[2023-03-16 10:09:24,148] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:09:24,149] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:09:24,149] [INFO] DQC Reference Directory: /var/lib/cwl/stgbba91cfd-e4d3-439b-8dee-fefeb3c7afdb/dqc_reference
[2023-03-16 10:09:25,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:09:25,271] [INFO] Task started: Prodigal
[2023-03-16 10:09:25,271] [INFO] Running command: cat /var/lib/cwl/stg6da9d6b5-1400-4b16-8645-16a85cb39331/OceanDNA-b31333.fa | prodigal -d OceanDNA-b31333/cds.fna -a OceanDNA-b31333/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:09:29,608] [INFO] Task succeeded: Prodigal
[2023-03-16 10:09:29,608] [INFO] Task started: HMMsearch
[2023-03-16 10:09:29,609] [INFO] Running command: hmmsearch --tblout OceanDNA-b31333/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbba91cfd-e4d3-439b-8dee-fefeb3c7afdb/dqc_reference/reference_markers.hmm OceanDNA-b31333/protein.faa > /dev/null
[2023-03-16 10:09:29,769] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:09:29,769] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6da9d6b5-1400-4b16-8645-16a85cb39331/OceanDNA-b31333.fa]
[2023-03-16 10:09:29,778] [INFO] Query marker FASTA was written to OceanDNA-b31333/markers.fasta
[2023-03-16 10:09:29,779] [INFO] Task started: Blastn
[2023-03-16 10:09:29,779] [INFO] Running command: blastn -query OceanDNA-b31333/markers.fasta -db /var/lib/cwl/stgbba91cfd-e4d3-439b-8dee-fefeb3c7afdb/dqc_reference/reference_markers.fasta -out OceanDNA-b31333/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:09:30,368] [INFO] Task succeeded: Blastn
[2023-03-16 10:09:30,370] [INFO] Selected 21 target genomes.
[2023-03-16 10:09:30,370] [INFO] Target genome list was writen to OceanDNA-b31333/target_genomes.txt
[2023-03-16 10:09:30,433] [INFO] Task started: fastANI
[2023-03-16 10:09:30,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg6da9d6b5-1400-4b16-8645-16a85cb39331/OceanDNA-b31333.fa --refList OceanDNA-b31333/target_genomes.txt --output OceanDNA-b31333/fastani_result.tsv --threads 1
[2023-03-16 10:09:41,925] [INFO] Task succeeded: fastANI
[2023-03-16 10:09:41,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbba91cfd-e4d3-439b-8dee-fefeb3c7afdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:09:41,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbba91cfd-e4d3-439b-8dee-fefeb3c7afdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:09:41,926] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:09:41,926] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:09:41,926] [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 10:09:41,926] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31333/tc_result.tsv
[2023-03-16 10:09:41,926] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:09:41,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:09:41,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbba91cfd-e4d3-439b-8dee-fefeb3c7afdb/dqc_reference/checkm_data
[2023-03-16 10:09:41,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:09:41,932] [INFO] Task started: CheckM
[2023-03-16 10:09:41,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31333/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31333/checkm_input OceanDNA-b31333/checkm_result
[2023-03-16 10:09:58,689] [INFO] Task succeeded: CheckM
[2023-03-16 10:09:58,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:09:58,691] [INFO] ===== Completeness check finished =====
[2023-03-16 10:09:58,691] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:09:58,691] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31333/markers.fasta)
[2023-03-16 10:09:58,692] [INFO] Task started: Blastn
[2023-03-16 10:09:58,693] [INFO] Running command: blastn -query OceanDNA-b31333/markers.fasta -db /var/lib/cwl/stgbba91cfd-e4d3-439b-8dee-fefeb3c7afdb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31333/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:09:59,765] [INFO] Task succeeded: Blastn
[2023-03-16 10:09:59,766] [INFO] Selected 27 target genomes.
[2023-03-16 10:09:59,766] [INFO] Target genome list was writen to OceanDNA-b31333/target_genomes_gtdb.txt
[2023-03-16 10:09:59,817] [INFO] Task started: fastANI
[2023-03-16 10:09:59,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg6da9d6b5-1400-4b16-8645-16a85cb39331/OceanDNA-b31333.fa --refList OceanDNA-b31333/target_genomes_gtdb.txt --output OceanDNA-b31333/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:10:07,705] [INFO] Task succeeded: fastANI
[2023-03-16 10:10:07,707] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:10:07,707] [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_905479865.1	s__GCA-2402195 sp905479865	76.335	50	266	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__GCA-2402195	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:10:07,707] [INFO] GTDB search result was written to OceanDNA-b31333/result_gtdb.tsv
[2023-03-16 10:10:07,707] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:10:07,708] [INFO] DFAST_QC result json was written to OceanDNA-b31333/dqc_result.json
[2023-03-16 10:10:07,708] [INFO] DFAST_QC completed!
[2023-03-16 10:10:07,708] [INFO] Total running time: 0h0m44s