[2023-03-16 10:22:20,863] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:22:20,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:22:20,863] [INFO] DQC Reference Directory: /var/lib/cwl/stg30e647b8-4d23-454e-8da5-8e0d888f97a8/dqc_reference
[2023-03-16 10:22:22,663] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:22:22,664] [INFO] Task started: Prodigal
[2023-03-16 10:22:22,665] [INFO] Running command: cat /var/lib/cwl/stg2991f807-dc58-4455-875e-8e002a4e47b6/OceanDNA-b32661.fa | prodigal -d OceanDNA-b32661/cds.fna -a OceanDNA-b32661/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:22:54,761] [INFO] Task succeeded: Prodigal
[2023-03-16 10:22:54,761] [INFO] Task started: HMMsearch
[2023-03-16 10:22:54,761] [INFO] Running command: hmmsearch --tblout OceanDNA-b32661/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30e647b8-4d23-454e-8da5-8e0d888f97a8/dqc_reference/reference_markers.hmm OceanDNA-b32661/protein.faa > /dev/null
[2023-03-16 10:22:55,245] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:22:55,246] [INFO] Found 6/6 markers.
[2023-03-16 10:22:55,295] [INFO] Query marker FASTA was written to OceanDNA-b32661/markers.fasta
[2023-03-16 10:22:55,299] [INFO] Task started: Blastn
[2023-03-16 10:22:55,299] [INFO] Running command: blastn -query OceanDNA-b32661/markers.fasta -db /var/lib/cwl/stg30e647b8-4d23-454e-8da5-8e0d888f97a8/dqc_reference/reference_markers.fasta -out OceanDNA-b32661/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:22:56,484] [INFO] Task succeeded: Blastn
[2023-03-16 10:22:56,485] [INFO] Selected 32 target genomes.
[2023-03-16 10:22:56,486] [INFO] Target genome list was writen to OceanDNA-b32661/target_genomes.txt
[2023-03-16 10:22:56,561] [INFO] Task started: fastANI
[2023-03-16 10:22:56,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg2991f807-dc58-4455-875e-8e002a4e47b6/OceanDNA-b32661.fa --refList OceanDNA-b32661/target_genomes.txt --output OceanDNA-b32661/fastani_result.tsv --threads 1
[2023-03-16 10:23:14,765] [INFO] Task succeeded: fastANI
[2023-03-16 10:23:14,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30e647b8-4d23-454e-8da5-8e0d888f97a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:23:14,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30e647b8-4d23-454e-8da5-8e0d888f97a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:23:14,766] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:23:14,766] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:23:14,766] [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
--------------------------------------------------------------------------------
[2023-03-16 10:23:14,766] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32661/tc_result.tsv
[2023-03-16 10:23:14,766] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:23:14,766] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:23:14,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30e647b8-4d23-454e-8da5-8e0d888f97a8/dqc_reference/checkm_data
[2023-03-16 10:23:14,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:23:15,068] [INFO] Task started: CheckM
[2023-03-16 10:23:15,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32661/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32661/checkm_input OceanDNA-b32661/checkm_result
[2023-03-16 10:24:33,725] [INFO] Task succeeded: CheckM
[2023-03-16 10:24:33,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:24:33,728] [INFO] ===== Completeness check finished =====
[2023-03-16 10:24:33,729] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:24:33,729] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32661/markers.fasta)
[2023-03-16 10:24:33,730] [INFO] Task started: Blastn
[2023-03-16 10:24:33,730] [INFO] Running command: blastn -query OceanDNA-b32661/markers.fasta -db /var/lib/cwl/stg30e647b8-4d23-454e-8da5-8e0d888f97a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32661/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:24:34,810] [INFO] Task succeeded: Blastn
[2023-03-16 10:24:34,811] [INFO] Selected 24 target genomes.
[2023-03-16 10:24:34,811] [INFO] Target genome list was writen to OceanDNA-b32661/target_genomes_gtdb.txt
[2023-03-16 10:24:34,947] [INFO] Task started: fastANI
[2023-03-16 10:24:34,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg2991f807-dc58-4455-875e-8e002a4e47b6/OceanDNA-b32661.fa --refList OceanDNA-b32661/target_genomes_gtdb.txt --output OceanDNA-b32661/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:24:57,316] [INFO] Task succeeded: fastANI
[2023-03-16 10:24:57,319] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:24:57,319] [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_018654745.1	s__JABILA01 sp018654745	99.9489	1518	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__JABILA01	95.0	99.91	99.83	0.93	0.89	4	conclusive
GCA_018650465.1	s__JABILA01 sp018650465	80.6478	774	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__JABILA01	95.0	99.90	99.89	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2023-03-16 10:24:57,320] [INFO] GTDB search result was written to OceanDNA-b32661/result_gtdb.tsv
[2023-03-16 10:24:57,320] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:24:57,321] [INFO] DFAST_QC result json was written to OceanDNA-b32661/dqc_result.json
[2023-03-16 10:24:57,321] [INFO] DFAST_QC completed!
[2023-03-16 10:24:57,321] [INFO] Total running time: 0h2m36s