[2023-03-18 23:11:06,946] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,946] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,946] [INFO] DQC Reference Directory: /var/lib/cwl/stg22426637-0a2a-439a-aad2-229f44aa7fff/dqc_reference
[2023-03-18 23:11:08,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,270] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,270] [INFO] Running command: cat /var/lib/cwl/stgf286e5e3-87ea-4756-84c3-10a07968eccf/OceanDNA-b13294.fa | prodigal -d OceanDNA-b13294/cds.fna -a OceanDNA-b13294/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:16,927] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:16,927] [INFO] Task started: HMMsearch
[2023-03-18 23:11:16,927] [INFO] Running command: hmmsearch --tblout OceanDNA-b13294/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22426637-0a2a-439a-aad2-229f44aa7fff/dqc_reference/reference_markers.hmm OceanDNA-b13294/protein.faa > /dev/null
[2023-03-18 23:11:17,147] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:17,148] [INFO] Found 6/6 markers.
[2023-03-18 23:11:17,164] [INFO] Query marker FASTA was written to OceanDNA-b13294/markers.fasta
[2023-03-18 23:11:17,164] [INFO] Task started: Blastn
[2023-03-18 23:11:17,164] [INFO] Running command: blastn -query OceanDNA-b13294/markers.fasta -db /var/lib/cwl/stg22426637-0a2a-439a-aad2-229f44aa7fff/dqc_reference/reference_markers.fasta -out OceanDNA-b13294/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:17,781] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:17,782] [INFO] Selected 29 target genomes.
[2023-03-18 23:11:17,782] [INFO] Target genome list was writen to OceanDNA-b13294/target_genomes.txt
[2023-03-18 23:11:17,799] [INFO] Task started: fastANI
[2023-03-18 23:11:17,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgf286e5e3-87ea-4756-84c3-10a07968eccf/OceanDNA-b13294.fa --refList OceanDNA-b13294/target_genomes.txt --output OceanDNA-b13294/fastani_result.tsv --threads 1
[2023-03-18 23:11:35,778] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:35,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22426637-0a2a-439a-aad2-229f44aa7fff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:35,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22426637-0a2a-439a-aad2-229f44aa7fff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:35,778] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:35,779] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:35,779] [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 23:11:35,779] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13294/tc_result.tsv
[2023-03-18 23:11:35,779] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:35,779] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:35,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22426637-0a2a-439a-aad2-229f44aa7fff/dqc_reference/checkm_data
[2023-03-18 23:11:35,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:35,789] [INFO] Task started: CheckM
[2023-03-18 23:11:35,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13294/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13294/checkm_input OceanDNA-b13294/checkm_result
[2023-03-18 23:12:02,453] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:02,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.26%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:02,456] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:02,456] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:02,456] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13294/markers.fasta)
[2023-03-18 23:12:02,457] [INFO] Task started: Blastn
[2023-03-18 23:12:02,457] [INFO] Running command: blastn -query OceanDNA-b13294/markers.fasta -db /var/lib/cwl/stg22426637-0a2a-439a-aad2-229f44aa7fff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13294/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:03,413] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:03,414] [INFO] Selected 16 target genomes.
[2023-03-18 23:12:03,414] [INFO] Target genome list was writen to OceanDNA-b13294/target_genomes_gtdb.txt
[2023-03-18 23:12:03,428] [INFO] Task started: fastANI
[2023-03-18 23:12:03,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgf286e5e3-87ea-4756-84c3-10a07968eccf/OceanDNA-b13294.fa --refList OceanDNA-b13294/target_genomes_gtdb.txt --output OceanDNA-b13294/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:11,349] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:11,353] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:12:11,353] [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_002311335.1	s__UBA1149 sp002311335	98.0389	376	406	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA1149;f__UBA1149;g__UBA1149	95.0	98.21	98.21	0.88	0.88	2	conclusive
GCA_012960245.1	s__UBA1149 sp012960245	94.6068	388	406	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA1149;f__UBA1149;g__UBA1149	95.0	99.91	99.91	0.97	0.97	2	-
GCA_014382245.1	s__UBA1149 sp014382245	93.6978	389	406	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA1149;f__UBA1149;g__UBA1149	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:11,353] [INFO] GTDB search result was written to OceanDNA-b13294/result_gtdb.tsv
[2023-03-18 23:12:11,353] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:11,354] [INFO] DFAST_QC result json was written to OceanDNA-b13294/dqc_result.json
[2023-03-18 23:12:11,354] [INFO] DFAST_QC completed!
[2023-03-18 23:12:11,354] [INFO] Total running time: 0h1m4s