[2024-01-24 13:31:29,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:29,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:29,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg22b36713-b50f-4186-b225-087c06761fc7/dqc_reference
[2024-01-24 13:31:31,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:31,157] [INFO] Task started: Prodigal
[2024-01-24 13:31:31,158] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7d018be-e927-400f-aa68-7ff554b746d2/GCF_003987645.1_ASM398764v1_genomic.fna.gz | prodigal -d GCF_003987645.1_ASM398764v1_genomic.fna/cds.fna -a GCF_003987645.1_ASM398764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:37,601] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:37,602] [INFO] Task started: HMMsearch
[2024-01-24 13:31:37,602] [INFO] Running command: hmmsearch --tblout GCF_003987645.1_ASM398764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22b36713-b50f-4186-b225-087c06761fc7/dqc_reference/reference_markers.hmm GCF_003987645.1_ASM398764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:37,863] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:37,864] [INFO] Found 6/6 markers.
[2024-01-24 13:31:37,896] [INFO] Query marker FASTA was written to GCF_003987645.1_ASM398764v1_genomic.fna/markers.fasta
[2024-01-24 13:31:37,896] [INFO] Task started: Blastn
[2024-01-24 13:31:37,897] [INFO] Running command: blastn -query GCF_003987645.1_ASM398764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22b36713-b50f-4186-b225-087c06761fc7/dqc_reference/reference_markers.fasta -out GCF_003987645.1_ASM398764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:38,582] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:38,586] [INFO] Selected 18 target genomes.
[2024-01-24 13:31:38,586] [INFO] Target genome list was writen to GCF_003987645.1_ASM398764v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:38,603] [INFO] Task started: fastANI
[2024-01-24 13:31:38,603] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7d018be-e927-400f-aa68-7ff554b746d2/GCF_003987645.1_ASM398764v1_genomic.fna.gz --refList GCF_003987645.1_ASM398764v1_genomic.fna/target_genomes.txt --output GCF_003987645.1_ASM398764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:47,700] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:47,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22b36713-b50f-4186-b225-087c06761fc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:47,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22b36713-b50f-4186-b225-087c06761fc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:47,709] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:47,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:47,710] [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
Vagococcus elongatus	strain=CCUG 51432	GCA_003987645.1	180344	180344	type	True	100.0	926	931	95	conclusive
Vagococcus acidifermentans	strain=LMG 24798	GCA_003987655.1	564710	564710	type	True	78.374	70	931	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	76.5714	58	931	95	below_threshold
Enterococcus wangshanyuanii	strain=CGMCC 1.15942	GCA_014644255.1	2005703	2005703	type	True	76.4102	50	931	95	below_threshold
Enterococcus wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	76.3226	50	931	95	below_threshold
Enterococcus silesiacus	strain=DSM 22801	GCA_001886225.1	332949	332949	type	True	76.1267	62	931	95	below_threshold
Enterococcus caccae	strain=ATCC BAA-1240	GCA_000407145.1	317735	317735	type	True	76.0866	57	931	95	below_threshold
Enterococcus caccae	strain=ATCC BAA-1240	GCA_000394055.1	317735	317735	type	True	76.0018	58	931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:47,711] [INFO] DFAST Taxonomy check result was written to GCF_003987645.1_ASM398764v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:47,712] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:47,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:47,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22b36713-b50f-4186-b225-087c06761fc7/dqc_reference/checkm_data
[2024-01-24 13:31:47,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:47,744] [INFO] Task started: CheckM
[2024-01-24 13:31:47,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987645.1_ASM398764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987645.1_ASM398764v1_genomic.fna/checkm_input GCF_003987645.1_ASM398764v1_genomic.fna/checkm_result
[2024-01-24 13:32:13,448] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:13,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:13,472] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:13,472] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:13,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987645.1_ASM398764v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:13,473] [INFO] Task started: Blastn
[2024-01-24 13:32:13,473] [INFO] Running command: blastn -query GCF_003987645.1_ASM398764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22b36713-b50f-4186-b225-087c06761fc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987645.1_ASM398764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:14,531] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:14,534] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:14,534] [INFO] Target genome list was writen to GCF_003987645.1_ASM398764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:14,549] [INFO] Task started: fastANI
[2024-01-24 13:32:14,549] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7d018be-e927-400f-aa68-7ff554b746d2/GCF_003987645.1_ASM398764v1_genomic.fna.gz --refList GCF_003987645.1_ASM398764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987645.1_ASM398764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:25,045] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:25,056] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:25,057] [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_003987645.1	s__Vagococcus_A elongatus	100.0	926	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003987655.1	s__Vagococcus_B acidifermentans	78.2472	69	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017829975.1	s__Vagococcus_D sp017829975	76.5714	58	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197645.1	s__Enterococcus wangshanyuanii	76.3226	50	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000407145.1	s__Enterococcus caccae	76.0866	57	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:25,059] [INFO] GTDB search result was written to GCF_003987645.1_ASM398764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:25,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:25,065] [INFO] DFAST_QC result json was written to GCF_003987645.1_ASM398764v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:25,066] [INFO] DFAST_QC completed!
[2024-01-24 13:32:25,066] [INFO] Total running time: 0h0m55s