[2023-03-19 00:44:19,940] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:44:19,940] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:44:19,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg0490dd91-1f2c-43e0-9691-1ce7300d3e72/dqc_reference
[2023-03-19 00:44:21,069] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:44:21,069] [INFO] Task started: Prodigal
[2023-03-19 00:44:21,069] [INFO] Running command: cat /var/lib/cwl/stgc0fb1b72-85ca-4ba9-94b4-bb9efd0235f5/OceanDNA-b34257.fa | prodigal -d OceanDNA-b34257/cds.fna -a OceanDNA-b34257/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:44:30,624] [INFO] Task succeeded: Prodigal
[2023-03-19 00:44:30,624] [INFO] Task started: HMMsearch
[2023-03-19 00:44:30,624] [INFO] Running command: hmmsearch --tblout OceanDNA-b34257/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0490dd91-1f2c-43e0-9691-1ce7300d3e72/dqc_reference/reference_markers.hmm OceanDNA-b34257/protein.faa > /dev/null
[2023-03-19 00:44:30,795] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:44:30,795] [INFO] Found 6/6 markers.
[2023-03-19 00:44:30,808] [INFO] Query marker FASTA was written to OceanDNA-b34257/markers.fasta
[2023-03-19 00:44:30,809] [INFO] Task started: Blastn
[2023-03-19 00:44:30,809] [INFO] Running command: blastn -query OceanDNA-b34257/markers.fasta -db /var/lib/cwl/stg0490dd91-1f2c-43e0-9691-1ce7300d3e72/dqc_reference/reference_markers.fasta -out OceanDNA-b34257/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:44:31,374] [INFO] Task succeeded: Blastn
[2023-03-19 00:44:31,375] [INFO] Selected 24 target genomes.
[2023-03-19 00:44:31,375] [INFO] Target genome list was writen to OceanDNA-b34257/target_genomes.txt
[2023-03-19 00:44:31,388] [INFO] Task started: fastANI
[2023-03-19 00:44:31,388] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fb1b72-85ca-4ba9-94b4-bb9efd0235f5/OceanDNA-b34257.fa --refList OceanDNA-b34257/target_genomes.txt --output OceanDNA-b34257/fastani_result.tsv --threads 1
[2023-03-19 00:44:44,807] [INFO] Task succeeded: fastANI
[2023-03-19 00:44:44,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0490dd91-1f2c-43e0-9691-1ce7300d3e72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:44:44,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0490dd91-1f2c-43e0-9691-1ce7300d3e72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:44:44,807] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:44:44,808] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:44:44,808] [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
--------------------------------------------------------------------------------
[2023-03-19 00:44:44,808] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34257/tc_result.tsv
[2023-03-19 00:44:44,808] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:44:44,808] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:44:44,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0490dd91-1f2c-43e0-9691-1ce7300d3e72/dqc_reference/checkm_data
[2023-03-19 00:44:44,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:44:44,819] [INFO] Task started: CheckM
[2023-03-19 00:44:44,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34257/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34257/checkm_input OceanDNA-b34257/checkm_result
[2023-03-19 00:45:13,529] [INFO] Task succeeded: CheckM
[2023-03-19 00:45:13,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:45:13,532] [INFO] ===== Completeness check finished =====
[2023-03-19 00:45:13,532] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:45:13,532] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34257/markers.fasta)
[2023-03-19 00:45:13,533] [INFO] Task started: Blastn
[2023-03-19 00:45:13,533] [INFO] Running command: blastn -query OceanDNA-b34257/markers.fasta -db /var/lib/cwl/stg0490dd91-1f2c-43e0-9691-1ce7300d3e72/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34257/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:45:14,446] [INFO] Task succeeded: Blastn
[2023-03-19 00:45:14,447] [INFO] Selected 21 target genomes.
[2023-03-19 00:45:14,447] [INFO] Target genome list was writen to OceanDNA-b34257/target_genomes_gtdb.txt
[2023-03-19 00:45:14,475] [INFO] Task started: fastANI
[2023-03-19 00:45:14,475] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fb1b72-85ca-4ba9-94b4-bb9efd0235f5/OceanDNA-b34257.fa --refList OceanDNA-b34257/target_genomes_gtdb.txt --output OceanDNA-b34257/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:45:21,888] [INFO] Task succeeded: fastANI
[2023-03-19 00:45:21,892] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:45:21,892] [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_002323325.1	s__UBA9148 sp002323325	99.8265	527	581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__UBA9148	95.0	99.86	99.86	0.93	0.93	2	conclusive
GCA_011523685.1	s__UBA9148 sp011523685	81.7676	268	581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__UBA9148	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623005.1	s__UBA9148 sp902623005	79.0756	79	581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__UBA9148	95.0	99.42	99.42	0.82	0.82	2	-
GCA_014238445.1	s__UBA9148 sp014238445	77.5168	79	581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Coxiellales;f__Coxiellaceae;g__UBA9148	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:45:21,892] [INFO] GTDB search result was written to OceanDNA-b34257/result_gtdb.tsv
[2023-03-19 00:45:21,893] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:45:21,893] [INFO] DFAST_QC result json was written to OceanDNA-b34257/dqc_result.json
[2023-03-19 00:45:21,894] [INFO] DFAST_QC completed!
[2023-03-19 00:45:21,894] [INFO] Total running time: 0h1m2s