[2023-03-17 02:31:12,846] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,846] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,846] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfbd0413-28ea-4d5c-81bc-1cf7f7cbb789/dqc_reference
[2023-03-17 02:31:14,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,379] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,379] [INFO] Running command: cat /var/lib/cwl/stgafb362cd-d737-40af-b8cf-e4e670fc0701/OceanDNA-b43685.fa | prodigal -d OceanDNA-b43685/cds.fna -a OceanDNA-b43685/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:24,382] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:24,383] [INFO] Task started: HMMsearch
[2023-03-17 02:31:24,383] [INFO] Running command: hmmsearch --tblout OceanDNA-b43685/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfbd0413-28ea-4d5c-81bc-1cf7f7cbb789/dqc_reference/reference_markers.hmm OceanDNA-b43685/protein.faa > /dev/null
[2023-03-17 02:31:24,554] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:24,554] [INFO] Found 6/6 markers.
[2023-03-17 02:31:24,568] [INFO] Query marker FASTA was written to OceanDNA-b43685/markers.fasta
[2023-03-17 02:31:24,569] [INFO] Task started: Blastn
[2023-03-17 02:31:24,569] [INFO] Running command: blastn -query OceanDNA-b43685/markers.fasta -db /var/lib/cwl/stgcfbd0413-28ea-4d5c-81bc-1cf7f7cbb789/dqc_reference/reference_markers.fasta -out OceanDNA-b43685/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:25,170] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:25,171] [INFO] Selected 40 target genomes.
[2023-03-17 02:31:25,171] [INFO] Target genome list was writen to OceanDNA-b43685/target_genomes.txt
[2023-03-17 02:31:25,191] [INFO] Task started: fastANI
[2023-03-17 02:31:25,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgafb362cd-d737-40af-b8cf-e4e670fc0701/OceanDNA-b43685.fa --refList OceanDNA-b43685/target_genomes.txt --output OceanDNA-b43685/fastani_result.tsv --threads 1
[2023-03-17 02:31:49,793] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:49,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfbd0413-28ea-4d5c-81bc-1cf7f7cbb789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:49,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfbd0413-28ea-4d5c-81bc-1cf7f7cbb789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:49,794] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:49,794] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:31:49,794] [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
--------------------------------------------------------------------------------
[2023-03-17 02:31:49,794] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43685/tc_result.tsv
[2023-03-17 02:31:49,794] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:49,794] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:49,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfbd0413-28ea-4d5c-81bc-1cf7f7cbb789/dqc_reference/checkm_data
[2023-03-17 02:31:49,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:49,801] [INFO] Task started: CheckM
[2023-03-17 02:31:49,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43685/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43685/checkm_input OceanDNA-b43685/checkm_result
[2023-03-17 02:32:19,086] [INFO] Task succeeded: CheckM
[2023-03-17 02:32:19,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:32:19,089] [INFO] ===== Completeness check finished =====
[2023-03-17 02:32:19,089] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:32:19,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43685/markers.fasta)
[2023-03-17 02:32:19,090] [INFO] Task started: Blastn
[2023-03-17 02:32:19,090] [INFO] Running command: blastn -query OceanDNA-b43685/markers.fasta -db /var/lib/cwl/stgcfbd0413-28ea-4d5c-81bc-1cf7f7cbb789/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43685/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:32:20,118] [INFO] Task succeeded: Blastn
[2023-03-17 02:32:20,119] [INFO] Selected 32 target genomes.
[2023-03-17 02:32:20,119] [INFO] Target genome list was writen to OceanDNA-b43685/target_genomes_gtdb.txt
[2023-03-17 02:32:21,102] [INFO] Task started: fastANI
[2023-03-17 02:32:21,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgafb362cd-d737-40af-b8cf-e4e670fc0701/OceanDNA-b43685.fa --refList OceanDNA-b43685/target_genomes_gtdb.txt --output OceanDNA-b43685/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:32:37,952] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:37,954] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:32:37,954] [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_002729195.1	s__UBA12578 sp002729195	98.9383	437	527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA12578	95.0	97.26	96.05	0.75	0.72	3	conclusive
--------------------------------------------------------------------------------
[2023-03-17 02:32:37,955] [INFO] GTDB search result was written to OceanDNA-b43685/result_gtdb.tsv
[2023-03-17 02:32:37,955] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:32:37,955] [INFO] DFAST_QC result json was written to OceanDNA-b43685/dqc_result.json
[2023-03-17 02:32:37,955] [INFO] DFAST_QC completed!
[2023-03-17 02:32:37,955] [INFO] Total running time: 0h1m25s