[2023-03-18 10:12:10,186] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:12:10,186] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:12:10,186] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbba0846-021d-47e5-9d6a-9189ed98eb7d/dqc_reference
[2023-03-18 10:12:11,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:12:11,280] [INFO] Task started: Prodigal
[2023-03-18 10:12:11,280] [INFO] Running command: cat /var/lib/cwl/stg907c8f6d-d253-4965-9d3c-5a48cabf19c0/OceanDNA-b35682.fa | prodigal -d OceanDNA-b35682/cds.fna -a OceanDNA-b35682/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:12:15,543] [INFO] Task succeeded: Prodigal
[2023-03-18 10:12:15,544] [INFO] Task started: HMMsearch
[2023-03-18 10:12:15,544] [INFO] Running command: hmmsearch --tblout OceanDNA-b35682/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbba0846-021d-47e5-9d6a-9189ed98eb7d/dqc_reference/reference_markers.hmm OceanDNA-b35682/protein.faa > /dev/null
[2023-03-18 10:12:15,703] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:12:15,704] [INFO] Found 6/6 markers.
[2023-03-18 10:12:15,713] [INFO] Query marker FASTA was written to OceanDNA-b35682/markers.fasta
[2023-03-18 10:12:15,714] [INFO] Task started: Blastn
[2023-03-18 10:12:15,715] [INFO] Running command: blastn -query OceanDNA-b35682/markers.fasta -db /var/lib/cwl/stgcbba0846-021d-47e5-9d6a-9189ed98eb7d/dqc_reference/reference_markers.fasta -out OceanDNA-b35682/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:12:16,213] [INFO] Task succeeded: Blastn
[2023-03-18 10:12:16,215] [INFO] Selected 22 target genomes.
[2023-03-18 10:12:16,215] [INFO] Target genome list was writen to OceanDNA-b35682/target_genomes.txt
[2023-03-18 10:12:16,229] [INFO] Task started: fastANI
[2023-03-18 10:12:16,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg907c8f6d-d253-4965-9d3c-5a48cabf19c0/OceanDNA-b35682.fa --refList OceanDNA-b35682/target_genomes.txt --output OceanDNA-b35682/fastani_result.tsv --threads 1
[2023-03-18 10:12:25,214] [INFO] Task succeeded: fastANI
[2023-03-18 10:12:25,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbba0846-021d-47e5-9d6a-9189ed98eb7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:12:25,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbba0846-021d-47e5-9d6a-9189ed98eb7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:12:25,215] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:12:25,215] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:12:25,215] [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 10:12:25,215] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35682/tc_result.tsv
[2023-03-18 10:12:25,216] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:12:25,217] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:12:25,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbba0846-021d-47e5-9d6a-9189ed98eb7d/dqc_reference/checkm_data
[2023-03-18 10:12:25,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:12:25,222] [INFO] Task started: CheckM
[2023-03-18 10:12:25,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35682/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35682/checkm_input OceanDNA-b35682/checkm_result
[2023-03-18 10:12:42,181] [INFO] Task succeeded: CheckM
[2023-03-18 10:12:42,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:12:42,189] [INFO] ===== Completeness check finished =====
[2023-03-18 10:12:42,189] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:12:42,190] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35682/markers.fasta)
[2023-03-18 10:12:42,190] [INFO] Task started: Blastn
[2023-03-18 10:12:42,190] [INFO] Running command: blastn -query OceanDNA-b35682/markers.fasta -db /var/lib/cwl/stgcbba0846-021d-47e5-9d6a-9189ed98eb7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35682/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:12:42,896] [INFO] Task succeeded: Blastn
[2023-03-18 10:12:42,899] [INFO] Selected 26 target genomes.
[2023-03-18 10:12:42,899] [INFO] Target genome list was writen to OceanDNA-b35682/target_genomes_gtdb.txt
[2023-03-18 10:12:42,918] [INFO] Task started: fastANI
[2023-03-18 10:12:42,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg907c8f6d-d253-4965-9d3c-5a48cabf19c0/OceanDNA-b35682.fa --refList OceanDNA-b35682/target_genomes_gtdb.txt --output OceanDNA-b35682/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:12:53,512] [INFO] Task succeeded: fastANI
[2023-03-18 10:12:53,514] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:12:53,514] [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_002728355.1	s__GCA-2728355 sp002728355	99.0882	246	271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2728355	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 10:12:53,516] [INFO] GTDB search result was written to OceanDNA-b35682/result_gtdb.tsv
[2023-03-18 10:12:53,517] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:12:53,517] [INFO] DFAST_QC result json was written to OceanDNA-b35682/dqc_result.json
[2023-03-18 10:12:53,517] [INFO] DFAST_QC completed!
[2023-03-18 10:12:53,517] [INFO] Total running time: 0h0m43s