[2024-01-25 18:43:50,760] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:50,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:50,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg26df98cd-195e-4dfc-8203-1240ecdb5f9e/dqc_reference
[2024-01-25 18:43:51,887] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:51,888] [INFO] Task started: Prodigal
[2024-01-25 18:43:51,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg85f7edd4-92a9-41ac-9137-b8a0e201afbb/GCF_016651435.1_ASM1665143v1_genomic.fna.gz | prodigal -d GCF_016651435.1_ASM1665143v1_genomic.fna/cds.fna -a GCF_016651435.1_ASM1665143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:57,457] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:57,458] [INFO] Task started: HMMsearch
[2024-01-25 18:43:57,458] [INFO] Running command: hmmsearch --tblout GCF_016651435.1_ASM1665143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26df98cd-195e-4dfc-8203-1240ecdb5f9e/dqc_reference/reference_markers.hmm GCF_016651435.1_ASM1665143v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:57,676] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:57,677] [INFO] Found 6/6 markers.
[2024-01-25 18:43:57,701] [INFO] Query marker FASTA was written to GCF_016651435.1_ASM1665143v1_genomic.fna/markers.fasta
[2024-01-25 18:43:57,701] [INFO] Task started: Blastn
[2024-01-25 18:43:57,702] [INFO] Running command: blastn -query GCF_016651435.1_ASM1665143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26df98cd-195e-4dfc-8203-1240ecdb5f9e/dqc_reference/reference_markers.fasta -out GCF_016651435.1_ASM1665143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:58,269] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:58,272] [INFO] Selected 20 target genomes.
[2024-01-25 18:43:58,272] [INFO] Target genome list was writen to GCF_016651435.1_ASM1665143v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:58,278] [INFO] Task started: fastANI
[2024-01-25 18:43:58,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg85f7edd4-92a9-41ac-9137-b8a0e201afbb/GCF_016651435.1_ASM1665143v1_genomic.fna.gz --refList GCF_016651435.1_ASM1665143v1_genomic.fna/target_genomes.txt --output GCF_016651435.1_ASM1665143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:09,234] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:09,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26df98cd-195e-4dfc-8203-1240ecdb5f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:09,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26df98cd-195e-4dfc-8203-1240ecdb5f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:09,239] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:44:09,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:09,240] [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
Catonella massiliensis	strain=Marseille-Q4567	GCA_016651435.1	2799636	2799636	type	True	100.0	1039	1039	95	conclusive
Catonella morbi	strain=ATCC 51271	GCA_000160035.2	43997	43997	type	True	81.034	530	1039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:09,241] [INFO] DFAST Taxonomy check result was written to GCF_016651435.1_ASM1665143v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:09,241] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:09,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:09,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26df98cd-195e-4dfc-8203-1240ecdb5f9e/dqc_reference/checkm_data
[2024-01-25 18:44:09,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:09,273] [INFO] Task started: CheckM
[2024-01-25 18:44:09,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016651435.1_ASM1665143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016651435.1_ASM1665143v1_genomic.fna/checkm_input GCF_016651435.1_ASM1665143v1_genomic.fna/checkm_result
[2024-01-25 18:44:30,623] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:30,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:30,643] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:30,643] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:30,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016651435.1_ASM1665143v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:30,644] [INFO] Task started: Blastn
[2024-01-25 18:44:30,644] [INFO] Running command: blastn -query GCF_016651435.1_ASM1665143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26df98cd-195e-4dfc-8203-1240ecdb5f9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016651435.1_ASM1665143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:31,585] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:31,588] [INFO] Selected 24 target genomes.
[2024-01-25 18:44:31,588] [INFO] Target genome list was writen to GCF_016651435.1_ASM1665143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:31,601] [INFO] Task started: fastANI
[2024-01-25 18:44:31,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg85f7edd4-92a9-41ac-9137-b8a0e201afbb/GCF_016651435.1_ASM1665143v1_genomic.fna.gz --refList GCF_016651435.1_ASM1665143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016651435.1_ASM1665143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:43,749] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:43,752] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:43,752] [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_016651435.1	s__Catonella massiliensis	100.0	1039	1039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catonella	95.0	95.56	95.38	0.94	0.93	3	conclusive
GCF_000160035.2	s__Catonella morbi	81.0381	529	1039	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:43,755] [INFO] GTDB search result was written to GCF_016651435.1_ASM1665143v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:43,756] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:43,759] [INFO] DFAST_QC result json was written to GCF_016651435.1_ASM1665143v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:43,759] [INFO] DFAST_QC completed!
[2024-01-25 18:44:43,760] [INFO] Total running time: 0h0m53s