[2023-06-17 08:40:45,643] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:40:45,646] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:40:45,646] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2f20315-2d90-4cf0-8d48-1cbc78fb8c00/dqc_reference
[2023-06-17 08:40:46,976] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:40:46,977] [INFO] Task started: Prodigal
[2023-06-17 08:40:46,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg01d46da5-62b5-4944-a0b0-9ab662317d85/GCA_009705635.1_ASM970563v1_genomic.fna.gz | prodigal -d GCA_009705635.1_ASM970563v1_genomic.fna/cds.fna -a GCA_009705635.1_ASM970563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:40:48,527] [INFO] Task succeeded: Prodigal
[2023-06-17 08:40:48,528] [INFO] Task started: HMMsearch
[2023-06-17 08:40:48,528] [INFO] Running command: hmmsearch --tblout GCA_009705635.1_ASM970563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2f20315-2d90-4cf0-8d48-1cbc78fb8c00/dqc_reference/reference_markers.hmm GCA_009705635.1_ASM970563v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:40:48,707] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:40:48,710] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg01d46da5-62b5-4944-a0b0-9ab662317d85/GCA_009705635.1_ASM970563v1_genomic.fna.gz]
[2023-06-17 08:40:48,726] [INFO] Query marker FASTA was written to GCA_009705635.1_ASM970563v1_genomic.fna/markers.fasta
[2023-06-17 08:40:48,727] [INFO] Task started: Blastn
[2023-06-17 08:40:48,727] [INFO] Running command: blastn -query GCA_009705635.1_ASM970563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2f20315-2d90-4cf0-8d48-1cbc78fb8c00/dqc_reference/reference_markers.fasta -out GCA_009705635.1_ASM970563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:40:49,791] [INFO] Task succeeded: Blastn
[2023-06-17 08:40:49,795] [INFO] Selected 7 target genomes.
[2023-06-17 08:40:49,795] [INFO] Target genome list was writen to GCA_009705635.1_ASM970563v1_genomic.fna/target_genomes.txt
[2023-06-17 08:40:49,799] [INFO] Task started: fastANI
[2023-06-17 08:40:49,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg01d46da5-62b5-4944-a0b0-9ab662317d85/GCA_009705635.1_ASM970563v1_genomic.fna.gz --refList GCA_009705635.1_ASM970563v1_genomic.fna/target_genomes.txt --output GCA_009705635.1_ASM970563v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:40:54,670] [INFO] Task succeeded: fastANI
[2023-06-17 08:40:54,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2f20315-2d90-4cf0-8d48-1cbc78fb8c00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:40:54,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2f20315-2d90-4cf0-8d48-1cbc78fb8c00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:40:54,673] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:40:54,673] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 08:40:54,673] [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
--------------------------------------------------------------------------------
[2023-06-17 08:40:54,674] [INFO] DFAST Taxonomy check result was written to GCA_009705635.1_ASM970563v1_genomic.fna/tc_result.tsv
[2023-06-17 08:40:54,675] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:40:54,675] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:40:54,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2f20315-2d90-4cf0-8d48-1cbc78fb8c00/dqc_reference/checkm_data
[2023-06-17 08:40:54,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:40:54,689] [INFO] Task started: CheckM
[2023-06-17 08:40:54,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009705635.1_ASM970563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009705635.1_ASM970563v1_genomic.fna/checkm_input GCA_009705635.1_ASM970563v1_genomic.fna/checkm_result
[2023-06-17 08:41:08,032] [INFO] Task succeeded: CheckM
[2023-06-17 08:41:08,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:41:08,056] [INFO] ===== Completeness check finished =====
[2023-06-17 08:41:08,056] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:41:08,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009705635.1_ASM970563v1_genomic.fna/markers.fasta)
[2023-06-17 08:41:08,057] [INFO] Task started: Blastn
[2023-06-17 08:41:08,057] [INFO] Running command: blastn -query GCA_009705635.1_ASM970563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2f20315-2d90-4cf0-8d48-1cbc78fb8c00/dqc_reference/reference_markers_gtdb.fasta -out GCA_009705635.1_ASM970563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:41:08,704] [INFO] Task succeeded: Blastn
[2023-06-17 08:41:08,708] [INFO] Selected 8 target genomes.
[2023-06-17 08:41:08,708] [INFO] Target genome list was writen to GCA_009705635.1_ASM970563v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:41:08,715] [INFO] Task started: fastANI
[2023-06-17 08:41:08,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg01d46da5-62b5-4944-a0b0-9ab662317d85/GCA_009705635.1_ASM970563v1_genomic.fna.gz --refList GCA_009705635.1_ASM970563v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009705635.1_ASM970563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:41:10,711] [INFO] Task succeeded: fastANI
[2023-06-17 08:41:10,718] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 08:41:10,718] [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_002346305.1	s__UBA3012 sp002346305	88.3689	157	209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	95.05	95.05	0.74	0.74	2	-
GCA_903902965.1	s__UBA3012 sp903902965	86.9832	167	209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	99.39	99.39	0.86	0.86	2	-
GCA_009701305.1	s__UBA3012 sp009701305	85.3252	165	209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	99.65	99.63	0.87	0.87	3	-
GCA_014190175.1	s__UBA3012 sp014190175	85.1499	176	209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010031635.1	s__UBA3012 sp010031635	84.4105	163	209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694285.1	s__UBA3012 sp009694285	84.1622	164	209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__UBA3012	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 08:41:10,720] [INFO] GTDB search result was written to GCA_009705635.1_ASM970563v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:41:10,721] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:41:10,723] [INFO] DFAST_QC result json was written to GCA_009705635.1_ASM970563v1_genomic.fna/dqc_result.json
[2023-06-17 08:41:10,723] [INFO] DFAST_QC completed!
[2023-06-17 08:41:10,724] [INFO] Total running time: 0h0m25s