[2024-01-24 13:55:16,976] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:16,978] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:16,978] [INFO] DQC Reference Directory: /var/lib/cwl/stg85a7afe6-444a-4f1e-901e-24807fafd52e/dqc_reference
[2024-01-24 13:55:18,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:18,247] [INFO] Task started: Prodigal
[2024-01-24 13:55:18,247] [INFO] Running command: gunzip -c /var/lib/cwl/stgad9a876d-c0e4-42d3-8d2f-f354c19f76e6/GCF_004309355.1_ASM430935v1_genomic.fna.gz | prodigal -d GCF_004309355.1_ASM430935v1_genomic.fna/cds.fna -a GCF_004309355.1_ASM430935v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:28,528] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:28,529] [INFO] Task started: HMMsearch
[2024-01-24 13:55:28,529] [INFO] Running command: hmmsearch --tblout GCF_004309355.1_ASM430935v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85a7afe6-444a-4f1e-901e-24807fafd52e/dqc_reference/reference_markers.hmm GCF_004309355.1_ASM430935v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:28,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:28,846] [INFO] Found 6/6 markers.
[2024-01-24 13:55:28,891] [INFO] Query marker FASTA was written to GCF_004309355.1_ASM430935v1_genomic.fna/markers.fasta
[2024-01-24 13:55:28,892] [INFO] Task started: Blastn
[2024-01-24 13:55:28,892] [INFO] Running command: blastn -query GCF_004309355.1_ASM430935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85a7afe6-444a-4f1e-901e-24807fafd52e/dqc_reference/reference_markers.fasta -out GCF_004309355.1_ASM430935v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:29,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:29,536] [INFO] Selected 22 target genomes.
[2024-01-24 13:55:29,537] [INFO] Target genome list was writen to GCF_004309355.1_ASM430935v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:29,552] [INFO] Task started: fastANI
[2024-01-24 13:55:29,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgad9a876d-c0e4-42d3-8d2f-f354c19f76e6/GCF_004309355.1_ASM430935v1_genomic.fna.gz --refList GCF_004309355.1_ASM430935v1_genomic.fna/target_genomes.txt --output GCF_004309355.1_ASM430935v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:43,336] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:43,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85a7afe6-444a-4f1e-901e-24807fafd52e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:43,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85a7afe6-444a-4f1e-901e-24807fafd52e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:43,350] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:43,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:43,351] [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 florum	strain=Gos25-1	GCA_004309355.1	2480627	2480627	type	True	100.0	1304	1305	95	conclusive
Enterococcus pallens	strain=ATCC BAA-351	GCA_000393975.1	160454	160454	type	True	79.4502	382	1305	95	below_threshold
Enterococcus pallens	strain=ATCC BAA-351	GCA_000407485.1	160454	160454	type	True	79.3895	384	1305	95	below_threshold
Enterococcus pallens	strain=DSM 15690	GCA_001886075.1	160454	160454	type	True	79.2759	378	1305	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	78.5452	86	1305	95	below_threshold
Enterococcus dongliensis	strain=63-4	GCA_005405225.1	2559925	2559925	type	True	78.5222	145	1305	95	below_threshold
Enterococcus lactis	strain=LMG 25958	GCA_015904215.1	357441	357441	type	True	78.5068	84	1305	95	below_threshold
Enterococcus pingfangensis	strain=241-2-2	GCA_005405205.1	2559924	2559924	type	True	78.4007	170	1305	95	below_threshold
Enterococcus gilvus	strain=ATCC BAA-350	GCA_000394615.1	160453	160453	type	True	78.2769	225	1305	95	below_threshold
Enterococcus raffinosus	strain=NBRC 100492	GCA_001544115.1	71452	71452	type	True	78.2484	222	1305	95	below_threshold
Enterococcus raffinosus	strain=DSM 5633	GCA_001886185.1	71452	71452	type	True	78.2089	226	1305	95	below_threshold
Enterococcus gilvus	strain=ATCC BAA-350	GCA_000407545.1	160453	160453	type	True	78.1833	227	1305	95	below_threshold
Enterococcus gilvus	strain=DSM 15689	GCA_001885915.1	160453	160453	type	True	78.1535	224	1305	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	78.0998	222	1305	95	below_threshold
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	77.9163	257	1305	95	below_threshold
Enterococcus devriesei	strain=DSM 22802	GCA_001885905.1	319970	319970	type	True	77.8189	213	1305	95	below_threshold
Enterococcus larvae	strain=BWM-S5	GCA_017830045.1	2794352	2794352	type	True	77.4072	73	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:43,353] [INFO] DFAST Taxonomy check result was written to GCF_004309355.1_ASM430935v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:43,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:43,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:43,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85a7afe6-444a-4f1e-901e-24807fafd52e/dqc_reference/checkm_data
[2024-01-24 13:55:43,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:43,403] [INFO] Task started: CheckM
[2024-01-24 13:55:43,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004309355.1_ASM430935v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004309355.1_ASM430935v1_genomic.fna/checkm_input GCF_004309355.1_ASM430935v1_genomic.fna/checkm_result
[2024-01-24 13:56:18,219] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:18,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:18,241] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:18,242] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:18,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004309355.1_ASM430935v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:18,243] [INFO] Task started: Blastn
[2024-01-24 13:56:18,243] [INFO] Running command: blastn -query GCF_004309355.1_ASM430935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85a7afe6-444a-4f1e-901e-24807fafd52e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004309355.1_ASM430935v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:18,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:18,982] [INFO] Selected 21 target genomes.
[2024-01-24 13:56:18,983] [INFO] Target genome list was writen to GCF_004309355.1_ASM430935v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:19,018] [INFO] Task started: fastANI
[2024-01-24 13:56:19,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgad9a876d-c0e4-42d3-8d2f-f354c19f76e6/GCF_004309355.1_ASM430935v1_genomic.fna.gz --refList GCF_004309355.1_ASM430935v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004309355.1_ASM430935v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:32,265] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:32,283] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:32,283] [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_004309355.1	s__Enterococcus_A florum	100.0	1304	1305	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_000407485.1	s__Enterococcus_A pallens	79.3876	383	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.99	99.98	1.00	0.99	3	-
GCF_017377655.1	s__Enterococcus_A sp017377655	79.2884	325	1305	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_017377575.1	s__Enterococcus_A sp017377575	78.6512	296	1305	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_015751045.1	s__Enterococcus_B lactis	78.6401	84	1305	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_005405225.1	s__Enterococcus_A dongliensis	78.5503	144	1305	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_005405205.1	s__Enterococcus_A pingfangensis	78.4007	170	1305	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	78.3396	224	1305	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_005405365.1	s__Enterococcus_A xiangfangensis	78.2744	198	1305	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_001886185.1	s__Enterococcus_A raffinosus	78.2089	226	1305	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_000407545.1	s__Enterococcus_A gilvus	78.1833	227	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.79	97.90	0.91	0.83	8	-
GCF_000407185.1	s__Enterococcus_A malodoratus	78.0818	248	1305	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_001544295.1	s__Enterococcus_A pseudoavium	78.0137	186	1305	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	77.9301	256	1305	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_001297065.1	s__Enterococcus_D sp001297065	77.8976	89	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.01	96.72	0.90	0.84	5	-
GCF_001885905.1	s__Enterococcus_A devriesei	77.8347	212	1305	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_000415185.1	s__Enterococcus_B faecalis_A	77.4978	92	1305	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_017830045.1	s__Enterococcus sp017830045	77.4072	73	1305	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:32,285] [INFO] GTDB search result was written to GCF_004309355.1_ASM430935v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:32,285] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:32,289] [INFO] DFAST_QC result json was written to GCF_004309355.1_ASM430935v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:32,289] [INFO] DFAST_QC completed!
[2024-01-24 13:56:32,289] [INFO] Total running time: 0h1m15s