[2024-01-25 18:43:05,666] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:05,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:05,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg84e283f6-8243-4186-8083-2fd6e64b16b6/dqc_reference
[2024-01-25 18:43:06,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:06,791] [INFO] Task started: Prodigal
[2024-01-25 18:43:06,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg779e116d-07af-4d14-b984-44b07e322635/GCF_009734185.1_ASM973418v1_genomic.fna.gz | prodigal -d GCF_009734185.1_ASM973418v1_genomic.fna/cds.fna -a GCF_009734185.1_ASM973418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:10,809] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:10,809] [INFO] Task started: HMMsearch
[2024-01-25 18:43:10,809] [INFO] Running command: hmmsearch --tblout GCF_009734185.1_ASM973418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84e283f6-8243-4186-8083-2fd6e64b16b6/dqc_reference/reference_markers.hmm GCF_009734185.1_ASM973418v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:11,031] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:11,032] [INFO] Found 6/6 markers.
[2024-01-25 18:43:11,051] [INFO] Query marker FASTA was written to GCF_009734185.1_ASM973418v1_genomic.fna/markers.fasta
[2024-01-25 18:43:11,051] [INFO] Task started: Blastn
[2024-01-25 18:43:11,051] [INFO] Running command: blastn -query GCF_009734185.1_ASM973418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84e283f6-8243-4186-8083-2fd6e64b16b6/dqc_reference/reference_markers.fasta -out GCF_009734185.1_ASM973418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:11,631] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:11,633] [INFO] Selected 22 target genomes.
[2024-01-25 18:43:11,634] [INFO] Target genome list was writen to GCF_009734185.1_ASM973418v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:11,646] [INFO] Task started: fastANI
[2024-01-25 18:43:11,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg779e116d-07af-4d14-b984-44b07e322635/GCF_009734185.1_ASM973418v1_genomic.fna.gz --refList GCF_009734185.1_ASM973418v1_genomic.fna/target_genomes.txt --output GCF_009734185.1_ASM973418v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:23,860] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:23,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84e283f6-8243-4186-8083-2fd6e64b16b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:23,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84e283f6-8243-4186-8083-2fd6e64b16b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:23,864] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:43:23,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:43:23,864] [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
Commensalibacter intestini	strain=A911	GCA_000231445.2	479936	479936	type	True	77.5997	109	653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:23,866] [INFO] DFAST Taxonomy check result was written to GCF_009734185.1_ASM973418v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:23,866] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:23,866] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:23,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84e283f6-8243-4186-8083-2fd6e64b16b6/dqc_reference/checkm_data
[2024-01-25 18:43:23,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:23,890] [INFO] Task started: CheckM
[2024-01-25 18:43:23,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009734185.1_ASM973418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009734185.1_ASM973418v1_genomic.fna/checkm_input GCF_009734185.1_ASM973418v1_genomic.fna/checkm_result
[2024-01-25 18:43:41,876] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:41,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:41,889] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:41,890] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:41,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009734185.1_ASM973418v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:41,890] [INFO] Task started: Blastn
[2024-01-25 18:43:41,890] [INFO] Running command: blastn -query GCF_009734185.1_ASM973418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84e283f6-8243-4186-8083-2fd6e64b16b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009734185.1_ASM973418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:42,861] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:42,864] [INFO] Selected 22 target genomes.
[2024-01-25 18:43:42,864] [INFO] Target genome list was writen to GCF_009734185.1_ASM973418v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:42,880] [INFO] Task started: fastANI
[2024-01-25 18:43:42,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg779e116d-07af-4d14-b984-44b07e322635/GCF_009734185.1_ASM973418v1_genomic.fna.gz --refList GCF_009734185.1_ASM973418v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009734185.1_ASM973418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:50,128] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:50,132] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:50,132] [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
GCF_003691365.1	s__Commensalibacter sp003202795	98.6986	643	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Commensalibacter	95.0	98.46	98.25	0.98	0.95	26	conclusive
GCF_000231445.1	s__Commensalibacter intestini	77.5997	109	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Commensalibacter	95.0	98.89	98.89	0.96	0.96	2	-
GCF_000527695.1	s__Commensalibacter sp000527695	77.0493	103	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Commensalibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:50,134] [INFO] GTDB search result was written to GCF_009734185.1_ASM973418v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:50,135] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:50,136] [INFO] DFAST_QC result json was written to GCF_009734185.1_ASM973418v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:50,136] [INFO] DFAST_QC completed!
[2024-01-25 18:43:50,137] [INFO] Total running time: 0h0m44s