[2024-01-24 13:40:55,678] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg920a132f-c257-4214-ace1-0aced94435ae/dqc_reference
[2024-01-24 13:40:56,970] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,971] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,971] [INFO] Running command: gunzip -c /var/lib/cwl/stgd446b6de-3fe8-4286-8983-0fa7d42978a4/GCF_005405365.1_ASM540536v1_genomic.fna.gz | prodigal -d GCF_005405365.1_ASM540536v1_genomic.fna/cds.fna -a GCF_005405365.1_ASM540536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:02,244] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:02,245] [INFO] Task started: HMMsearch
[2024-01-24 13:41:02,245] [INFO] Running command: hmmsearch --tblout GCF_005405365.1_ASM540536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg920a132f-c257-4214-ace1-0aced94435ae/dqc_reference/reference_markers.hmm GCF_005405365.1_ASM540536v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:02,520] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:02,521] [INFO] Found 6/6 markers.
[2024-01-24 13:41:02,546] [INFO] Query marker FASTA was written to GCF_005405365.1_ASM540536v1_genomic.fna/markers.fasta
[2024-01-24 13:41:02,546] [INFO] Task started: Blastn
[2024-01-24 13:41:02,546] [INFO] Running command: blastn -query GCF_005405365.1_ASM540536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg920a132f-c257-4214-ace1-0aced94435ae/dqc_reference/reference_markers.fasta -out GCF_005405365.1_ASM540536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:03,098] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:03,101] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:03,101] [INFO] Target genome list was writen to GCF_005405365.1_ASM540536v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:03,112] [INFO] Task started: fastANI
[2024-01-24 13:41:03,112] [INFO] Running command: fastANI --query /var/lib/cwl/stgd446b6de-3fe8-4286-8983-0fa7d42978a4/GCF_005405365.1_ASM540536v1_genomic.fna.gz --refList GCF_005405365.1_ASM540536v1_genomic.fna/target_genomes.txt --output GCF_005405365.1_ASM540536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,468] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg920a132f-c257-4214-ace1-0aced94435ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg920a132f-c257-4214-ace1-0aced94435ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,476] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:13,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:13,476] [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	100.0	873	875	95	conclusive
Enterococcus pingfangensis	strain=241-2-2	GCA_005405205.1	2559924	2559924	type	True	92.0222	578	875	95	below_threshold
Enterococcus dongliensis	strain=63-4	GCA_005405225.1	2559925	2559925	type	True	83.3494	475	875	95	below_threshold
Enterococcus malodoratus	strain=ATCC 43197	GCA_000407185.1	71451	71451	type	True	81.6478	525	875	95	below_threshold
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	81.5911	521	875	95	below_threshold
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	81.5095	501	875	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	81.101	450	875	95	below_threshold
Enterococcus gilvus	strain=ATCC BAA-350	GCA_000394615.1	160453	160453	type	True	81.0805	452	875	95	below_threshold
Enterococcus pseudoavium	strain=NBRC 100491	GCA_001544295.1	44007	44007	type	True	80.9833	469	875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,477] [INFO] DFAST Taxonomy check result was written to GCF_005405365.1_ASM540536v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,478] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,478] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg920a132f-c257-4214-ace1-0aced94435ae/dqc_reference/checkm_data
[2024-01-24 13:41:13,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,508] [INFO] Task started: CheckM
[2024-01-24 13:41:13,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405365.1_ASM540536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405365.1_ASM540536v1_genomic.fna/checkm_input GCF_005405365.1_ASM540536v1_genomic.fna/checkm_result
[2024-01-24 13:41:34,608] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:34,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:34,629] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:34,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:34,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405365.1_ASM540536v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:34,629] [INFO] Task started: Blastn
[2024-01-24 13:41:34,630] [INFO] Running command: blastn -query GCF_005405365.1_ASM540536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg920a132f-c257-4214-ace1-0aced94435ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405365.1_ASM540536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:35,400] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:35,403] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:35,403] [INFO] Target genome list was writen to GCF_005405365.1_ASM540536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:35,408] [INFO] Task started: fastANI
[2024-01-24 13:41:35,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgd446b6de-3fe8-4286-8983-0fa7d42978a4/GCF_005405365.1_ASM540536v1_genomic.fna.gz --refList GCF_005405365.1_ASM540536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405365.1_ASM540536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:42,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:42,525] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:42,526] [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	100.0	873	875	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	92.0222	578	875	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	83.3494	475	875	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	81.6205	527	875	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	81.5156	500	875	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	81.0845	473	875	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	81.0541	460	875	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	81.0021	467	875	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 13:41:42,527] [INFO] GTDB search result was written to GCF_005405365.1_ASM540536v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:42,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:42,530] [INFO] DFAST_QC result json was written to GCF_005405365.1_ASM540536v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:42,530] [INFO] DFAST_QC completed!
[2024-01-24 13:41:42,530] [INFO] Total running time: 0h0m47s