[2023-03-18 23:45:35,837] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:45:35,837] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:45:35,838] [INFO] DQC Reference Directory: /var/lib/cwl/stgb86cbef4-f8d0-4b2e-9f27-f6174931c171/dqc_reference
[2023-03-18 23:45:37,730] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:45:37,730] [INFO] Task started: Prodigal
[2023-03-18 23:45:37,730] [INFO] Running command: cat /var/lib/cwl/stg5f3b2adc-9d49-4d88-b751-f7bdd9b27f05/OceanDNA-b37225.fa | prodigal -d OceanDNA-b37225/cds.fna -a OceanDNA-b37225/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:45:55,261] [INFO] Task succeeded: Prodigal
[2023-03-18 23:45:55,262] [INFO] Task started: HMMsearch
[2023-03-18 23:45:55,262] [INFO] Running command: hmmsearch --tblout OceanDNA-b37225/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb86cbef4-f8d0-4b2e-9f27-f6174931c171/dqc_reference/reference_markers.hmm OceanDNA-b37225/protein.faa > /dev/null
[2023-03-18 23:45:55,457] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:45:55,457] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5f3b2adc-9d49-4d88-b751-f7bdd9b27f05/OceanDNA-b37225.fa]
[2023-03-18 23:45:55,478] [INFO] Query marker FASTA was written to OceanDNA-b37225/markers.fasta
[2023-03-18 23:45:55,478] [INFO] Task started: Blastn
[2023-03-18 23:45:55,479] [INFO] Running command: blastn -query OceanDNA-b37225/markers.fasta -db /var/lib/cwl/stgb86cbef4-f8d0-4b2e-9f27-f6174931c171/dqc_reference/reference_markers.fasta -out OceanDNA-b37225/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:56,032] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:56,032] [INFO] Selected 25 target genomes.
[2023-03-18 23:45:56,033] [INFO] Target genome list was writen to OceanDNA-b37225/target_genomes.txt
[2023-03-18 23:45:56,046] [INFO] Task started: fastANI
[2023-03-18 23:45:56,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f3b2adc-9d49-4d88-b751-f7bdd9b27f05/OceanDNA-b37225.fa --refList OceanDNA-b37225/target_genomes.txt --output OceanDNA-b37225/fastani_result.tsv --threads 1
[2023-03-18 23:46:11,408] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:11,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb86cbef4-f8d0-4b2e-9f27-f6174931c171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:46:11,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb86cbef4-f8d0-4b2e-9f27-f6174931c171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:46:11,408] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:46:11,408] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:46:11,408] [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 23:46:11,409] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37225/tc_result.tsv
[2023-03-18 23:46:11,409] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:46:11,409] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:46:11,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb86cbef4-f8d0-4b2e-9f27-f6174931c171/dqc_reference/checkm_data
[2023-03-18 23:46:11,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:46:11,416] [INFO] Task started: CheckM
[2023-03-18 23:46:11,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37225/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37225/checkm_input OceanDNA-b37225/checkm_result
[2023-03-18 23:46:57,797] [INFO] Task succeeded: CheckM
[2023-03-18 23:46:57,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:46:57,800] [INFO] ===== Completeness check finished =====
[2023-03-18 23:46:57,800] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:46:57,800] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37225/markers.fasta)
[2023-03-18 23:46:57,801] [INFO] Task started: Blastn
[2023-03-18 23:46:57,801] [INFO] Running command: blastn -query OceanDNA-b37225/markers.fasta -db /var/lib/cwl/stgb86cbef4-f8d0-4b2e-9f27-f6174931c171/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37225/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:46:58,639] [INFO] Task succeeded: Blastn
[2023-03-18 23:46:58,640] [INFO] Selected 29 target genomes.
[2023-03-18 23:46:58,641] [INFO] Target genome list was writen to OceanDNA-b37225/target_genomes_gtdb.txt
[2023-03-18 23:46:58,684] [INFO] Task started: fastANI
[2023-03-18 23:46:58,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f3b2adc-9d49-4d88-b751-f7bdd9b27f05/OceanDNA-b37225.fa --refList OceanDNA-b37225/target_genomes_gtdb.txt --output OceanDNA-b37225/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:47:15,900] [INFO] Task succeeded: fastANI
[2023-03-18 23:47:15,902] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:47:15,902] [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_002457275.1	s__UBA7451 sp002457275	77.8764	158	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7451	95.0	99.69	99.68	0.87	0.82	3	-
--------------------------------------------------------------------------------
[2023-03-18 23:47:15,902] [INFO] GTDB search result was written to OceanDNA-b37225/result_gtdb.tsv
[2023-03-18 23:47:15,903] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:47:15,903] [INFO] DFAST_QC result json was written to OceanDNA-b37225/dqc_result.json
[2023-03-18 23:47:15,903] [INFO] DFAST_QC completed!
[2023-03-18 23:47:15,903] [INFO] Total running time: 0h1m40s