[2023-03-17 23:17:40,226] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:17:40,226] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:17:40,226] [INFO] DQC Reference Directory: /var/lib/cwl/stg28847e20-972c-4710-b1f5-32f47e1b58e7/dqc_reference
[2023-03-17 23:17:41,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:17:41,368] [INFO] Task started: Prodigal
[2023-03-17 23:17:41,368] [INFO] Running command: cat /var/lib/cwl/stg08bea2c8-a11f-4f0a-bcf0-6903848a4366/OceanDNA-b38033.fa | prodigal -d OceanDNA-b38033/cds.fna -a OceanDNA-b38033/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:17:54,214] [INFO] Task succeeded: Prodigal
[2023-03-17 23:17:54,214] [INFO] Task started: HMMsearch
[2023-03-17 23:17:54,214] [INFO] Running command: hmmsearch --tblout OceanDNA-b38033/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28847e20-972c-4710-b1f5-32f47e1b58e7/dqc_reference/reference_markers.hmm OceanDNA-b38033/protein.faa > /dev/null
[2023-03-17 23:17:54,407] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:17:54,408] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg08bea2c8-a11f-4f0a-bcf0-6903848a4366/OceanDNA-b38033.fa]
[2023-03-17 23:17:54,426] [INFO] Query marker FASTA was written to OceanDNA-b38033/markers.fasta
[2023-03-17 23:17:54,427] [INFO] Task started: Blastn
[2023-03-17 23:17:54,428] [INFO] Running command: blastn -query OceanDNA-b38033/markers.fasta -db /var/lib/cwl/stg28847e20-972c-4710-b1f5-32f47e1b58e7/dqc_reference/reference_markers.fasta -out OceanDNA-b38033/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:17:55,073] [INFO] Task succeeded: Blastn
[2023-03-17 23:17:55,073] [INFO] Selected 27 target genomes.
[2023-03-17 23:17:55,074] [INFO] Target genome list was writen to OceanDNA-b38033/target_genomes.txt
[2023-03-17 23:17:55,225] [INFO] Task started: fastANI
[2023-03-17 23:17:55,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg08bea2c8-a11f-4f0a-bcf0-6903848a4366/OceanDNA-b38033.fa --refList OceanDNA-b38033/target_genomes.txt --output OceanDNA-b38033/fastani_result.tsv --threads 1
[2023-03-17 23:18:10,528] [INFO] Task succeeded: fastANI
[2023-03-17 23:18:10,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28847e20-972c-4710-b1f5-32f47e1b58e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:18:10,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28847e20-972c-4710-b1f5-32f47e1b58e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:18:10,529] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:18:10,529] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:18:10,529] [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
--------------------------------------------------------------------------------
[2023-03-17 23:18:10,529] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38033/tc_result.tsv
[2023-03-17 23:18:10,529] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:18:10,529] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:18:10,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28847e20-972c-4710-b1f5-32f47e1b58e7/dqc_reference/checkm_data
[2023-03-17 23:18:10,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:18:10,537] [INFO] Task started: CheckM
[2023-03-17 23:18:10,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38033/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38033/checkm_input OceanDNA-b38033/checkm_result
[2023-03-17 23:18:47,051] [INFO] Task succeeded: CheckM
[2023-03-17 23:18:47,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:18:47,053] [INFO] ===== Completeness check finished =====
[2023-03-17 23:18:47,054] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:18:47,054] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38033/markers.fasta)
[2023-03-17 23:18:47,080] [INFO] Task started: Blastn
[2023-03-17 23:18:47,080] [INFO] Running command: blastn -query OceanDNA-b38033/markers.fasta -db /var/lib/cwl/stg28847e20-972c-4710-b1f5-32f47e1b58e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38033/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:18:48,351] [INFO] Task succeeded: Blastn
[2023-03-17 23:18:48,352] [INFO] Selected 26 target genomes.
[2023-03-17 23:18:48,352] [INFO] Target genome list was writen to OceanDNA-b38033/target_genomes_gtdb.txt
[2023-03-17 23:18:48,714] [INFO] Task started: fastANI
[2023-03-17 23:18:48,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg08bea2c8-a11f-4f0a-bcf0-6903848a4366/OceanDNA-b38033.fa --refList OceanDNA-b38033/target_genomes_gtdb.txt --output OceanDNA-b38033/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:19:01,751] [INFO] Task succeeded: fastANI
[2023-03-17 23:19:01,754] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:19:01,755] [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_000169115.1	s__Luminiphilus sp000169115	97.5247	649	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.96	96.76	0.93	0.91	5	conclusive
GCA_009886815.1	s__Luminiphilus sp009886815	80.2708	345	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.45	98.43	0.82	0.81	3	-
GCA_012270045.1	s__Luminiphilus sp012270045	76.4234	71	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.26	98.26	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:19:01,755] [INFO] GTDB search result was written to OceanDNA-b38033/result_gtdb.tsv
[2023-03-17 23:19:01,755] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:19:01,755] [INFO] DFAST_QC result json was written to OceanDNA-b38033/dqc_result.json
[2023-03-17 23:19:01,755] [INFO] DFAST_QC completed!
[2023-03-17 23:19:01,756] [INFO] Total running time: 0h1m22s