[2023-03-15 07:52:40,251] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,251] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,251] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1605ba6-4ecd-45ea-8e4e-0f24339f2315/dqc_reference
[2023-03-15 07:52:41,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,410] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,411] [INFO] Running command: cat /var/lib/cwl/stg66cc2820-a08b-4763-b040-7ba50f66613b/OceanDNA-b36729.fa | prodigal -d OceanDNA-b36729/cds.fna -a OceanDNA-b36729/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:53:06,150] [INFO] Task succeeded: Prodigal
[2023-03-15 07:53:06,151] [INFO] Task started: HMMsearch
[2023-03-15 07:53:06,151] [INFO] Running command: hmmsearch --tblout OceanDNA-b36729/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1605ba6-4ecd-45ea-8e4e-0f24339f2315/dqc_reference/reference_markers.hmm OceanDNA-b36729/protein.faa > /dev/null
[2023-03-15 07:53:06,411] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:53:06,412] [INFO] Found 6/6 markers.
[2023-03-15 07:53:06,438] [INFO] Query marker FASTA was written to OceanDNA-b36729/markers.fasta
[2023-03-15 07:53:06,438] [INFO] Task started: Blastn
[2023-03-15 07:53:06,438] [INFO] Running command: blastn -query OceanDNA-b36729/markers.fasta -db /var/lib/cwl/stgb1605ba6-4ecd-45ea-8e4e-0f24339f2315/dqc_reference/reference_markers.fasta -out OceanDNA-b36729/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:07,070] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:07,071] [INFO] Selected 30 target genomes.
[2023-03-15 07:53:07,071] [INFO] Target genome list was writen to OceanDNA-b36729/target_genomes.txt
[2023-03-15 07:53:07,086] [INFO] Task started: fastANI
[2023-03-15 07:53:07,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg66cc2820-a08b-4763-b040-7ba50f66613b/OceanDNA-b36729.fa --refList OceanDNA-b36729/target_genomes.txt --output OceanDNA-b36729/fastani_result.tsv --threads 1
[2023-03-15 07:53:27,799] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:27,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1605ba6-4ecd-45ea-8e4e-0f24339f2315/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:27,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1605ba6-4ecd-45ea-8e4e-0f24339f2315/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:27,800] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:53:27,800] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:53:27,800] [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 07:53:27,800] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36729/tc_result.tsv
[2023-03-15 07:53:27,801] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:27,801] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:27,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1605ba6-4ecd-45ea-8e4e-0f24339f2315/dqc_reference/checkm_data
[2023-03-15 07:53:27,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:27,895] [INFO] Task started: CheckM
[2023-03-15 07:53:27,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36729/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36729/checkm_input OceanDNA-b36729/checkm_result
[2023-03-15 07:54:27,690] [INFO] Task succeeded: CheckM
[2023-03-15 07:54:27,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:54:27,693] [INFO] ===== Completeness check finished =====
[2023-03-15 07:54:27,693] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:54:27,693] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36729/markers.fasta)
[2023-03-15 07:54:27,695] [INFO] Task started: Blastn
[2023-03-15 07:54:27,695] [INFO] Running command: blastn -query OceanDNA-b36729/markers.fasta -db /var/lib/cwl/stgb1605ba6-4ecd-45ea-8e4e-0f24339f2315/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36729/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:54:28,677] [INFO] Task succeeded: Blastn
[2023-03-15 07:54:28,678] [INFO] Selected 29 target genomes.
[2023-03-15 07:54:28,678] [INFO] Target genome list was writen to OceanDNA-b36729/target_genomes_gtdb.txt
[2023-03-15 07:54:28,742] [INFO] Task started: fastANI
[2023-03-15 07:54:28,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg66cc2820-a08b-4763-b040-7ba50f66613b/OceanDNA-b36729.fa --refList OceanDNA-b36729/target_genomes_gtdb.txt --output OceanDNA-b36729/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:54:44,868] [INFO] Task succeeded: fastANI
[2023-03-15 07:54:44,870] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:54:44,870] [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_002480525.1	s__UBA7803 sp002480525	75.5323	63	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	99.35	98.95	0.83	0.81	3	-
--------------------------------------------------------------------------------
[2023-03-15 07:54:44,870] [INFO] GTDB search result was written to OceanDNA-b36729/result_gtdb.tsv
[2023-03-15 07:54:44,871] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:54:44,871] [INFO] DFAST_QC result json was written to OceanDNA-b36729/dqc_result.json
[2023-03-15 07:54:44,871] [INFO] DFAST_QC completed!
[2023-03-15 07:54:44,871] [INFO] Total running time: 0h2m5s