[2023-03-18 09:19:06,959] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:19:06,959] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:19:06,959] [INFO] DQC Reference Directory: /var/lib/cwl/stgb402c5f1-b800-45e2-8d1e-af5e30baf436/dqc_reference
[2023-03-18 09:19:08,108] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:19:08,109] [INFO] Task started: Prodigal
[2023-03-18 09:19:08,109] [INFO] Running command: cat /var/lib/cwl/stgb7a33289-a7c7-44a1-b847-161d24c1ac0f/OceanDNA-b37076.fa | prodigal -d OceanDNA-b37076/cds.fna -a OceanDNA-b37076/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:19:29,087] [INFO] Task succeeded: Prodigal
[2023-03-18 09:19:29,087] [INFO] Task started: HMMsearch
[2023-03-18 09:19:29,087] [INFO] Running command: hmmsearch --tblout OceanDNA-b37076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb402c5f1-b800-45e2-8d1e-af5e30baf436/dqc_reference/reference_markers.hmm OceanDNA-b37076/protein.faa > /dev/null
[2023-03-18 09:19:29,304] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:19:29,304] [INFO] Found 6/6 markers.
[2023-03-18 09:19:29,331] [INFO] Query marker FASTA was written to OceanDNA-b37076/markers.fasta
[2023-03-18 09:19:29,332] [INFO] Task started: Blastn
[2023-03-18 09:19:29,332] [INFO] Running command: blastn -query OceanDNA-b37076/markers.fasta -db /var/lib/cwl/stgb402c5f1-b800-45e2-8d1e-af5e30baf436/dqc_reference/reference_markers.fasta -out OceanDNA-b37076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:19:29,918] [INFO] Task succeeded: Blastn
[2023-03-18 09:19:29,921] [INFO] Selected 29 target genomes.
[2023-03-18 09:19:29,921] [INFO] Target genome list was writen to OceanDNA-b37076/target_genomes.txt
[2023-03-18 09:19:29,937] [INFO] Task started: fastANI
[2023-03-18 09:19:29,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7a33289-a7c7-44a1-b847-161d24c1ac0f/OceanDNA-b37076.fa --refList OceanDNA-b37076/target_genomes.txt --output OceanDNA-b37076/fastani_result.tsv --threads 1
[2023-03-18 09:19:45,912] [INFO] Task succeeded: fastANI
[2023-03-18 09:19:45,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb402c5f1-b800-45e2-8d1e-af5e30baf436/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:19:45,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb402c5f1-b800-45e2-8d1e-af5e30baf436/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:19:45,913] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:19:45,913] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:19:45,913] [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 09:19:45,914] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37076/tc_result.tsv
[2023-03-18 09:19:45,914] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:19:45,915] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:19:45,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb402c5f1-b800-45e2-8d1e-af5e30baf436/dqc_reference/checkm_data
[2023-03-18 09:19:45,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:19:45,925] [INFO] Task started: CheckM
[2023-03-18 09:19:45,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37076/checkm_input OceanDNA-b37076/checkm_result
[2023-03-18 09:20:38,852] [INFO] Task succeeded: CheckM
[2023-03-18 09:20:38,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:20:38,880] [INFO] ===== Completeness check finished =====
[2023-03-18 09:20:38,880] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:20:38,880] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37076/markers.fasta)
[2023-03-18 09:20:38,881] [INFO] Task started: Blastn
[2023-03-18 09:20:38,881] [INFO] Running command: blastn -query OceanDNA-b37076/markers.fasta -db /var/lib/cwl/stgb402c5f1-b800-45e2-8d1e-af5e30baf436/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:20:39,850] [INFO] Task succeeded: Blastn
[2023-03-18 09:20:39,854] [INFO] Selected 25 target genomes.
[2023-03-18 09:20:39,854] [INFO] Target genome list was writen to OceanDNA-b37076/target_genomes_gtdb.txt
[2023-03-18 09:20:40,068] [INFO] Task started: fastANI
[2023-03-18 09:20:40,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7a33289-a7c7-44a1-b847-161d24c1ac0f/OceanDNA-b37076.fa --refList OceanDNA-b37076/target_genomes_gtdb.txt --output OceanDNA-b37076/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:20:53,604] [INFO] Task succeeded: fastANI
[2023-03-18 09:20:53,605] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:20:53,606] [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_002389675.1	s__UBA4421 sp002389675	99.89	945	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.80	99.68	0.93	0.91	3	conclusive
--------------------------------------------------------------------------------
[2023-03-18 09:20:53,608] [INFO] GTDB search result was written to OceanDNA-b37076/result_gtdb.tsv
[2023-03-18 09:20:53,609] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:20:53,611] [INFO] DFAST_QC result json was written to OceanDNA-b37076/dqc_result.json
[2023-03-18 09:20:53,611] [INFO] DFAST_QC completed!
[2023-03-18 09:20:53,611] [INFO] Total running time: 0h1m47s