[2024-01-24 12:05:59,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:59,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:59,075] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cf2dc9b-18a1-4610-92a0-98da9b26bebf/dqc_reference
[2024-01-24 12:06:00,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:00,376] [INFO] Task started: Prodigal
[2024-01-24 12:06:00,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg1756bb64-df77-4c96-a14d-0ee14bd980a2/GCF_007990225.1_ASM799022v1_genomic.fna.gz | prodigal -d GCF_007990225.1_ASM799022v1_genomic.fna/cds.fna -a GCF_007990225.1_ASM799022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:06,058] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:06,058] [INFO] Task started: HMMsearch
[2024-01-24 12:06:06,058] [INFO] Running command: hmmsearch --tblout GCF_007990225.1_ASM799022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cf2dc9b-18a1-4610-92a0-98da9b26bebf/dqc_reference/reference_markers.hmm GCF_007990225.1_ASM799022v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:06,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:06,391] [INFO] Found 6/6 markers.
[2024-01-24 12:06:06,434] [INFO] Query marker FASTA was written to GCF_007990225.1_ASM799022v1_genomic.fna/markers.fasta
[2024-01-24 12:06:06,435] [INFO] Task started: Blastn
[2024-01-24 12:06:06,435] [INFO] Running command: blastn -query GCF_007990225.1_ASM799022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf2dc9b-18a1-4610-92a0-98da9b26bebf/dqc_reference/reference_markers.fasta -out GCF_007990225.1_ASM799022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:07,100] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:07,103] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:07,104] [INFO] Target genome list was writen to GCF_007990225.1_ASM799022v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:07,118] [INFO] Task started: fastANI
[2024-01-24 12:06:07,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg1756bb64-df77-4c96-a14d-0ee14bd980a2/GCF_007990225.1_ASM799022v1_genomic.fna.gz --refList GCF_007990225.1_ASM799022v1_genomic.fna/target_genomes.txt --output GCF_007990225.1_ASM799022v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:15,619] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:15,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cf2dc9b-18a1-4610-92a0-98da9b26bebf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:15,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cf2dc9b-18a1-4610-92a0-98da9b26bebf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:15,633] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:15,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:15,633] [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 villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	100.0	916	920	95	conclusive
Enterococcus hirae	strain=FDAARGOS_1123	GCA_016766815.1	1354	1354	type	True	81.9592	569	920	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	81.9566	559	920	95	below_threshold
Enterococcus hirae	strain=DSM 20160	GCA_001885955.1	1354	1354	type	True	81.9249	561	920	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	81.9129	560	920	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000393835.1	1354	1354	type	True	81.9012	567	920	95	below_threshold
Enterococcus ratti	strain=DSM 15687	GCA_001886195.1	150033	150033	type	True	81.4726	476	920	95	below_threshold
Enterococcus durans	strain=NBRC 100479	GCA_001544215.1	53345	53345	type	True	80.8959	445	920	95	below_threshold
Enterococcus durans	strain=FDAARGOS 1437	GCA_019048325.1	53345	53345	type	True	80.7549	457	920	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	79.4319	359	920	95	below_threshold
Enterococcus thailandicus	strain=NBRC 101867	GCA_007989705.1	417368	417368	type	True	79.0787	331	920	95	below_threshold
Enterococcus thailandicus	strain=DSM 21767	GCA_001886265.1	417368	417368	type	True	79.041	336	920	95	below_threshold
Enterococcus faecalis	strain=ATCC 19433	GCA_000392875.1	1351	1351	type	True	77.7571	145	920	95	below_threshold
Enterococcus faecalis	strain=NBRC 100480	GCA_001544235.1	1351	1351	type	True	77.6675	145	920	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	77.4289	73	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:15,635] [INFO] DFAST Taxonomy check result was written to GCF_007990225.1_ASM799022v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:15,636] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:15,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:15,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cf2dc9b-18a1-4610-92a0-98da9b26bebf/dqc_reference/checkm_data
[2024-01-24 12:06:15,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:15,670] [INFO] Task started: CheckM
[2024-01-24 12:06:15,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990225.1_ASM799022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990225.1_ASM799022v1_genomic.fna/checkm_input GCF_007990225.1_ASM799022v1_genomic.fna/checkm_result
[2024-01-24 12:06:41,187] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:41,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:41,207] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:41,207] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:41,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990225.1_ASM799022v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:41,208] [INFO] Task started: Blastn
[2024-01-24 12:06:41,208] [INFO] Running command: blastn -query GCF_007990225.1_ASM799022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf2dc9b-18a1-4610-92a0-98da9b26bebf/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990225.1_ASM799022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:42,006] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:42,009] [INFO] Selected 9 target genomes.
[2024-01-24 12:06:42,010] [INFO] Target genome list was writen to GCF_007990225.1_ASM799022v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:42,016] [INFO] Task started: fastANI
[2024-01-24 12:06:42,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg1756bb64-df77-4c96-a14d-0ee14bd980a2/GCF_007990225.1_ASM799022v1_genomic.fna.gz --refList GCF_007990225.1_ASM799022v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990225.1_ASM799022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:47,596] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:47,609] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:47,609] [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_007990225.1	s__Enterococcus_B villorum	100.0	916	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.96	97.46	0.94	0.89	6	conclusive
GCA_015680865.1	s__Enterococcus_B lacertideformus	82.2255	563	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000271405.2	s__Enterococcus_B hirae	81.9566	559	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.97	97.87	0.92	0.86	203	-
GCF_001886195.1	s__Enterococcus_B ratti	81.502	474	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544215.1	s__Enterococcus_B durans	80.8914	446	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.77	96.42	0.88	0.77	135	-
GCF_011038845.1	s__Enterococcus_B sp011038845	79.7165	333	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.61	99.61	0.98	0.98	2	-
GCF_015751045.1	s__Enterococcus_B lactis	79.4319	359	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.26	97.66	0.89	0.81	335	-
GCF_001886265.1	s__Enterococcus_B thailandicus	79.0548	335	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.46	99.20	0.93	0.90	6	-
GCF_017426705.1	s__Enterococcus_F sp017426705	77.6258	149	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:47,611] [INFO] GTDB search result was written to GCF_007990225.1_ASM799022v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:47,612] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:47,615] [INFO] DFAST_QC result json was written to GCF_007990225.1_ASM799022v1_genomic.fna/dqc_result.json
[2024-01-24 12:06:47,616] [INFO] DFAST_QC completed!
[2024-01-24 12:06:47,616] [INFO] Total running time: 0h0m49s