[2023-03-18 10:53:04,371] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:53:04,373] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:53:04,373] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf21beb0-cb1c-433d-8d9d-ea973b8e1865/dqc_reference
[2023-03-18 10:53:05,541] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:53:05,541] [INFO] Task started: Prodigal
[2023-03-18 10:53:05,541] [INFO] Running command: cat /var/lib/cwl/stg09d7b1a4-2cc8-4b69-835c-337d5a402e79/OceanDNA-b229.fa | prodigal -d OceanDNA-b229/cds.fna -a OceanDNA-b229/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:53:15,404] [INFO] Task succeeded: Prodigal
[2023-03-18 10:53:15,405] [INFO] Task started: HMMsearch
[2023-03-18 10:53:15,405] [INFO] Running command: hmmsearch --tblout OceanDNA-b229/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf21beb0-cb1c-433d-8d9d-ea973b8e1865/dqc_reference/reference_markers.hmm OceanDNA-b229/protein.faa > /dev/null
[2023-03-18 10:53:15,594] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:53:15,595] [INFO] Found 6/6 markers.
[2023-03-18 10:53:15,616] [INFO] Query marker FASTA was written to OceanDNA-b229/markers.fasta
[2023-03-18 10:53:15,618] [INFO] Task started: Blastn
[2023-03-18 10:53:15,618] [INFO] Running command: blastn -query OceanDNA-b229/markers.fasta -db /var/lib/cwl/stgbf21beb0-cb1c-433d-8d9d-ea973b8e1865/dqc_reference/reference_markers.fasta -out OceanDNA-b229/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:53:16,230] [INFO] Task succeeded: Blastn
[2023-03-18 10:53:16,236] [INFO] Selected 20 target genomes.
[2023-03-18 10:53:16,236] [INFO] Target genome list was writen to OceanDNA-b229/target_genomes.txt
[2023-03-18 10:53:16,273] [INFO] Task started: fastANI
[2023-03-18 10:53:16,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d7b1a4-2cc8-4b69-835c-337d5a402e79/OceanDNA-b229.fa --refList OceanDNA-b229/target_genomes.txt --output OceanDNA-b229/fastani_result.tsv --threads 1
[2023-03-18 10:53:26,791] [INFO] Task succeeded: fastANI
[2023-03-18 10:53:26,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf21beb0-cb1c-433d-8d9d-ea973b8e1865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:53:26,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf21beb0-cb1c-433d-8d9d-ea973b8e1865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:53:26,792] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:53:26,792] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:53:26,792] [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
--------------------------------------------------------------------------------
[2023-03-18 10:53:26,794] [INFO] DFAST Taxonomy check result was written to OceanDNA-b229/tc_result.tsv
[2023-03-18 10:53:26,794] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:53:26,794] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:53:26,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf21beb0-cb1c-433d-8d9d-ea973b8e1865/dqc_reference/checkm_data
[2023-03-18 10:53:26,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:53:26,810] [INFO] Task started: CheckM
[2023-03-18 10:53:26,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b229/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b229/checkm_input OceanDNA-b229/checkm_result
[2023-03-18 10:53:56,163] [INFO] Task succeeded: CheckM
[2023-03-18 10:53:56,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.40%
Contamintation: 1.22%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 10:53:56,173] [INFO] ===== Completeness check finished =====
[2023-03-18 10:53:56,173] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:53:56,173] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b229/markers.fasta)
[2023-03-18 10:53:56,174] [INFO] Task started: Blastn
[2023-03-18 10:53:56,174] [INFO] Running command: blastn -query OceanDNA-b229/markers.fasta -db /var/lib/cwl/stgbf21beb0-cb1c-433d-8d9d-ea973b8e1865/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b229/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:53:57,137] [INFO] Task succeeded: Blastn
[2023-03-18 10:53:57,141] [INFO] Selected 26 target genomes.
[2023-03-18 10:53:57,141] [INFO] Target genome list was writen to OceanDNA-b229/target_genomes_gtdb.txt
[2023-03-18 10:53:57,156] [INFO] Task started: fastANI
[2023-03-18 10:53:57,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d7b1a4-2cc8-4b69-835c-337d5a402e79/OceanDNA-b229.fa --refList OceanDNA-b229/target_genomes_gtdb.txt --output OceanDNA-b229/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:54:09,446] [INFO] Task succeeded: fastANI
[2023-03-18 10:54:09,448] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:54:09,449] [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_012963185.1	s__DTWD01 sp012963185	81.7185	274	506	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__DTWD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:54:09,451] [INFO] GTDB search result was written to OceanDNA-b229/result_gtdb.tsv
[2023-03-18 10:54:09,455] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:54:09,459] [INFO] DFAST_QC result json was written to OceanDNA-b229/dqc_result.json
[2023-03-18 10:54:09,459] [INFO] DFAST_QC completed!
[2023-03-18 10:54:09,459] [INFO] Total running time: 0h1m5s