[2023-03-16 08:39:00,436] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:39:00,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:39:00,437] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d3e4b42-91b4-4eea-a314-5ddae4451664/dqc_reference
[2023-03-16 08:39:01,518] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:39:01,519] [INFO] Task started: Prodigal
[2023-03-16 08:39:01,519] [INFO] Running command: cat /var/lib/cwl/stgd930a3ed-f390-4662-8040-780d5848c40b/OceanDNA-a4418.fa | prodigal -d OceanDNA-a4418/cds.fna -a OceanDNA-a4418/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:39:09,377] [INFO] Task succeeded: Prodigal
[2023-03-16 08:39:09,378] [INFO] Task started: HMMsearch
[2023-03-16 08:39:09,378] [INFO] Running command: hmmsearch --tblout OceanDNA-a4418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d3e4b42-91b4-4eea-a314-5ddae4451664/dqc_reference/reference_markers.hmm OceanDNA-a4418/protein.faa > /dev/null
[2023-03-16 08:39:09,548] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:39:09,549] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd930a3ed-f390-4662-8040-780d5848c40b/OceanDNA-a4418.fa]
[2023-03-16 08:39:09,559] [INFO] Query marker FASTA was written to OceanDNA-a4418/markers.fasta
[2023-03-16 08:39:09,560] [INFO] Task started: Blastn
[2023-03-16 08:39:09,560] [INFO] Running command: blastn -query OceanDNA-a4418/markers.fasta -db /var/lib/cwl/stg4d3e4b42-91b4-4eea-a314-5ddae4451664/dqc_reference/reference_markers.fasta -out OceanDNA-a4418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:39:10,054] [INFO] Task succeeded: Blastn
[2023-03-16 08:39:10,055] [INFO] Selected 4 target genomes.
[2023-03-16 08:39:10,055] [INFO] Target genome list was writen to OceanDNA-a4418/target_genomes.txt
[2023-03-16 08:39:10,060] [INFO] Task started: fastANI
[2023-03-16 08:39:10,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgd930a3ed-f390-4662-8040-780d5848c40b/OceanDNA-a4418.fa --refList OceanDNA-a4418/target_genomes.txt --output OceanDNA-a4418/fastani_result.tsv --threads 1
[2023-03-16 08:39:12,067] [INFO] Task succeeded: fastANI
[2023-03-16 08:39:12,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d3e4b42-91b4-4eea-a314-5ddae4451664/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:39:12,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d3e4b42-91b4-4eea-a314-5ddae4451664/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:39:12,067] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:39:12,067] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:39:12,067] [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
--------------------------------------------------------------------------------
[2023-03-16 08:39:12,067] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4418/tc_result.tsv
[2023-03-16 08:39:12,068] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:39:12,068] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:39:12,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d3e4b42-91b4-4eea-a314-5ddae4451664/dqc_reference/checkm_data
[2023-03-16 08:39:12,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:39:12,074] [INFO] Task started: CheckM
[2023-03-16 08:39:12,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4418/checkm_input OceanDNA-a4418/checkm_result
[2023-03-16 08:39:37,941] [INFO] Task succeeded: CheckM
[2023-03-16 08:39:37,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:39:37,946] [INFO] ===== Completeness check finished =====
[2023-03-16 08:39:37,946] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:39:37,946] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4418/markers.fasta)
[2023-03-16 08:39:37,947] [INFO] Task started: Blastn
[2023-03-16 08:39:37,947] [INFO] Running command: blastn -query OceanDNA-a4418/markers.fasta -db /var/lib/cwl/stg4d3e4b42-91b4-4eea-a314-5ddae4451664/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:39:38,637] [INFO] Task succeeded: Blastn
[2023-03-16 08:39:38,639] [INFO] Selected 5 target genomes.
[2023-03-16 08:39:38,639] [INFO] Target genome list was writen to OceanDNA-a4418/target_genomes_gtdb.txt
[2023-03-16 08:39:38,641] [INFO] Task started: fastANI
[2023-03-16 08:39:38,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgd930a3ed-f390-4662-8040-780d5848c40b/OceanDNA-a4418.fa --refList OceanDNA-a4418/target_genomes_gtdb.txt --output OceanDNA-a4418/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:39:39,792] [INFO] Task succeeded: fastANI
[2023-03-16 08:39:39,794] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:39:39,794] [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_002725315.1	s__MGIIb-O3 sp002725315	99.2559	404	442	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.12	98.81	0.90	0.86	5	conclusive
--------------------------------------------------------------------------------
[2023-03-16 08:39:39,795] [INFO] GTDB search result was written to OceanDNA-a4418/result_gtdb.tsv
[2023-03-16 08:39:39,795] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:39:39,796] [INFO] DFAST_QC result json was written to OceanDNA-a4418/dqc_result.json
[2023-03-16 08:39:39,797] [INFO] DFAST_QC completed!
[2023-03-16 08:39:39,797] [INFO] Total running time: 0h0m39s