[2023-03-17 07:28:31,303] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,303] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg62f5d62c-6cc8-47ec-b73b-e46db5da3b49/dqc_reference
[2023-03-17 07:28:33,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,079] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,079] [INFO] Running command: cat /var/lib/cwl/stg5480cf05-6d2f-4810-8821-fb0d3a334bd3/OceanDNA-b17033.fa | prodigal -d OceanDNA-b17033/cds.fna -a OceanDNA-b17033/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:45,925] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:45,925] [INFO] Task started: HMMsearch
[2023-03-17 07:28:45,925] [INFO] Running command: hmmsearch --tblout OceanDNA-b17033/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62f5d62c-6cc8-47ec-b73b-e46db5da3b49/dqc_reference/reference_markers.hmm OceanDNA-b17033/protein.faa > /dev/null
[2023-03-17 07:28:46,176] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:46,176] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5480cf05-6d2f-4810-8821-fb0d3a334bd3/OceanDNA-b17033.fa]
[2023-03-17 07:28:46,197] [INFO] Query marker FASTA was written to OceanDNA-b17033/markers.fasta
[2023-03-17 07:28:46,198] [INFO] Task started: Blastn
[2023-03-17 07:28:46,198] [INFO] Running command: blastn -query OceanDNA-b17033/markers.fasta -db /var/lib/cwl/stg62f5d62c-6cc8-47ec-b73b-e46db5da3b49/dqc_reference/reference_markers.fasta -out OceanDNA-b17033/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:46,741] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:46,742] [INFO] Selected 19 target genomes.
[2023-03-17 07:28:46,742] [INFO] Target genome list was writen to OceanDNA-b17033/target_genomes.txt
[2023-03-17 07:28:46,754] [INFO] Task started: fastANI
[2023-03-17 07:28:46,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg5480cf05-6d2f-4810-8821-fb0d3a334bd3/OceanDNA-b17033.fa --refList OceanDNA-b17033/target_genomes.txt --output OceanDNA-b17033/fastani_result.tsv --threads 1
[2023-03-17 07:28:56,608] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:56,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62f5d62c-6cc8-47ec-b73b-e46db5da3b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:56,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62f5d62c-6cc8-47ec-b73b-e46db5da3b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:56,612] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:56,612] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:28:56,612] [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
Truepera radiovictrix	strain=DSM 17093	GCA_000092425.1	332249	332249	type	True	76.5929	98	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:28:56,612] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17033/tc_result.tsv
[2023-03-17 07:28:56,612] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:56,612] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:56,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62f5d62c-6cc8-47ec-b73b-e46db5da3b49/dqc_reference/checkm_data
[2023-03-17 07:28:56,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:56,617] [INFO] Task started: CheckM
[2023-03-17 07:28:56,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17033/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17033/checkm_input OceanDNA-b17033/checkm_result
[2023-03-17 07:29:32,110] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:32,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:32,113] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:32,114] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:32,114] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17033/markers.fasta)
[2023-03-17 07:29:32,114] [INFO] Task started: Blastn
[2023-03-17 07:29:32,114] [INFO] Running command: blastn -query OceanDNA-b17033/markers.fasta -db /var/lib/cwl/stg62f5d62c-6cc8-47ec-b73b-e46db5da3b49/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17033/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:32,830] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:32,831] [INFO] Selected 24 target genomes.
[2023-03-17 07:29:32,831] [INFO] Target genome list was writen to OceanDNA-b17033/target_genomes_gtdb.txt
[2023-03-17 07:29:33,165] [INFO] Task started: fastANI
[2023-03-17 07:29:33,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg5480cf05-6d2f-4810-8821-fb0d3a334bd3/OceanDNA-b17033.fa --refList OceanDNA-b17033/target_genomes_gtdb.txt --output OceanDNA-b17033/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:46,220] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:46,223] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:29:46,223] [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_000092425.1	s__Truepera radiovictrix	76.5929	98	699	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__Truepera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806425.1	s__Truepera sp902806425	76.0153	65	699	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__Truepera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:46,223] [INFO] GTDB search result was written to OceanDNA-b17033/result_gtdb.tsv
[2023-03-17 07:29:46,223] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:46,224] [INFO] DFAST_QC result json was written to OceanDNA-b17033/dqc_result.json
[2023-03-17 07:29:46,224] [INFO] DFAST_QC completed!
[2023-03-17 07:29:46,224] [INFO] Total running time: 0h1m15s