[2023-03-15 11:36:00,595] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:36:00,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:36:00,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg44154de3-5728-4b43-822c-f76798bcf04e/dqc_reference
[2023-03-15 11:36:02,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:36:02,577] [INFO] Task started: Prodigal
[2023-03-15 11:36:02,577] [INFO] Running command: cat /var/lib/cwl/stg8e9e4d5e-5b81-471f-af2d-cbfa6f640108/OceanDNA-b12499.fa | prodigal -d OceanDNA-b12499/cds.fna -a OceanDNA-b12499/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:36:24,912] [INFO] Task succeeded: Prodigal
[2023-03-15 11:36:24,912] [INFO] Task started: HMMsearch
[2023-03-15 11:36:24,912] [INFO] Running command: hmmsearch --tblout OceanDNA-b12499/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44154de3-5728-4b43-822c-f76798bcf04e/dqc_reference/reference_markers.hmm OceanDNA-b12499/protein.faa > /dev/null
[2023-03-15 11:36:25,124] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:36:25,125] [INFO] Found 6/6 markers.
[2023-03-15 11:36:25,202] [INFO] Query marker FASTA was written to OceanDNA-b12499/markers.fasta
[2023-03-15 11:36:25,203] [INFO] Task started: Blastn
[2023-03-15 11:36:25,203] [INFO] Running command: blastn -query OceanDNA-b12499/markers.fasta -db /var/lib/cwl/stg44154de3-5728-4b43-822c-f76798bcf04e/dqc_reference/reference_markers.fasta -out OceanDNA-b12499/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:36:25,759] [INFO] Task succeeded: Blastn
[2023-03-15 11:36:25,768] [INFO] Selected 32 target genomes.
[2023-03-15 11:36:25,768] [INFO] Target genome list was writen to OceanDNA-b12499/target_genomes.txt
[2023-03-15 11:36:25,786] [INFO] Task started: fastANI
[2023-03-15 11:36:25,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e9e4d5e-5b81-471f-af2d-cbfa6f640108/OceanDNA-b12499.fa --refList OceanDNA-b12499/target_genomes.txt --output OceanDNA-b12499/fastani_result.tsv --threads 1
[2023-03-15 11:36:47,227] [INFO] Task succeeded: fastANI
[2023-03-15 11:36:47,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44154de3-5728-4b43-822c-f76798bcf04e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:36:47,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44154de3-5728-4b43-822c-f76798bcf04e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:36:47,228] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:36:47,228] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:36:47,228] [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
--------------------------------------------------------------------------------
[2023-03-15 11:36:47,233] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12499/tc_result.tsv
[2023-03-15 11:36:47,241] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:36:47,242] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:36:47,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44154de3-5728-4b43-822c-f76798bcf04e/dqc_reference/checkm_data
[2023-03-15 11:36:47,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:36:47,256] [INFO] Task started: CheckM
[2023-03-15 11:36:47,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12499/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12499/checkm_input OceanDNA-b12499/checkm_result
[2023-03-15 11:37:46,079] [INFO] Task succeeded: CheckM
[2023-03-15 11:37:46,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:37:46,173] [INFO] ===== Completeness check finished =====
[2023-03-15 11:37:46,174] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:37:46,174] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12499/markers.fasta)
[2023-03-15 11:37:46,175] [INFO] Task started: Blastn
[2023-03-15 11:37:46,175] [INFO] Running command: blastn -query OceanDNA-b12499/markers.fasta -db /var/lib/cwl/stg44154de3-5728-4b43-822c-f76798bcf04e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12499/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:37:46,868] [INFO] Task succeeded: Blastn
[2023-03-15 11:37:46,878] [INFO] Selected 29 target genomes.
[2023-03-15 11:37:46,878] [INFO] Target genome list was writen to OceanDNA-b12499/target_genomes_gtdb.txt
[2023-03-15 11:37:46,969] [INFO] Task started: fastANI
[2023-03-15 11:37:46,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e9e4d5e-5b81-471f-af2d-cbfa6f640108/OceanDNA-b12499.fa --refList OceanDNA-b12499/target_genomes_gtdb.txt --output OceanDNA-b12499/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:38:04,771] [INFO] Task succeeded: fastANI
[2023-03-15 11:38:04,774] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:38:04,774] [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_003456455.1	s__UBA10329 sp003456455	79.3975	227	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10329;g__UBA10329	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402015.1	s__UBA10329 sp018402015	77.0936	142	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10329;g__UBA10329	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124845.1	s__UBA10329 sp016124845	76.9135	137	778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10329;g__UBA10329	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:38:04,778] [INFO] GTDB search result was written to OceanDNA-b12499/result_gtdb.tsv
[2023-03-15 11:38:04,783] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:38:04,788] [INFO] DFAST_QC result json was written to OceanDNA-b12499/dqc_result.json
[2023-03-15 11:38:04,788] [INFO] DFAST_QC completed!
[2023-03-15 11:38:04,788] [INFO] Total running time: 0h2m4s