[2023-03-15 14:21:30,607] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:21:30,619] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:21:30,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgabcfff8f-3c53-4443-bb38-badaf1a8fe32/dqc_reference
[2023-03-15 14:21:31,722] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:21:31,723] [INFO] Task started: Prodigal
[2023-03-15 14:21:31,723] [INFO] Running command: cat /var/lib/cwl/stg7f43fc00-b6ca-4f11-b020-2ec5891402da/OceanDNA-b23083.fa | prodigal -d OceanDNA-b23083/cds.fna -a OceanDNA-b23083/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:21:41,761] [INFO] Task succeeded: Prodigal
[2023-03-15 14:21:41,762] [INFO] Task started: HMMsearch
[2023-03-15 14:21:41,762] [INFO] Running command: hmmsearch --tblout OceanDNA-b23083/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabcfff8f-3c53-4443-bb38-badaf1a8fe32/dqc_reference/reference_markers.hmm OceanDNA-b23083/protein.faa > /dev/null
[2023-03-15 14:21:41,912] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:21:41,913] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7f43fc00-b6ca-4f11-b020-2ec5891402da/OceanDNA-b23083.fa]
[2023-03-15 14:21:42,009] [INFO] Query marker FASTA was written to OceanDNA-b23083/markers.fasta
[2023-03-15 14:21:42,010] [INFO] Task started: Blastn
[2023-03-15 14:21:42,010] [INFO] Running command: blastn -query OceanDNA-b23083/markers.fasta -db /var/lib/cwl/stgabcfff8f-3c53-4443-bb38-badaf1a8fe32/dqc_reference/reference_markers.fasta -out OceanDNA-b23083/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:21:42,525] [INFO] Task succeeded: Blastn
[2023-03-15 14:21:42,562] [INFO] Selected 7 target genomes.
[2023-03-15 14:21:42,563] [INFO] Target genome list was writen to OceanDNA-b23083/target_genomes.txt
[2023-03-15 14:21:42,567] [INFO] Task started: fastANI
[2023-03-15 14:21:42,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f43fc00-b6ca-4f11-b020-2ec5891402da/OceanDNA-b23083.fa --refList OceanDNA-b23083/target_genomes.txt --output OceanDNA-b23083/fastani_result.tsv --threads 1
[2023-03-15 14:21:45,889] [INFO] Task succeeded: fastANI
[2023-03-15 14:21:45,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabcfff8f-3c53-4443-bb38-badaf1a8fe32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:21:45,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabcfff8f-3c53-4443-bb38-badaf1a8fe32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:21:45,890] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:21:45,890] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:21:45,890] [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
--------------------------------------------------------------------------------
[2023-03-15 14:21:45,899] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23083/tc_result.tsv
[2023-03-15 14:21:45,920] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:21:45,920] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:21:45,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabcfff8f-3c53-4443-bb38-badaf1a8fe32/dqc_reference/checkm_data
[2023-03-15 14:21:45,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:21:46,041] [INFO] Task started: CheckM
[2023-03-15 14:21:46,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23083/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23083/checkm_input OceanDNA-b23083/checkm_result
[2023-03-15 14:22:15,830] [INFO] Task succeeded: CheckM
[2023-03-15 14:22:15,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:22:15,914] [INFO] ===== Completeness check finished =====
[2023-03-15 14:22:15,914] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:22:15,914] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23083/markers.fasta)
[2023-03-15 14:22:15,916] [INFO] Task started: Blastn
[2023-03-15 14:22:15,916] [INFO] Running command: blastn -query OceanDNA-b23083/markers.fasta -db /var/lib/cwl/stgabcfff8f-3c53-4443-bb38-badaf1a8fe32/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23083/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:22:16,559] [INFO] Task succeeded: Blastn
[2023-03-15 14:22:16,564] [INFO] Selected 15 target genomes.
[2023-03-15 14:22:16,564] [INFO] Target genome list was writen to OceanDNA-b23083/target_genomes_gtdb.txt
[2023-03-15 14:22:16,575] [INFO] Task started: fastANI
[2023-03-15 14:22:16,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f43fc00-b6ca-4f11-b020-2ec5891402da/OceanDNA-b23083.fa --refList OceanDNA-b23083/target_genomes_gtdb.txt --output OceanDNA-b23083/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:22:23,840] [INFO] Task succeeded: fastANI
[2023-03-15 14:22:23,842] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:22:23,842] [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_002311925.1	s__UBA1135 sp002311925	98.6712	258	274	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__UBA1135;g__UBA1135	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-15 14:22:23,851] [INFO] GTDB search result was written to OceanDNA-b23083/result_gtdb.tsv
[2023-03-15 14:22:23,855] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:22:23,859] [INFO] DFAST_QC result json was written to OceanDNA-b23083/dqc_result.json
[2023-03-15 14:22:23,859] [INFO] DFAST_QC completed!
[2023-03-15 14:22:23,859] [INFO] Total running time: 0h0m53s