[2023-03-15 17:24:01,268] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,268] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg05af35c6-f3a9-4dfc-b351-3f1947f37beb/dqc_reference
[2023-03-15 17:24:02,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,564] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,564] [INFO] Running command: cat /var/lib/cwl/stg11db009d-e144-4ec6-b998-df9be40291ac/OceanDNA-b29543.fa | prodigal -d OceanDNA-b29543/cds.fna -a OceanDNA-b29543/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:13,254] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:13,254] [INFO] Task started: HMMsearch
[2023-03-15 17:24:13,254] [INFO] Running command: hmmsearch --tblout OceanDNA-b29543/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05af35c6-f3a9-4dfc-b351-3f1947f37beb/dqc_reference/reference_markers.hmm OceanDNA-b29543/protein.faa > /dev/null
[2023-03-15 17:24:13,460] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:13,461] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg11db009d-e144-4ec6-b998-df9be40291ac/OceanDNA-b29543.fa]
[2023-03-15 17:24:13,478] [INFO] Query marker FASTA was written to OceanDNA-b29543/markers.fasta
[2023-03-15 17:24:13,479] [INFO] Task started: Blastn
[2023-03-15 17:24:13,479] [INFO] Running command: blastn -query OceanDNA-b29543/markers.fasta -db /var/lib/cwl/stg05af35c6-f3a9-4dfc-b351-3f1947f37beb/dqc_reference/reference_markers.fasta -out OceanDNA-b29543/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:13,987] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:13,988] [INFO] Selected 20 target genomes.
[2023-03-15 17:24:13,988] [INFO] Target genome list was writen to OceanDNA-b29543/target_genomes.txt
[2023-03-15 17:24:13,998] [INFO] Task started: fastANI
[2023-03-15 17:24:13,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg11db009d-e144-4ec6-b998-df9be40291ac/OceanDNA-b29543.fa --refList OceanDNA-b29543/target_genomes.txt --output OceanDNA-b29543/fastani_result.tsv --threads 1
[2023-03-15 17:24:26,199] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:26,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05af35c6-f3a9-4dfc-b351-3f1947f37beb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:26,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05af35c6-f3a9-4dfc-b351-3f1947f37beb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:26,200] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:24:26,200] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:24:26,200] [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 17:24:26,200] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29543/tc_result.tsv
[2023-03-15 17:24:26,200] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:26,200] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:26,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05af35c6-f3a9-4dfc-b351-3f1947f37beb/dqc_reference/checkm_data
[2023-03-15 17:24:26,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:26,206] [INFO] Task started: CheckM
[2023-03-15 17:24:26,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29543/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29543/checkm_input OceanDNA-b29543/checkm_result
[2023-03-15 17:24:57,271] [INFO] Task succeeded: CheckM
[2023-03-15 17:24:57,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:24:57,274] [INFO] ===== Completeness check finished =====
[2023-03-15 17:24:57,274] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:24:57,275] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29543/markers.fasta)
[2023-03-15 17:24:57,276] [INFO] Task started: Blastn
[2023-03-15 17:24:57,276] [INFO] Running command: blastn -query OceanDNA-b29543/markers.fasta -db /var/lib/cwl/stg05af35c6-f3a9-4dfc-b351-3f1947f37beb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29543/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:57,857] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:57,858] [INFO] Selected 17 target genomes.
[2023-03-15 17:24:57,858] [INFO] Target genome list was writen to OceanDNA-b29543/target_genomes_gtdb.txt
[2023-03-15 17:24:57,880] [INFO] Task started: fastANI
[2023-03-15 17:24:57,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg11db009d-e144-4ec6-b998-df9be40291ac/OceanDNA-b29543.fa --refList OceanDNA-b29543/target_genomes_gtdb.txt --output OceanDNA-b29543/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:25:08,731] [INFO] Task succeeded: fastANI
[2023-03-15 17:25:08,734] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:25:08,734] [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
GCF_004145845.1	s__Marivivens sp004145845	76.8836	108	540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:25:08,734] [INFO] GTDB search result was written to OceanDNA-b29543/result_gtdb.tsv
[2023-03-15 17:25:08,734] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:25:08,735] [INFO] DFAST_QC result json was written to OceanDNA-b29543/dqc_result.json
[2023-03-15 17:25:08,735] [INFO] DFAST_QC completed!
[2023-03-15 17:25:08,735] [INFO] Total running time: 0h1m7s