[2023-03-17 00:45:47,088] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,088] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bec06c8-b561-478b-b07d-9f8694c4ae48/dqc_reference
[2023-03-17 00:45:48,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,285] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,285] [INFO] Running command: cat /var/lib/cwl/stg302b6af5-03ff-418d-87e0-ed2c98fb6ec3/OceanDNA-b23273.fa | prodigal -d OceanDNA-b23273/cds.fna -a OceanDNA-b23273/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:01,228] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:01,228] [INFO] Task started: HMMsearch
[2023-03-17 00:46:01,228] [INFO] Running command: hmmsearch --tblout OceanDNA-b23273/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bec06c8-b561-478b-b07d-9f8694c4ae48/dqc_reference/reference_markers.hmm OceanDNA-b23273/protein.faa > /dev/null
[2023-03-17 00:46:01,395] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:01,396] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg302b6af5-03ff-418d-87e0-ed2c98fb6ec3/OceanDNA-b23273.fa]
[2023-03-17 00:46:01,416] [INFO] Query marker FASTA was written to OceanDNA-b23273/markers.fasta
[2023-03-17 00:46:01,416] [INFO] Task started: Blastn
[2023-03-17 00:46:01,416] [INFO] Running command: blastn -query OceanDNA-b23273/markers.fasta -db /var/lib/cwl/stg5bec06c8-b561-478b-b07d-9f8694c4ae48/dqc_reference/reference_markers.fasta -out OceanDNA-b23273/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:01,951] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:01,952] [INFO] Selected 26 target genomes.
[2023-03-17 00:46:01,952] [INFO] Target genome list was writen to OceanDNA-b23273/target_genomes.txt
[2023-03-17 00:46:01,970] [INFO] Task started: fastANI
[2023-03-17 00:46:01,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg302b6af5-03ff-418d-87e0-ed2c98fb6ec3/OceanDNA-b23273.fa --refList OceanDNA-b23273/target_genomes.txt --output OceanDNA-b23273/fastani_result.tsv --threads 1
[2023-03-17 00:46:20,072] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:20,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bec06c8-b561-478b-b07d-9f8694c4ae48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:20,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bec06c8-b561-478b-b07d-9f8694c4ae48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:20,076] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:20,076] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:46:20,076] [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
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.0252	53	658	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:20,076] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23273/tc_result.tsv
[2023-03-17 00:46:20,076] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:20,076] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:20,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bec06c8-b561-478b-b07d-9f8694c4ae48/dqc_reference/checkm_data
[2023-03-17 00:46:20,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:20,089] [INFO] Task started: CheckM
[2023-03-17 00:46:20,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23273/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23273/checkm_input OceanDNA-b23273/checkm_result
[2023-03-17 00:46:55,512] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:55,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.41%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:55,534] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:55,534] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:55,534] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23273/markers.fasta)
[2023-03-17 00:46:55,535] [INFO] Task started: Blastn
[2023-03-17 00:46:55,535] [INFO] Running command: blastn -query OceanDNA-b23273/markers.fasta -db /var/lib/cwl/stg5bec06c8-b561-478b-b07d-9f8694c4ae48/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23273/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:56,317] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:56,318] [INFO] Selected 24 target genomes.
[2023-03-17 00:46:56,318] [INFO] Target genome list was writen to OceanDNA-b23273/target_genomes_gtdb.txt
[2023-03-17 00:46:56,793] [INFO] Task started: fastANI
[2023-03-17 00:46:56,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg302b6af5-03ff-418d-87e0-ed2c98fb6ec3/OceanDNA-b23273.fa --refList OceanDNA-b23273/target_genomes_gtdb.txt --output OceanDNA-b23273/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:13,780] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:13,781] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:47:13,781] [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
--------------------------------------------------------------------------------
[2023-03-17 00:47:13,781] [INFO] GTDB search result was written to OceanDNA-b23273/result_gtdb.tsv
[2023-03-17 00:47:13,781] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:13,782] [INFO] DFAST_QC result json was written to OceanDNA-b23273/dqc_result.json
[2023-03-17 00:47:13,782] [INFO] DFAST_QC completed!
[2023-03-17 00:47:13,782] [INFO] Total running time: 0h1m27s