[2023-03-14 14:40:53,147] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:40:53,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:40:53,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg5684bcef-f5c8-4858-a887-d54ae8c29daa/dqc_reference
[2023-03-14 14:40:54,240] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:40:54,240] [INFO] Task started: Prodigal
[2023-03-14 14:40:54,240] [INFO] Running command: cat /var/lib/cwl/stgb5347e11-a794-4067-9460-3beed5aeb5da/OceanDNA-b36777.fa | prodigal -d OceanDNA-b36777/cds.fna -a OceanDNA-b36777/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:41:21,239] [INFO] Task succeeded: Prodigal
[2023-03-14 14:41:21,239] [INFO] Task started: HMMsearch
[2023-03-14 14:41:21,239] [INFO] Running command: hmmsearch --tblout OceanDNA-b36777/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5684bcef-f5c8-4858-a887-d54ae8c29daa/dqc_reference/reference_markers.hmm OceanDNA-b36777/protein.faa > /dev/null
[2023-03-14 14:41:21,467] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:41:21,468] [INFO] Found 6/6 markers.
[2023-03-14 14:41:21,494] [INFO] Query marker FASTA was written to OceanDNA-b36777/markers.fasta
[2023-03-14 14:41:21,495] [INFO] Task started: Blastn
[2023-03-14 14:41:21,495] [INFO] Running command: blastn -query OceanDNA-b36777/markers.fasta -db /var/lib/cwl/stg5684bcef-f5c8-4858-a887-d54ae8c29daa/dqc_reference/reference_markers.fasta -out OceanDNA-b36777/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:41:22,086] [INFO] Task succeeded: Blastn
[2023-03-14 14:41:22,087] [INFO] Selected 29 target genomes.
[2023-03-14 14:41:22,087] [INFO] Target genome list was writen to OceanDNA-b36777/target_genomes.txt
[2023-03-14 14:41:22,135] [INFO] Task started: fastANI
[2023-03-14 14:41:22,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5347e11-a794-4067-9460-3beed5aeb5da/OceanDNA-b36777.fa --refList OceanDNA-b36777/target_genomes.txt --output OceanDNA-b36777/fastani_result.tsv --threads 1
[2023-03-14 14:41:39,089] [INFO] Task succeeded: fastANI
[2023-03-14 14:41:39,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5684bcef-f5c8-4858-a887-d54ae8c29daa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:41:39,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5684bcef-f5c8-4858-a887-d54ae8c29daa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:41:39,090] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:41:39,090] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:41:39,090] [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
--------------------------------------------------------------------------------
[2023-03-14 14:41:39,090] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36777/tc_result.tsv
[2023-03-14 14:41:39,090] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:41:39,091] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:41:39,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5684bcef-f5c8-4858-a887-d54ae8c29daa/dqc_reference/checkm_data
[2023-03-14 14:41:39,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:41:39,106] [INFO] Task started: CheckM
[2023-03-14 14:41:39,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36777/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36777/checkm_input OceanDNA-b36777/checkm_result
[2023-03-14 14:43:01,453] [INFO] Task succeeded: CheckM
[2023-03-14 14:43:01,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:43:01,457] [INFO] ===== Completeness check finished =====
[2023-03-14 14:43:01,457] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:43:01,457] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36777/markers.fasta)
[2023-03-14 14:43:01,485] [INFO] Task started: Blastn
[2023-03-14 14:43:01,485] [INFO] Running command: blastn -query OceanDNA-b36777/markers.fasta -db /var/lib/cwl/stg5684bcef-f5c8-4858-a887-d54ae8c29daa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36777/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:43:04,075] [INFO] Task succeeded: Blastn
[2023-03-14 14:43:04,076] [INFO] Selected 30 target genomes.
[2023-03-14 14:43:04,076] [INFO] Target genome list was writen to OceanDNA-b36777/target_genomes_gtdb.txt
[2023-03-14 14:43:04,120] [INFO] Task started: fastANI
[2023-03-14 14:43:04,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5347e11-a794-4067-9460-3beed5aeb5da/OceanDNA-b36777.fa --refList OceanDNA-b36777/target_genomes_gtdb.txt --output OceanDNA-b36777/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:43:25,359] [INFO] Task succeeded: fastANI
[2023-03-14 14:43:25,360] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:43:25,360] [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
--------------------------------------------------------------------------------
[2023-03-14 14:43:25,360] [INFO] GTDB search result was written to OceanDNA-b36777/result_gtdb.tsv
[2023-03-14 14:43:25,360] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:43:25,361] [INFO] DFAST_QC result json was written to OceanDNA-b36777/dqc_result.json
[2023-03-14 14:43:25,361] [INFO] DFAST_QC completed!
[2023-03-14 14:43:25,361] [INFO] Total running time: 0h2m32s