[2023-03-15 10:49:28,646] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,646] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg0493a676-a119-4395-8d10-d7e2a3aed72a/dqc_reference
[2023-03-15 10:49:29,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,831] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,831] [INFO] Running command: cat /var/lib/cwl/stgb913cceb-b8f2-48d1-9204-2d7db35faefb/OceanDNA-b32641.fa | prodigal -d OceanDNA-b32641/cds.fna -a OceanDNA-b32641/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:40,444] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:40,444] [INFO] Task started: HMMsearch
[2023-03-15 10:49:40,444] [INFO] Running command: hmmsearch --tblout OceanDNA-b32641/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0493a676-a119-4395-8d10-d7e2a3aed72a/dqc_reference/reference_markers.hmm OceanDNA-b32641/protein.faa > /dev/null
[2023-03-15 10:49:40,645] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:40,646] [INFO] Found 6/6 markers.
[2023-03-15 10:49:40,659] [INFO] Query marker FASTA was written to OceanDNA-b32641/markers.fasta
[2023-03-15 10:49:40,660] [INFO] Task started: Blastn
[2023-03-15 10:49:40,660] [INFO] Running command: blastn -query OceanDNA-b32641/markers.fasta -db /var/lib/cwl/stg0493a676-a119-4395-8d10-d7e2a3aed72a/dqc_reference/reference_markers.fasta -out OceanDNA-b32641/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:41,199] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:41,200] [INFO] Selected 27 target genomes.
[2023-03-15 10:49:41,200] [INFO] Target genome list was writen to OceanDNA-b32641/target_genomes.txt
[2023-03-15 10:49:41,217] [INFO] Task started: fastANI
[2023-03-15 10:49:41,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgb913cceb-b8f2-48d1-9204-2d7db35faefb/OceanDNA-b32641.fa --refList OceanDNA-b32641/target_genomes.txt --output OceanDNA-b32641/fastani_result.tsv --threads 1
[2023-03-15 10:49:57,573] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:57,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0493a676-a119-4395-8d10-d7e2a3aed72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:57,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0493a676-a119-4395-8d10-d7e2a3aed72a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:57,573] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:57,573] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:49:57,573] [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 10:49:57,574] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32641/tc_result.tsv
[2023-03-15 10:49:57,574] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:57,574] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:57,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0493a676-a119-4395-8d10-d7e2a3aed72a/dqc_reference/checkm_data
[2023-03-15 10:49:57,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:57,582] [INFO] Task started: CheckM
[2023-03-15 10:49:57,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32641/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32641/checkm_input OceanDNA-b32641/checkm_result
[2023-03-15 10:50:28,658] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:28,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:28,661] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:28,661] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:28,662] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32641/markers.fasta)
[2023-03-15 10:50:28,663] [INFO] Task started: Blastn
[2023-03-15 10:50:28,663] [INFO] Running command: blastn -query OceanDNA-b32641/markers.fasta -db /var/lib/cwl/stg0493a676-a119-4395-8d10-d7e2a3aed72a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32641/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:29,382] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:29,384] [INFO] Selected 24 target genomes.
[2023-03-15 10:50:29,384] [INFO] Target genome list was writen to OceanDNA-b32641/target_genomes_gtdb.txt
[2023-03-15 10:50:29,412] [INFO] Task started: fastANI
[2023-03-15 10:50:29,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgb913cceb-b8f2-48d1-9204-2d7db35faefb/OceanDNA-b32641.fa --refList OceanDNA-b32641/target_genomes_gtdb.txt --output OceanDNA-b32641/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:42,177] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:42,179] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:50:42,179] [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_002436405.1	s__UBA6503 sp002436405	99.9987	580	588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA1280;f__UBA6503;g__UBA6503	95.0	99.95	99.85	0.99	0.96	4	conclusive
--------------------------------------------------------------------------------
[2023-03-15 10:50:42,180] [INFO] GTDB search result was written to OceanDNA-b32641/result_gtdb.tsv
[2023-03-15 10:50:42,180] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:42,181] [INFO] DFAST_QC result json was written to OceanDNA-b32641/dqc_result.json
[2023-03-15 10:50:42,181] [INFO] DFAST_QC completed!
[2023-03-15 10:50:42,181] [INFO] Total running time: 0h1m14s