[2023-03-16 23:35:12,979] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:12,980] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:12,980] [INFO] DQC Reference Directory: /var/lib/cwl/stg70ecaadf-3e0a-4215-9a56-32980535ea45/dqc_reference
[2023-03-16 23:35:14,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,100] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,100] [INFO] Running command: cat /var/lib/cwl/stg31f0d150-0049-4b5e-a5ca-990cba798cb1/OceanDNA-b32917.fa | prodigal -d OceanDNA-b32917/cds.fna -a OceanDNA-b32917/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:28,928] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:28,928] [INFO] Task started: HMMsearch
[2023-03-16 23:35:28,929] [INFO] Running command: hmmsearch --tblout OceanDNA-b32917/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70ecaadf-3e0a-4215-9a56-32980535ea45/dqc_reference/reference_markers.hmm OceanDNA-b32917/protein.faa > /dev/null
[2023-03-16 23:35:29,104] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:29,104] [INFO] Found 6/6 markers.
[2023-03-16 23:35:29,122] [INFO] Query marker FASTA was written to OceanDNA-b32917/markers.fasta
[2023-03-16 23:35:29,123] [INFO] Task started: Blastn
[2023-03-16 23:35:29,123] [INFO] Running command: blastn -query OceanDNA-b32917/markers.fasta -db /var/lib/cwl/stg70ecaadf-3e0a-4215-9a56-32980535ea45/dqc_reference/reference_markers.fasta -out OceanDNA-b32917/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:29,677] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:29,678] [INFO] Selected 38 target genomes.
[2023-03-16 23:35:29,678] [INFO] Target genome list was writen to OceanDNA-b32917/target_genomes.txt
[2023-03-16 23:35:29,708] [INFO] Task started: fastANI
[2023-03-16 23:35:29,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg31f0d150-0049-4b5e-a5ca-990cba798cb1/OceanDNA-b32917.fa --refList OceanDNA-b32917/target_genomes.txt --output OceanDNA-b32917/fastani_result.tsv --threads 1
[2023-03-16 23:35:56,073] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:56,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70ecaadf-3e0a-4215-9a56-32980535ea45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:56,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70ecaadf-3e0a-4215-9a56-32980535ea45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:56,074] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:56,074] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:35:56,074] [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 23:35:56,074] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32917/tc_result.tsv
[2023-03-16 23:35:56,074] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:56,074] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:56,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70ecaadf-3e0a-4215-9a56-32980535ea45/dqc_reference/checkm_data
[2023-03-16 23:35:56,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:56,081] [INFO] Task started: CheckM
[2023-03-16 23:35:56,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32917/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32917/checkm_input OceanDNA-b32917/checkm_result
[2023-03-16 23:36:36,295] [INFO] Task succeeded: CheckM
[2023-03-16 23:36:36,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 23:36:36,298] [INFO] ===== Completeness check finished =====
[2023-03-16 23:36:36,298] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:36:36,298] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32917/markers.fasta)
[2023-03-16 23:36:36,300] [INFO] Task started: Blastn
[2023-03-16 23:36:36,300] [INFO] Running command: blastn -query OceanDNA-b32917/markers.fasta -db /var/lib/cwl/stg70ecaadf-3e0a-4215-9a56-32980535ea45/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32917/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:36:37,108] [INFO] Task succeeded: Blastn
[2023-03-16 23:36:37,109] [INFO] Selected 25 target genomes.
[2023-03-16 23:36:37,109] [INFO] Target genome list was writen to OceanDNA-b32917/target_genomes_gtdb.txt
[2023-03-16 23:36:37,647] [INFO] Task started: fastANI
[2023-03-16 23:36:37,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg31f0d150-0049-4b5e-a5ca-990cba798cb1/OceanDNA-b32917.fa --refList OceanDNA-b32917/target_genomes_gtdb.txt --output OceanDNA-b32917/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:36:53,648] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:53,651] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:36:53,651] [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_002717225.1	s__PTKB01 sp002717225	99.2245	658	823	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018666805.1	s__PTKB01 sp018666805	76.6723	172	823	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
GCA_002937555.1	s__PTKB01 sp002937555	76.538	144	823	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:36:53,651] [INFO] GTDB search result was written to OceanDNA-b32917/result_gtdb.tsv
[2023-03-16 23:36:53,651] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:36:53,652] [INFO] DFAST_QC result json was written to OceanDNA-b32917/dqc_result.json
[2023-03-16 23:36:53,652] [INFO] DFAST_QC completed!
[2023-03-16 23:36:53,652] [INFO] Total running time: 0h1m41s