[2024-01-25 19:56:20,568] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:20,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:20,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg395a2bca-d97b-454f-a161-411100fa76e7/dqc_reference
[2024-01-25 19:56:21,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:21,723] [INFO] Task started: Prodigal
[2024-01-25 19:56:21,724] [INFO] Running command: gunzip -c /var/lib/cwl/stge3ef092a-7be3-4e1e-a564-9dedde8a48c7/GCF_015311765.1_PDT000701674.1_genomic.fna.gz | prodigal -d GCF_015311765.1_PDT000701674.1_genomic.fna/cds.fna -a GCF_015311765.1_PDT000701674.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:27,095] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:27,095] [INFO] Task started: HMMsearch
[2024-01-25 19:56:27,096] [INFO] Running command: hmmsearch --tblout GCF_015311765.1_PDT000701674.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg395a2bca-d97b-454f-a161-411100fa76e7/dqc_reference/reference_markers.hmm GCF_015311765.1_PDT000701674.1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:27,339] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:27,340] [INFO] Found 6/6 markers.
[2024-01-25 19:56:27,366] [INFO] Query marker FASTA was written to GCF_015311765.1_PDT000701674.1_genomic.fna/markers.fasta
[2024-01-25 19:56:27,366] [INFO] Task started: Blastn
[2024-01-25 19:56:27,366] [INFO] Running command: blastn -query GCF_015311765.1_PDT000701674.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg395a2bca-d97b-454f-a161-411100fa76e7/dqc_reference/reference_markers.fasta -out GCF_015311765.1_PDT000701674.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:27,927] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:27,930] [INFO] Selected 9 target genomes.
[2024-01-25 19:56:27,930] [INFO] Target genome list was writen to GCF_015311765.1_PDT000701674.1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:27,931] [INFO] Task started: fastANI
[2024-01-25 19:56:27,931] [INFO] Running command: fastANI --query /var/lib/cwl/stge3ef092a-7be3-4e1e-a564-9dedde8a48c7/GCF_015311765.1_PDT000701674.1_genomic.fna.gz --refList GCF_015311765.1_PDT000701674.1_genomic.fna/target_genomes.txt --output GCF_015311765.1_PDT000701674.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:33,085] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:33,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg395a2bca-d97b-454f-a161-411100fa76e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:33,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg395a2bca-d97b-454f-a161-411100fa76e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:33,090] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:56:33,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:33,090] [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 faecalis	strain=NCTC 775	GCA_015311765.1	1351	1351	type	True	100.0	939	961	95	conclusive
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	99.9945	925	961	95	conclusive
Enterococcus faecalis	strain=NBRC 100480	GCA_001544235.1	1351	1351	type	True	99.9935	920	961	95	conclusive
Enterococcus faecalis	strain=ATCC 19433	GCA_000392875.1	1351	1351	type	True	99.9902	924	961	95	conclusive
Enterococcus faecalis	strain=NCTC775	GCA_900447895.1	1351	1351	type	True	99.9519	884	961	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:56:33,092] [INFO] DFAST Taxonomy check result was written to GCF_015311765.1_PDT000701674.1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:33,092] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:33,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:33,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg395a2bca-d97b-454f-a161-411100fa76e7/dqc_reference/checkm_data
[2024-01-25 19:56:33,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:33,123] [INFO] Task started: CheckM
[2024-01-25 19:56:33,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015311765.1_PDT000701674.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015311765.1_PDT000701674.1_genomic.fna/checkm_input GCF_015311765.1_PDT000701674.1_genomic.fna/checkm_result
[2024-01-25 19:56:55,403] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:55,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:55,423] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:55,423] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:55,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015311765.1_PDT000701674.1_genomic.fna/markers.fasta)
[2024-01-25 19:56:55,424] [INFO] Task started: Blastn
[2024-01-25 19:56:55,424] [INFO] Running command: blastn -query GCF_015311765.1_PDT000701674.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg395a2bca-d97b-454f-a161-411100fa76e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_015311765.1_PDT000701674.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:56,215] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:56,218] [INFO] Selected 19 target genomes.
[2024-01-25 19:56:56,218] [INFO] Target genome list was writen to GCF_015311765.1_PDT000701674.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:56,219] [INFO] Task started: fastANI
[2024-01-25 19:56:56,219] [INFO] Running command: fastANI --query /var/lib/cwl/stge3ef092a-7be3-4e1e-a564-9dedde8a48c7/GCF_015311765.1_PDT000701674.1_genomic.fna.gz --refList GCF_015311765.1_PDT000701674.1_genomic.fna/target_genomes_gtdb.txt --output GCF_015311765.1_PDT000701674.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:06,867] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:06,878] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:06,879] [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_000392875.1	s__Enterococcus faecalis	99.9902	924	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.66	96.80	0.89	0.77	1902	conclusive
GCA_019116505.1	s__Enterococcus_I avicola	79.1843	91	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001465345.1	s__Enterococcus rotai	78.9196	222	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002140715.1	s__Enterococcus sp002140715	78.5176	223	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405345.1	s__Enterococcus_A viikkiensis	78.48	106	961	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_002148425.1	s__Enterococcus sp002148425	78.4699	247	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCF_000407445.1	s__Enterococcus moraviensis	78.457	233	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_017377505.1	s__Enterococcus sp017377505	78.4141	234	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_001730285.1	s__Enterococcus ureasiticus	78.34	236	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCF_001730295.1	s__Enterococcus plantarum	78.2971	226	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_001730315.1	s__Enterococcus ureilyticus	78.2822	214	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	-
GCF_017830045.1	s__Enterococcus sp017830045	78.2079	113	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730365.1	s__Enterococcus quebecensis	78.1011	216	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000407145.1	s__Enterococcus caccae	78.0876	241	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_002197645.1	s__Enterococcus wangshanyuanii	78.061	211	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001465115.1	s__Enterococcus silesiacus	78.052	235	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001742285.1	s__Enterococcus rivorum	77.902	203	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007990225.1	s__Enterococcus_B villorum	77.629	150	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.96	97.46	0.94	0.89	6	-
GCF_017426705.1	s__Enterococcus_F sp017426705	77.5276	158	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:06,880] [INFO] GTDB search result was written to GCF_015311765.1_PDT000701674.1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:06,881] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:06,884] [INFO] DFAST_QC result json was written to GCF_015311765.1_PDT000701674.1_genomic.fna/dqc_result.json
[2024-01-25 19:57:06,884] [INFO] DFAST_QC completed!
[2024-01-25 19:57:06,884] [INFO] Total running time: 0h0m46s