[2023-06-05 07:09:38,748] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:09:38,751] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:09:38,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg6cf985e8-8888-49ba-8c03-8e4eab051bee/dqc_reference
[2023-06-05 07:09:41,832] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:09:41,833] [INFO] Task started: Prodigal
[2023-06-05 07:09:41,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg58ec6aa9-96f9-4103-91d2-0130abe9c418/GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna.gz | prodigal -d GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/cds.fna -a GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:09:44,050] [INFO] Task succeeded: Prodigal
[2023-06-05 07:09:44,051] [INFO] Task started: HMMsearch
[2023-06-05 07:09:44,051] [INFO] Running command: hmmsearch --tblout GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6cf985e8-8888-49ba-8c03-8e4eab051bee/dqc_reference/reference_markers.hmm GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:09:44,334] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:09:44,335] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg58ec6aa9-96f9-4103-91d2-0130abe9c418/GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna.gz]
[2023-06-05 07:09:44,356] [INFO] Query marker FASTA was written to GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/markers.fasta
[2023-06-05 07:09:44,356] [INFO] Task started: Blastn
[2023-06-05 07:09:44,357] [INFO] Running command: blastn -query GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cf985e8-8888-49ba-8c03-8e4eab051bee/dqc_reference/reference_markers.fasta -out GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:09:47,656] [INFO] Task succeeded: Blastn
[2023-06-05 07:09:47,660] [INFO] Selected 22 target genomes.
[2023-06-05 07:09:47,660] [INFO] Target genome list was writen to GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/target_genomes.txt
[2023-06-05 07:09:47,665] [INFO] Task started: fastANI
[2023-06-05 07:09:47,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg58ec6aa9-96f9-4103-91d2-0130abe9c418/GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna.gz --refList GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/target_genomes.txt --output GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:09:55,338] [INFO] Task succeeded: fastANI
[2023-06-05 07:09:55,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6cf985e8-8888-49ba-8c03-8e4eab051bee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:09:55,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6cf985e8-8888-49ba-8c03-8e4eab051bee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:09:55,343] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:09:55,343] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:09:55,343] [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
Holdemanella biformis	strain=DSM 3989	GCA_000156655.1	1735	1735	suspected-type	True	77.275	55	261	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:09:55,345] [INFO] DFAST Taxonomy check result was written to GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/tc_result.tsv
[2023-06-05 07:09:55,346] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:09:55,346] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:09:55,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6cf985e8-8888-49ba-8c03-8e4eab051bee/dqc_reference/checkm_data
[2023-06-05 07:09:55,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:09:55,366] [INFO] Task started: CheckM
[2023-06-05 07:09:55,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/checkm_input GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/checkm_result
[2023-06-05 07:10:11,370] [INFO] Task succeeded: CheckM
[2023-06-05 07:10:11,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.95%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:10:11,403] [INFO] ===== Completeness check finished =====
[2023-06-05 07:10:11,403] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:10:11,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/markers.fasta)
[2023-06-05 07:10:11,404] [INFO] Task started: Blastn
[2023-06-05 07:10:11,404] [INFO] Running command: blastn -query GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cf985e8-8888-49ba-8c03-8e4eab051bee/dqc_reference/reference_markers_gtdb.fasta -out GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:10:12,301] [INFO] Task succeeded: Blastn
[2023-06-05 07:10:12,304] [INFO] Selected 14 target genomes.
[2023-06-05 07:10:12,305] [INFO] Target genome list was writen to GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:10:12,379] [INFO] Task started: fastANI
[2023-06-05 07:10:12,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg58ec6aa9-96f9-4103-91d2-0130abe9c418/GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna.gz --refList GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/target_genomes_gtdb.txt --output GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:10:16,488] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:16,495] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:10:16,496] [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_902797585.1	s__RUG14284 sp902797585	100.0	255	261	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__RUG14284	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003480165.1	s__Absicoccus sp000434355	77.7924	65	261	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Absicoccus	95.0	99.44	99.16	0.95	0.93	5	-
GCF_003436425.1	s__Holdemanella sp003436425	77.5533	52	261	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	98.46	97.77	0.88	0.82	5	-
GCF_000156655.1	s__Holdemanella biformis	77.2696	55	261	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.82	95.86	0.79	0.56	17	-
--------------------------------------------------------------------------------
[2023-06-05 07:10:16,497] [INFO] GTDB search result was written to GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/result_gtdb.tsv
[2023-06-05 07:10:16,498] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:10:16,500] [INFO] DFAST_QC result json was written to GCA_902797585.1_Rumen_uncultured_genome_RUG14284_genomic.fna/dqc_result.json
[2023-06-05 07:10:16,500] [INFO] DFAST_QC completed!
[2023-06-05 07:10:16,500] [INFO] Total running time: 0h0m38s