[2023-03-18 07:58:06,153] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:58:06,153] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:58:06,153] [INFO] DQC Reference Directory: /var/lib/cwl/stgd853c609-674b-48ad-96cd-25b5ad95a77f/dqc_reference
[2023-03-18 07:58:07,246] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:58:07,247] [INFO] Task started: Prodigal
[2023-03-18 07:58:07,248] [INFO] Running command: cat /var/lib/cwl/stg6d1253cf-5fbf-4dcf-82df-f41b16e96350/OceanDNA-b36757.fa | prodigal -d OceanDNA-b36757/cds.fna -a OceanDNA-b36757/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:58:22,542] [INFO] Task succeeded: Prodigal
[2023-03-18 07:58:22,542] [INFO] Task started: HMMsearch
[2023-03-18 07:58:22,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b36757/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd853c609-674b-48ad-96cd-25b5ad95a77f/dqc_reference/reference_markers.hmm OceanDNA-b36757/protein.faa > /dev/null
[2023-03-18 07:58:22,733] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:58:22,734] [INFO] Found 6/6 markers.
[2023-03-18 07:58:22,755] [INFO] Query marker FASTA was written to OceanDNA-b36757/markers.fasta
[2023-03-18 07:58:22,756] [INFO] Task started: Blastn
[2023-03-18 07:58:22,756] [INFO] Running command: blastn -query OceanDNA-b36757/markers.fasta -db /var/lib/cwl/stgd853c609-674b-48ad-96cd-25b5ad95a77f/dqc_reference/reference_markers.fasta -out OceanDNA-b36757/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:58:23,316] [INFO] Task succeeded: Blastn
[2023-03-18 07:58:23,317] [INFO] Selected 27 target genomes.
[2023-03-18 07:58:23,317] [INFO] Target genome list was writen to OceanDNA-b36757/target_genomes.txt
[2023-03-18 07:58:23,329] [INFO] Task started: fastANI
[2023-03-18 07:58:23,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d1253cf-5fbf-4dcf-82df-f41b16e96350/OceanDNA-b36757.fa --refList OceanDNA-b36757/target_genomes.txt --output OceanDNA-b36757/fastani_result.tsv --threads 1
[2023-03-18 07:58:38,819] [INFO] Task succeeded: fastANI
[2023-03-18 07:58:38,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd853c609-674b-48ad-96cd-25b5ad95a77f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:58:38,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd853c609-674b-48ad-96cd-25b5ad95a77f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:58:38,819] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:58:38,819] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:58:38,819] [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
--------------------------------------------------------------------------------
[2023-03-18 07:58:38,820] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36757/tc_result.tsv
[2023-03-18 07:58:38,820] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:58:38,820] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:58:38,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd853c609-674b-48ad-96cd-25b5ad95a77f/dqc_reference/checkm_data
[2023-03-18 07:58:38,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:58:38,827] [INFO] Task started: CheckM
[2023-03-18 07:58:38,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36757/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36757/checkm_input OceanDNA-b36757/checkm_result
[2023-03-18 07:59:19,875] [INFO] Task succeeded: CheckM
[2023-03-18 07:59:19,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.57%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:59:19,877] [INFO] ===== Completeness check finished =====
[2023-03-18 07:59:19,878] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:59:19,878] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36757/markers.fasta)
[2023-03-18 07:59:19,878] [INFO] Task started: Blastn
[2023-03-18 07:59:19,878] [INFO] Running command: blastn -query OceanDNA-b36757/markers.fasta -db /var/lib/cwl/stgd853c609-674b-48ad-96cd-25b5ad95a77f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36757/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:59:20,743] [INFO] Task succeeded: Blastn
[2023-03-18 07:59:20,744] [INFO] Selected 28 target genomes.
[2023-03-18 07:59:20,744] [INFO] Target genome list was writen to OceanDNA-b36757/target_genomes_gtdb.txt
[2023-03-18 07:59:20,772] [INFO] Task started: fastANI
[2023-03-18 07:59:20,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d1253cf-5fbf-4dcf-82df-f41b16e96350/OceanDNA-b36757.fa --refList OceanDNA-b36757/target_genomes_gtdb.txt --output OceanDNA-b36757/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:59:36,996] [INFO] Task succeeded: fastANI
[2023-03-18 07:59:36,998] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:59:36,999] [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_002714125.1	s__GCA-002728675 sp002714125	98.6602	701	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__GCA-002728675	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002728675.1	s__GCA-002728675 sp002728675	76.558	177	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__GCA-002728675	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:59:36,999] [INFO] GTDB search result was written to OceanDNA-b36757/result_gtdb.tsv
[2023-03-18 07:59:36,999] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:59:36,999] [INFO] DFAST_QC result json was written to OceanDNA-b36757/dqc_result.json
[2023-03-18 07:59:36,999] [INFO] DFAST_QC completed!
[2023-03-18 07:59:36,999] [INFO] Total running time: 0h1m31s