.json
[2023-03-17 15:31:43,706] [INFO] DFAST_QC completed!
[2023-03-17 15:31:43,706] [INFO] Total running time: 0h1m36s