[2023-03-14 11:13:58,988] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,988] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,988] [INFO] DQC Reference Directory: /var/lib/cwl/stg04c31199-8745-4a65-99bb-c4c3ec88f926/dqc_reference
[2023-03-14 11:14:00,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,597] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,597] [INFO] Running command: cat /var/lib/cwl/stg77031358-4b9b-4e22-a67b-08f486908f98/OceanDNA-b42423.fa | prodigal -d OceanDNA-b42423/cds.fna -a OceanDNA-b42423/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:04,768] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:04,768] [INFO] Task started: HMMsearch
[2023-03-14 11:14:04,769] [INFO] Running command: hmmsearch --tblout OceanDNA-b42423/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04c31199-8745-4a65-99bb-c4c3ec88f926/dqc_reference/reference_markers.hmm OceanDNA-b42423/protein.faa > /dev/null
[2023-03-14 11:14:04,920] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:04,921] [INFO] Found 6/6 markers.
[2023-03-14 11:14:04,930] [INFO] Query marker FASTA was written to OceanDNA-b42423/markers.fasta
[2023-03-14 11:14:04,931] [INFO] Task started: Blastn
[2023-03-14 11:14:04,931] [INFO] Running command: blastn -query OceanDNA-b42423/markers.fasta -db /var/lib/cwl/stg04c31199-8745-4a65-99bb-c4c3ec88f926/dqc_reference/reference_markers.fasta -out OceanDNA-b42423/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:06,772] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:06,773] [INFO] Selected 15 target genomes.
[2023-03-14 11:14:06,773] [INFO] Target genome list was writen to OceanDNA-b42423/target_genomes.txt
[2023-03-14 11:14:06,787] [INFO] Task started: fastANI
[2023-03-14 11:14:06,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg77031358-4b9b-4e22-a67b-08f486908f98/OceanDNA-b42423.fa --refList OceanDNA-b42423/target_genomes.txt --output OceanDNA-b42423/fastani_result.tsv --threads 1
[2023-03-14 11:14:13,811] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:13,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04c31199-8745-4a65-99bb-c4c3ec88f926/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:13,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04c31199-8745-4a65-99bb-c4c3ec88f926/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:13,812] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:13,812] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:13,812] [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
--------------------------------------------------------------------------------
[2023-03-14 11:14:13,812] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42423/tc_result.tsv
[2023-03-14 11:14:13,812] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:13,812] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:13,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04c31199-8745-4a65-99bb-c4c3ec88f926/dqc_reference/checkm_data
[2023-03-14 11:14:13,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:13,817] [INFO] Task started: CheckM
[2023-03-14 11:14:13,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42423/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42423/checkm_input OceanDNA-b42423/checkm_result
[2023-03-14 11:14:33,199] [INFO] Task succeeded: CheckM
[2023-03-14 11:14:33,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:14:33,201] [INFO] ===== Completeness check finished =====
[2023-03-14 11:14:33,202] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:14:33,202] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42423/markers.fasta)
[2023-03-14 11:14:33,203] [INFO] Task started: Blastn
[2023-03-14 11:14:33,203] [INFO] Running command: blastn -query OceanDNA-b42423/markers.fasta -db /var/lib/cwl/stg04c31199-8745-4a65-99bb-c4c3ec88f926/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42423/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:34,398] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:34,399] [INFO] Selected 26 target genomes.
[2023-03-14 11:14:34,399] [INFO] Target genome list was writen to OceanDNA-b42423/target_genomes_gtdb.txt
[2023-03-14 11:14:34,432] [INFO] Task started: fastANI
[2023-03-14 11:14:34,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg77031358-4b9b-4e22-a67b-08f486908f98/OceanDNA-b42423.fa --refList OceanDNA-b42423/target_genomes_gtdb.txt --output OceanDNA-b42423/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:14:42,422] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:42,424] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:14:42,424] [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_902628375.1	s__CACOMS01 sp902628375	98.7542	191	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__CACOMS01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-14 11:14:42,424] [INFO] GTDB search result was written to OceanDNA-b42423/result_gtdb.tsv
[2023-03-14 11:14:42,424] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:14:42,424] [INFO] DFAST_QC result json was written to OceanDNA-b42423/dqc_result.json
[2023-03-14 11:14:42,425] [INFO] DFAST_QC completed!
[2023-03-14 11:14:42,425] [INFO] Total running time: 0h0m43s