[2023-03-16 06:54:58,966] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:54:58,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:54:58,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9992168-2aa7-4290-8d5b-c53989fa6eb6/dqc_reference
[2023-03-16 06:55:00,091] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:55:00,091] [INFO] Task started: Prodigal
[2023-03-16 06:55:00,091] [INFO] Running command: cat /var/lib/cwl/stg46473a50-d72a-4aeb-aae7-a89304c73ef6/OceanDNA-b36771.fa | prodigal -d OceanDNA-b36771/cds.fna -a OceanDNA-b36771/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:55:16,992] [INFO] Task succeeded: Prodigal
[2023-03-16 06:55:16,992] [INFO] Task started: HMMsearch
[2023-03-16 06:55:16,992] [INFO] Running command: hmmsearch --tblout OceanDNA-b36771/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9992168-2aa7-4290-8d5b-c53989fa6eb6/dqc_reference/reference_markers.hmm OceanDNA-b36771/protein.faa > /dev/null
[2023-03-16 06:55:17,185] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:55:17,185] [INFO] Found 6/6 markers.
[2023-03-16 06:55:17,234] [INFO] Query marker FASTA was written to OceanDNA-b36771/markers.fasta
[2023-03-16 06:55:17,235] [INFO] Task started: Blastn
[2023-03-16 06:55:17,235] [INFO] Running command: blastn -query OceanDNA-b36771/markers.fasta -db /var/lib/cwl/stgd9992168-2aa7-4290-8d5b-c53989fa6eb6/dqc_reference/reference_markers.fasta -out OceanDNA-b36771/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:55:17,780] [INFO] Task succeeded: Blastn
[2023-03-16 06:55:17,795] [INFO] Selected 25 target genomes.
[2023-03-16 06:55:17,795] [INFO] Target genome list was writen to OceanDNA-b36771/target_genomes.txt
[2023-03-16 06:55:17,810] [INFO] Task started: fastANI
[2023-03-16 06:55:17,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg46473a50-d72a-4aeb-aae7-a89304c73ef6/OceanDNA-b36771.fa --refList OceanDNA-b36771/target_genomes.txt --output OceanDNA-b36771/fastani_result.tsv --threads 1
[2023-03-16 06:55:32,916] [INFO] Task succeeded: fastANI
[2023-03-16 06:55:32,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9992168-2aa7-4290-8d5b-c53989fa6eb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:55:32,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9992168-2aa7-4290-8d5b-c53989fa6eb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:55:32,917] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:55:32,917] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:55:32,917] [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 06:55:32,919] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36771/tc_result.tsv
[2023-03-16 06:55:32,921] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:55:32,922] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:55:32,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9992168-2aa7-4290-8d5b-c53989fa6eb6/dqc_reference/checkm_data
[2023-03-16 06:55:32,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:55:32,932] [INFO] Task started: CheckM
[2023-03-16 06:55:32,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36771/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36771/checkm_input OceanDNA-b36771/checkm_result
[2023-03-16 06:56:17,807] [INFO] Task succeeded: CheckM
[2023-03-16 06:56:17,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:56:17,850] [INFO] ===== Completeness check finished =====
[2023-03-16 06:56:17,850] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:56:17,850] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36771/markers.fasta)
[2023-03-16 06:56:17,851] [INFO] Task started: Blastn
[2023-03-16 06:56:17,851] [INFO] Running command: blastn -query OceanDNA-b36771/markers.fasta -db /var/lib/cwl/stgd9992168-2aa7-4290-8d5b-c53989fa6eb6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36771/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:56:18,661] [INFO] Task succeeded: Blastn
[2023-03-16 06:56:18,665] [INFO] Selected 16 target genomes.
[2023-03-16 06:56:18,666] [INFO] Target genome list was writen to OceanDNA-b36771/target_genomes_gtdb.txt
[2023-03-16 06:56:18,682] [INFO] Task started: fastANI
[2023-03-16 06:56:18,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg46473a50-d72a-4aeb-aae7-a89304c73ef6/OceanDNA-b36771.fa --refList OceanDNA-b36771/target_genomes_gtdb.txt --output OceanDNA-b36771/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:56:29,246] [INFO] Task succeeded: fastANI
[2023-03-16 06:56:29,249] [INFO] Found 3 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 06:56:29,250] [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_002697205.1	s__UBA9926 sp002697205	97.5912	831	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_012960535.1	s__UBA9926 sp012960535	95.358	876	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.93	99.93	0.95	0.95	2	inconclusive
GCA_018666555.1	s__UBA9926 sp018666555	77.7461	327	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.83	99.81	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-16 06:56:29,255] [INFO] GTDB search result was written to OceanDNA-b36771/result_gtdb.tsv
[2023-03-16 06:56:29,266] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:56:29,273] [INFO] DFAST_QC result json was written to OceanDNA-b36771/dqc_result.json
[2023-03-16 06:56:29,273] [INFO] DFAST_QC completed!
[2023-03-16 06:56:29,273] [INFO] Total running time: 0h1m30s