[2023-03-14 13:19:13,824] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:19:13,824] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:19:13,824] [INFO] DQC Reference Directory: /var/lib/cwl/stge348a095-babf-4e43-b180-ff23177144f0/dqc_reference
[2023-03-14 13:19:16,903] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:19:16,909] [INFO] Task started: Prodigal
[2023-03-14 13:19:16,909] [INFO] Running command: cat /var/lib/cwl/stg776def55-4ef4-405e-a9df-df17b685be1b/OceanDNA-b38906.fa | prodigal -d OceanDNA-b38906/cds.fna -a OceanDNA-b38906/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:19:51,853] [INFO] Task succeeded: Prodigal
[2023-03-14 13:19:51,853] [INFO] Task started: HMMsearch
[2023-03-14 13:19:51,854] [INFO] Running command: hmmsearch --tblout OceanDNA-b38906/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge348a095-babf-4e43-b180-ff23177144f0/dqc_reference/reference_markers.hmm OceanDNA-b38906/protein.faa > /dev/null
[2023-03-14 13:19:52,102] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:19:52,102] [INFO] Found 6/6 markers.
[2023-03-14 13:19:52,131] [INFO] Query marker FASTA was written to OceanDNA-b38906/markers.fasta
[2023-03-14 13:19:52,132] [INFO] Task started: Blastn
[2023-03-14 13:19:52,132] [INFO] Running command: blastn -query OceanDNA-b38906/markers.fasta -db /var/lib/cwl/stge348a095-babf-4e43-b180-ff23177144f0/dqc_reference/reference_markers.fasta -out OceanDNA-b38906/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:19:52,696] [INFO] Task succeeded: Blastn
[2023-03-14 13:19:52,697] [INFO] Selected 45 target genomes.
[2023-03-14 13:19:52,698] [INFO] Target genome list was writen to OceanDNA-b38906/target_genomes.txt
[2023-03-14 13:19:52,719] [INFO] Task started: fastANI
[2023-03-14 13:19:52,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg776def55-4ef4-405e-a9df-df17b685be1b/OceanDNA-b38906.fa --refList OceanDNA-b38906/target_genomes.txt --output OceanDNA-b38906/fastani_result.tsv --threads 1
[2023-03-14 13:20:20,628] [INFO] Task succeeded: fastANI
[2023-03-14 13:20:20,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge348a095-babf-4e43-b180-ff23177144f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:20:20,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge348a095-babf-4e43-b180-ff23177144f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:20:20,633] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:20:20,633] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:20:20,633] [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
Oleiphilus messinensis	strain=ME102	GCA_002162375.1	141451	141451	type	True	76.2112	51	1487	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	75.8662	52	1487	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:20:20,634] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38906/tc_result.tsv
[2023-03-14 13:20:20,634] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:20:20,634] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:20:20,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge348a095-babf-4e43-b180-ff23177144f0/dqc_reference/checkm_data
[2023-03-14 13:20:20,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:20:20,651] [INFO] Task started: CheckM
[2023-03-14 13:20:20,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38906/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38906/checkm_input OceanDNA-b38906/checkm_result
[2023-03-14 13:21:39,813] [INFO] Task succeeded: CheckM
[2023-03-14 13:21:39,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:21:39,818] [INFO] ===== Completeness check finished =====
[2023-03-14 13:21:39,818] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:21:39,818] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38906/markers.fasta)
[2023-03-14 13:21:39,820] [INFO] Task started: Blastn
[2023-03-14 13:21:39,820] [INFO] Running command: blastn -query OceanDNA-b38906/markers.fasta -db /var/lib/cwl/stge348a095-babf-4e43-b180-ff23177144f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38906/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:21:40,696] [INFO] Task succeeded: Blastn
[2023-03-14 13:21:40,698] [INFO] Selected 40 target genomes.
[2023-03-14 13:21:40,698] [INFO] Target genome list was writen to OceanDNA-b38906/target_genomes_gtdb.txt
[2023-03-14 13:21:40,820] [INFO] Task started: fastANI
[2023-03-14 13:21:40,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg776def55-4ef4-405e-a9df-df17b685be1b/OceanDNA-b38906.fa --refList OceanDNA-b38906/target_genomes_gtdb.txt --output OceanDNA-b38906/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:22:20,281] [INFO] Task succeeded: fastANI
[2023-03-14 13:22:20,283] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:22:20,283] [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_006212045.1	s__PZPK01 sp006212045	76.9065	77	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__PZPK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162375.1	s__Oleiphilus messinensis	76.1938	50	1487	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Oleiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:22:20,285] [INFO] GTDB search result was written to OceanDNA-b38906/result_gtdb.tsv
[2023-03-14 13:22:20,285] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:22:20,286] [INFO] DFAST_QC result json was written to OceanDNA-b38906/dqc_result.json
[2023-03-14 13:22:20,286] [INFO] DFAST_QC completed!
[2023-03-14 13:22:20,286] [INFO] Total running time: 0h3m6s