[2024-01-24 13:40:28,448] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c7d21f4-0aa2-47b3-8942-052f9369c24f/dqc_reference
[2024-01-24 13:40:29,849] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:29,850] [INFO] Task started: Prodigal
[2024-01-24 13:40:29,850] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c4de742-f285-4055-985d-e179478ea544/GCF_016909115.1_ASM1690911v1_genomic.fna.gz | prodigal -d GCF_016909115.1_ASM1690911v1_genomic.fna/cds.fna -a GCF_016909115.1_ASM1690911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:36,097] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:36,097] [INFO] Task started: HMMsearch
[2024-01-24 13:40:36,097] [INFO] Running command: hmmsearch --tblout GCF_016909115.1_ASM1690911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c7d21f4-0aa2-47b3-8942-052f9369c24f/dqc_reference/reference_markers.hmm GCF_016909115.1_ASM1690911v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:36,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:36,338] [INFO] Found 6/6 markers.
[2024-01-24 13:40:36,365] [INFO] Query marker FASTA was written to GCF_016909115.1_ASM1690911v1_genomic.fna/markers.fasta
[2024-01-24 13:40:36,365] [INFO] Task started: Blastn
[2024-01-24 13:40:36,365] [INFO] Running command: blastn -query GCF_016909115.1_ASM1690911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7d21f4-0aa2-47b3-8942-052f9369c24f/dqc_reference/reference_markers.fasta -out GCF_016909115.1_ASM1690911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:36,986] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:36,990] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:36,990] [INFO] Target genome list was writen to GCF_016909115.1_ASM1690911v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:36,999] [INFO] Task started: fastANI
[2024-01-24 13:40:37,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c4de742-f285-4055-985d-e179478ea544/GCF_016909115.1_ASM1690911v1_genomic.fna.gz --refList GCF_016909115.1_ASM1690911v1_genomic.fna/target_genomes.txt --output GCF_016909115.1_ASM1690911v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:46,284] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:46,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c7d21f4-0aa2-47b3-8942-052f9369c24f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:46,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c7d21f4-0aa2-47b3-8942-052f9369c24f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:46,293] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:46,293] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:46,294] [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
Enterococcus xiangfangensis	strain=11097	GCA_005405365.1	1296537	1296537	type	True	99.9988	868	876	95	conclusive
Enterococcus pingfangensis	strain=241-2-2	GCA_005405205.1	2559924	2559924	type	True	91.9983	574	876	95	below_threshold
Enterococcus dongliensis	strain=63-4	GCA_005405225.1	2559925	2559925	type	True	83.4891	467	876	95	below_threshold
Enterococcus malodoratus	strain=ATCC 43197	GCA_000407185.1	71451	71451	type	True	81.6334	529	876	95	below_threshold
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	81.5531	499	876	95	below_threshold
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	81.5276	524	876	95	below_threshold
Enterococcus gilvus	strain=ATCC BAA-350	GCA_000394615.1	160453	160453	type	True	81.1918	449	876	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	81.0389	453	876	95	below_threshold
Enterococcus pseudoavium	strain=NBRC 100491	GCA_001544295.1	44007	44007	type	True	80.9227	468	876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:46,297] [INFO] DFAST Taxonomy check result was written to GCF_016909115.1_ASM1690911v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:46,300] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:46,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:46,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c7d21f4-0aa2-47b3-8942-052f9369c24f/dqc_reference/checkm_data
[2024-01-24 13:40:46,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:46,333] [INFO] Task started: CheckM
[2024-01-24 13:40:46,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016909115.1_ASM1690911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016909115.1_ASM1690911v1_genomic.fna/checkm_input GCF_016909115.1_ASM1690911v1_genomic.fna/checkm_result
[2024-01-24 13:41:11,044] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:11,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:11,062] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:11,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:11,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016909115.1_ASM1690911v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:11,063] [INFO] Task started: Blastn
[2024-01-24 13:41:11,064] [INFO] Running command: blastn -query GCF_016909115.1_ASM1690911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7d21f4-0aa2-47b3-8942-052f9369c24f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016909115.1_ASM1690911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:11,938] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:11,942] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:11,942] [INFO] Target genome list was writen to GCF_016909115.1_ASM1690911v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:11,950] [INFO] Task started: fastANI
[2024-01-24 13:41:11,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c4de742-f285-4055-985d-e179478ea544/GCF_016909115.1_ASM1690911v1_genomic.fna.gz --refList GCF_016909115.1_ASM1690911v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016909115.1_ASM1690911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:19,829] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:19,837] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:19,837] [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_005405365.1	s__Enterococcus_A xiangfangensis	99.9988	868	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.65	99.31	0.96	0.92	3	conclusive
GCF_005405205.1	s__Enterococcus_A pingfangensis	91.9983	574	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405225.1	s__Enterococcus_A dongliensis	83.4891	467	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407185.1	s__Enterococcus_A malodoratus	81.6333	529	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.33	98.27	0.94	0.84	8	-
GCF_005405485.1	s__Enterococcus_A hulanensis	81.5531	499	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	97.15	97.02	0.83	0.81	4	-
GCF_018917525.1	s__Enterococcus_A raffinosus_A	81.154	471	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000406965.1	s__Enterococcus_A avium	81.0416	464	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.01	97.91	0.91	0.78	43	-
GCF_001544295.1	s__Enterococcus_A pseudoavium	80.9373	467	876	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,839] [INFO] GTDB search result was written to GCF_016909115.1_ASM1690911v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:19,839] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:19,842] [INFO] DFAST_QC result json was written to GCF_016909115.1_ASM1690911v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:19,843] [INFO] DFAST_QC completed!
[2024-01-24 13:41:19,843] [INFO] Total running time: 0h0m51s