[2024-01-24 15:18:27,506] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,509] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg053680f5-64df-4399-9e5b-cd11c7c6d82c/dqc_reference
[2024-01-24 15:18:28,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,994] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,995] [INFO] Running command: gunzip -c /var/lib/cwl/stgee327738-52bf-4f7d-a4b0-f403c21e73e2/GCF_005405345.1_ASM540534v1_genomic.fna.gz | prodigal -d GCF_005405345.1_ASM540534v1_genomic.fna/cds.fna -a GCF_005405345.1_ASM540534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:34,881] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:34,881] [INFO] Task started: HMMsearch
[2024-01-24 15:18:34,881] [INFO] Running command: hmmsearch --tblout GCF_005405345.1_ASM540534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg053680f5-64df-4399-9e5b-cd11c7c6d82c/dqc_reference/reference_markers.hmm GCF_005405345.1_ASM540534v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:35,189] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:35,190] [INFO] Found 6/6 markers.
[2024-01-24 15:18:35,214] [INFO] Query marker FASTA was written to GCF_005405345.1_ASM540534v1_genomic.fna/markers.fasta
[2024-01-24 15:18:35,214] [INFO] Task started: Blastn
[2024-01-24 15:18:35,214] [INFO] Running command: blastn -query GCF_005405345.1_ASM540534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg053680f5-64df-4399-9e5b-cd11c7c6d82c/dqc_reference/reference_markers.fasta -out GCF_005405345.1_ASM540534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:35,845] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:35,848] [INFO] Selected 20 target genomes.
[2024-01-24 15:18:35,848] [INFO] Target genome list was writen to GCF_005405345.1_ASM540534v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:36,227] [INFO] Task started: fastANI
[2024-01-24 15:18:36,227] [INFO] Running command: fastANI --query /var/lib/cwl/stgee327738-52bf-4f7d-a4b0-f403c21e73e2/GCF_005405345.1_ASM540534v1_genomic.fna.gz --refList GCF_005405345.1_ASM540534v1_genomic.fna/target_genomes.txt --output GCF_005405345.1_ASM540534v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:48,780] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:48,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg053680f5-64df-4399-9e5b-cd11c7c6d82c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:48,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg053680f5-64df-4399-9e5b-cd11c7c6d82c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:48,793] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:48,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:48,793] [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 viikkiensis	strain=LMG 26075	GCA_005405345.1	930854	930854	type	True	100.0	819	825	95	conclusive
Enterococcus devriesei	strain=DSM 22802	GCA_001885905.1	319970	319970	type	True	91.7632	731	825	95	below_threshold
Enterococcus pseudoavium	strain=NBRC 100491	GCA_001544295.1	44007	44007	type	True	81.0624	411	825	95	below_threshold
Enterococcus malodoratus	strain=NCTC12365	GCA_900447955.1	71451	71451	type	True	80.818	480	825	95	below_threshold
Enterococcus malodoratus	strain=ATCC 43197	GCA_000407185.1	71451	71451	type	True	80.7226	484	825	95	below_threshold
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	80.6761	475	825	95	below_threshold
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	80.5629	488	825	95	below_threshold
Enterococcus raffinosus	strain=DSM 5633	GCA_001886185.1	71452	71452	type	True	80.5305	433	825	95	below_threshold
Enterococcus dongliensis	strain=63-4	GCA_005405225.1	2559925	2559925	type	True	80.4986	286	825	95	below_threshold
Enterococcus avium	strain=NCTC9938	GCA_900447655.1	33945	33945	type	True	80.4917	446	825	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	80.4876	436	825	95	below_threshold
Enterococcus xiangfangensis	strain=11097	GCA_005405365.1	1296537	1296537	type	True	80.4689	396	825	95	below_threshold
Enterococcus raffinosus	strain=NBRC 100492	GCA_001544115.1	71452	71452	type	True	80.4627	433	825	95	below_threshold
Enterococcus avium	strain=ATCC 14025	GCA_000407245.1	33945	33945	type	True	80.4026	446	825	95	below_threshold
Enterococcus hermanniensis	strain=DSM 17122	GCA_001885945.1	249189	249189	type	True	79.9513	401	825	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:48,795] [INFO] DFAST Taxonomy check result was written to GCF_005405345.1_ASM540534v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:48,795] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:48,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:48,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg053680f5-64df-4399-9e5b-cd11c7c6d82c/dqc_reference/checkm_data
[2024-01-24 15:18:48,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:48,824] [INFO] Task started: CheckM
[2024-01-24 15:18:48,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405345.1_ASM540534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405345.1_ASM540534v1_genomic.fna/checkm_input GCF_005405345.1_ASM540534v1_genomic.fna/checkm_result
[2024-01-24 15:19:13,106] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:13,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:13,131] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:13,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:13,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405345.1_ASM540534v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:13,132] [INFO] Task started: Blastn
[2024-01-24 15:19:13,132] [INFO] Running command: blastn -query GCF_005405345.1_ASM540534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg053680f5-64df-4399-9e5b-cd11c7c6d82c/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405345.1_ASM540534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:13,937] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:13,941] [INFO] Selected 12 target genomes.
[2024-01-24 15:19:13,941] [INFO] Target genome list was writen to GCF_005405345.1_ASM540534v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:13,949] [INFO] Task started: fastANI
[2024-01-24 15:19:13,950] [INFO] Running command: fastANI --query /var/lib/cwl/stgee327738-52bf-4f7d-a4b0-f403c21e73e2/GCF_005405345.1_ASM540534v1_genomic.fna.gz --refList GCF_005405345.1_ASM540534v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405345.1_ASM540534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:22,761] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:22,771] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:22,771] [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_005405345.1	s__Enterococcus_A viikkiensis	100.0	819	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001885905.1	s__Enterococcus_A devriesei	91.7632	731	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.13	98.05	0.88	0.86	3	-
GCF_000407185.1	s__Enterococcus_A malodoratus	80.7226	484	825	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_018917525.1	s__Enterococcus_A raffinosus_A	80.6081	453	825	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_005405485.1	s__Enterococcus_A hulanensis	80.5507	489	825	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_001886185.1	s__Enterococcus_A raffinosus	80.5254	434	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.27	97.96	0.91	0.87	12	-
GCF_005405225.1	s__Enterococcus_A dongliensis	80.4986	286	825	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_017315985.1	s__Enterococcus_A sp017315985	80.4774	428	825	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_005405365.1	s__Enterococcus_A xiangfangensis	80.4598	397	825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.65	99.31	0.96	0.92	3	-
GCF_000406965.1	s__Enterococcus_A avium	80.3589	458	825	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_001885945.1	s__Enterococcus_A hermanniensis	79.9378	402	825	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 15:19:22,773] [INFO] GTDB search result was written to GCF_005405345.1_ASM540534v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:22,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:22,777] [INFO] DFAST_QC result json was written to GCF_005405345.1_ASM540534v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:22,778] [INFO] DFAST_QC completed!
[2024-01-24 15:19:22,778] [INFO] Total running time: 0h0m55s