[2023-03-17 00:45:49,118] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:49,119] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:49,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg22fad8ee-891b-4472-9dd7-ed790db17182/dqc_reference
[2023-03-17 00:45:50,221] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:50,221] [INFO] Task started: Prodigal
[2023-03-17 00:45:50,221] [INFO] Running command: cat /var/lib/cwl/stgbe29cdd7-7257-416c-a5ce-9f137d2da4c2/OceanDNA-b35180.fa | prodigal -d OceanDNA-b35180/cds.fna -a OceanDNA-b35180/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:00,040] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:00,040] [INFO] Task started: HMMsearch
[2023-03-17 00:46:00,040] [INFO] Running command: hmmsearch --tblout OceanDNA-b35180/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22fad8ee-891b-4472-9dd7-ed790db17182/dqc_reference/reference_markers.hmm OceanDNA-b35180/protein.faa > /dev/null
[2023-03-17 00:46:00,213] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:00,213] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbe29cdd7-7257-416c-a5ce-9f137d2da4c2/OceanDNA-b35180.fa]
[2023-03-17 00:46:00,234] [INFO] Query marker FASTA was written to OceanDNA-b35180/markers.fasta
[2023-03-17 00:46:00,234] [INFO] Task started: Blastn
[2023-03-17 00:46:00,234] [INFO] Running command: blastn -query OceanDNA-b35180/markers.fasta -db /var/lib/cwl/stg22fad8ee-891b-4472-9dd7-ed790db17182/dqc_reference/reference_markers.fasta -out OceanDNA-b35180/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:00,789] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:00,791] [INFO] Selected 25 target genomes.
[2023-03-17 00:46:00,791] [INFO] Target genome list was writen to OceanDNA-b35180/target_genomes.txt
[2023-03-17 00:46:00,847] [INFO] Task started: fastANI
[2023-03-17 00:46:00,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe29cdd7-7257-416c-a5ce-9f137d2da4c2/OceanDNA-b35180.fa --refList OceanDNA-b35180/target_genomes.txt --output OceanDNA-b35180/fastani_result.tsv --threads 1
[2023-03-17 00:46:14,356] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:14,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22fad8ee-891b-4472-9dd7-ed790db17182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:14,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22fad8ee-891b-4472-9dd7-ed790db17182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:14,359] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 00:46:14,359] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 00:46:14,360] [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
Pleionea mediterranea	strain=DSM 25350	GCA_003148745.1	523701	523701	type	True	97.4719	451	464	95	conclusive
Pleionea sediminis	strain=S1-5-21	GCA_007570825.1	2569479	2569479	type	True	78.0727	54	464	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:14,360] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35180/tc_result.tsv
[2023-03-17 00:46:14,360] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:14,361] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:14,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22fad8ee-891b-4472-9dd7-ed790db17182/dqc_reference/checkm_data
[2023-03-17 00:46:14,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:14,367] [INFO] Task started: CheckM
[2023-03-17 00:46:14,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35180/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35180/checkm_input OceanDNA-b35180/checkm_result
[2023-03-17 00:46:44,041] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:44,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:44,043] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:44,044] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:44,044] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35180/markers.fasta)
[2023-03-17 00:46:44,045] [INFO] Task started: Blastn
[2023-03-17 00:46:44,045] [INFO] Running command: blastn -query OceanDNA-b35180/markers.fasta -db /var/lib/cwl/stg22fad8ee-891b-4472-9dd7-ed790db17182/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35180/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:44,868] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:44,869] [INFO] Selected 24 target genomes.
[2023-03-17 00:46:44,869] [INFO] Target genome list was writen to OceanDNA-b35180/target_genomes_gtdb.txt
[2023-03-17 00:46:45,089] [INFO] Task started: fastANI
[2023-03-17 00:46:45,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe29cdd7-7257-416c-a5ce-9f137d2da4c2/OceanDNA-b35180.fa --refList OceanDNA-b35180/target_genomes_gtdb.txt --output OceanDNA-b35180/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:57,875] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:57,878] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:46:57,878] [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_003148745.1	s__Pleionea mediterranea	97.4719	451	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Pleionea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007570825.1	s__Pleionea sediminis	78.0727	54	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Pleionea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:57,878] [INFO] GTDB search result was written to OceanDNA-b35180/result_gtdb.tsv
[2023-03-17 00:46:57,878] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:57,879] [INFO] DFAST_QC result json was written to OceanDNA-b35180/dqc_result.json
[2023-03-17 00:46:57,879] [INFO] DFAST_QC completed!
[2023-03-17 00:46:57,879] [INFO] Total running time: 0h1m9s