[2024-01-24 13:41:10,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd7ca1dd-2de8-4ea0-8e8a-cdd21a2a5044/dqc_reference
[2024-01-24 13:41:12,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:12,105] [INFO] Task started: Prodigal
[2024-01-24 13:41:12,105] [INFO] Running command: gunzip -c /var/lib/cwl/stgc93d9712-03ee-423c-a424-7cf5d131a606/GCF_025595115.1_ASM2559511v1_genomic.fna.gz | prodigal -d GCF_025595115.1_ASM2559511v1_genomic.fna/cds.fna -a GCF_025595115.1_ASM2559511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:17,748] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:17,748] [INFO] Task started: HMMsearch
[2024-01-24 13:41:17,748] [INFO] Running command: hmmsearch --tblout GCF_025595115.1_ASM2559511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd7ca1dd-2de8-4ea0-8e8a-cdd21a2a5044/dqc_reference/reference_markers.hmm GCF_025595115.1_ASM2559511v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:18,024] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:18,025] [INFO] Found 6/6 markers.
[2024-01-24 13:41:18,055] [INFO] Query marker FASTA was written to GCF_025595115.1_ASM2559511v1_genomic.fna/markers.fasta
[2024-01-24 13:41:18,056] [INFO] Task started: Blastn
[2024-01-24 13:41:18,056] [INFO] Running command: blastn -query GCF_025595115.1_ASM2559511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd7ca1dd-2de8-4ea0-8e8a-cdd21a2a5044/dqc_reference/reference_markers.fasta -out GCF_025595115.1_ASM2559511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:18,689] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:18,693] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:18,694] [INFO] Target genome list was writen to GCF_025595115.1_ASM2559511v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:18,704] [INFO] Task started: fastANI
[2024-01-24 13:41:18,705] [INFO] Running command: fastANI --query /var/lib/cwl/stgc93d9712-03ee-423c-a424-7cf5d131a606/GCF_025595115.1_ASM2559511v1_genomic.fna.gz --refList GCF_025595115.1_ASM2559511v1_genomic.fna/target_genomes.txt --output GCF_025595115.1_ASM2559511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:28,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:28,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd7ca1dd-2de8-4ea0-8e8a-cdd21a2a5044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:28,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd7ca1dd-2de8-4ea0-8e8a-cdd21a2a5044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:28,701] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:28,701] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:28,701] [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
Turicibacter sanguinis	strain=MOL361	GCA_013046825.1	154288	154288	type	True	99.993	937	938	95	conclusive
Turicibacter bilis	strain=MMM721	GCA_024499055.1	2735723	2735723	type	True	80.8523	413	938	95	below_threshold
Turicibacter bilis	strain=MMM721	GCA_018305205.1	2735723	2735723	type	True	80.8071	406	938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:28,703] [INFO] DFAST Taxonomy check result was written to GCF_025595115.1_ASM2559511v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:28,704] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:28,704] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:28,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd7ca1dd-2de8-4ea0-8e8a-cdd21a2a5044/dqc_reference/checkm_data
[2024-01-24 13:41:28,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:28,739] [INFO] Task started: CheckM
[2024-01-24 13:41:28,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025595115.1_ASM2559511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025595115.1_ASM2559511v1_genomic.fna/checkm_input GCF_025595115.1_ASM2559511v1_genomic.fna/checkm_result
[2024-01-24 13:41:51,772] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:51,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:51,792] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:51,792] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:51,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025595115.1_ASM2559511v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:51,793] [INFO] Task started: Blastn
[2024-01-24 13:41:51,793] [INFO] Running command: blastn -query GCF_025595115.1_ASM2559511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd7ca1dd-2de8-4ea0-8e8a-cdd21a2a5044/dqc_reference/reference_markers_gtdb.fasta -out GCF_025595115.1_ASM2559511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:52,604] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:52,609] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:52,609] [INFO] Target genome list was writen to GCF_025595115.1_ASM2559511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:52,620] [INFO] Task started: fastANI
[2024-01-24 13:41:52,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgc93d9712-03ee-423c-a424-7cf5d131a606/GCF_025595115.1_ASM2559511v1_genomic.fna.gz --refList GCF_025595115.1_ASM2559511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025595115.1_ASM2559511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:00,901] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:00,912] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:00,913] [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_013046825.1	s__Turicibacter sanguinis	99.993	937	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	99.52	99.21	0.94	0.89	18	conclusive
GCF_001543345.1	s__Turicibacter sp001543345	80.773	398	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	98.30	97.82	0.87	0.78	10	-
GCA_017888305.1	s__Turicibacter sp017888305	80.7017	276	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009935875.1	s__Turicibacter sp002311155	79.4284	251	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	99.25	99.25	0.93	0.91	3	-
GCA_002493395.1	s__Turicibacter sp002493395	78.959	223	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003486705.1	s__Turicibacter sp003486705	78.6827	187	938	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:00,915] [INFO] GTDB search result was written to GCF_025595115.1_ASM2559511v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:00,916] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:00,918] [INFO] DFAST_QC result json was written to GCF_025595115.1_ASM2559511v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:00,918] [INFO] DFAST_QC completed!
[2024-01-24 13:42:00,919] [INFO] Total running time: 0h0m50s