[2023-03-18 00:21:54,210] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:54,210] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:54,210] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd980d1a-bc68-4aea-b247-633d606da5f2/dqc_reference
[2023-03-18 00:21:55,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:55,650] [INFO] Task started: Prodigal
[2023-03-18 00:21:55,651] [INFO] Running command: cat /var/lib/cwl/stg7c3ba777-1ef6-4d54-8d37-af0fb8f0212d/OceanDNA-b17770.fa | prodigal -d OceanDNA-b17770/cds.fna -a OceanDNA-b17770/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:02,695] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:02,695] [INFO] Task started: HMMsearch
[2023-03-18 00:22:02,695] [INFO] Running command: hmmsearch --tblout OceanDNA-b17770/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd980d1a-bc68-4aea-b247-633d606da5f2/dqc_reference/reference_markers.hmm OceanDNA-b17770/protein.faa > /dev/null
[2023-03-18 00:22:02,840] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:02,840] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7c3ba777-1ef6-4d54-8d37-af0fb8f0212d/OceanDNA-b17770.fa]
[2023-03-18 00:22:02,851] [INFO] Query marker FASTA was written to OceanDNA-b17770/markers.fasta
[2023-03-18 00:22:02,853] [INFO] Task started: Blastn
[2023-03-18 00:22:02,853] [INFO] Running command: blastn -query OceanDNA-b17770/markers.fasta -db /var/lib/cwl/stgbd980d1a-bc68-4aea-b247-633d606da5f2/dqc_reference/reference_markers.fasta -out OceanDNA-b17770/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:03,332] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:03,332] [INFO] Selected 12 target genomes.
[2023-03-18 00:22:03,333] [INFO] Target genome list was writen to OceanDNA-b17770/target_genomes.txt
[2023-03-18 00:22:03,340] [INFO] Task started: fastANI
[2023-03-18 00:22:03,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c3ba777-1ef6-4d54-8d37-af0fb8f0212d/OceanDNA-b17770.fa --refList OceanDNA-b17770/target_genomes.txt --output OceanDNA-b17770/fastani_result.tsv --threads 1
[2023-03-18 00:22:08,608] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:08,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd980d1a-bc68-4aea-b247-633d606da5f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:08,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd980d1a-bc68-4aea-b247-633d606da5f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:08,609] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:08,609] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:22:08,609] [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
--------------------------------------------------------------------------------
[2023-03-18 00:22:08,609] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17770/tc_result.tsv
[2023-03-18 00:22:08,609] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:08,609] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:08,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd980d1a-bc68-4aea-b247-633d606da5f2/dqc_reference/checkm_data
[2023-03-18 00:22:08,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:08,615] [INFO] Task started: CheckM
[2023-03-18 00:22:08,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17770/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17770/checkm_input OceanDNA-b17770/checkm_result
[2023-03-18 00:22:31,794] [INFO] Task succeeded: CheckM
[2023-03-18 00:22:31,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 00:22:31,796] [INFO] ===== Completeness check finished =====
[2023-03-18 00:22:31,796] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:22:31,796] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17770/markers.fasta)
[2023-03-18 00:22:31,797] [INFO] Task started: Blastn
[2023-03-18 00:22:31,797] [INFO] Running command: blastn -query OceanDNA-b17770/markers.fasta -db /var/lib/cwl/stgbd980d1a-bc68-4aea-b247-633d606da5f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17770/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:32,439] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:32,440] [INFO] Selected 14 target genomes.
[2023-03-18 00:22:32,440] [INFO] Target genome list was writen to OceanDNA-b17770/target_genomes_gtdb.txt
[2023-03-18 00:22:32,459] [INFO] Task started: fastANI
[2023-03-18 00:22:32,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c3ba777-1ef6-4d54-8d37-af0fb8f0212d/OceanDNA-b17770.fa --refList OceanDNA-b17770/target_genomes_gtdb.txt --output OceanDNA-b17770/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:22:38,582] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:38,584] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:22:38,584] [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_018646105.1	s__JABGVJ01 sp018646105	99.5052	381	445	d__Bacteria;p__Margulisbacteria;c__Marinamargulisbacteria;o__JABGVJ01;f__JABGVJ01;g__JABGVJ01	95.0	99.40	99.12	0.90	0.87	5	conclusive
--------------------------------------------------------------------------------
[2023-03-18 00:22:38,584] [INFO] GTDB search result was written to OceanDNA-b17770/result_gtdb.tsv
[2023-03-18 00:22:38,584] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:22:38,584] [INFO] DFAST_QC result json was written to OceanDNA-b17770/dqc_result.json
[2023-03-18 00:22:38,585] [INFO] DFAST_QC completed!
[2023-03-18 00:22:38,585] [INFO] Total running time: 0h0m44s