[2024-01-24 13:37:05,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg313a4b98-521a-4fc6-8bd4-a8f166fbd4f7/dqc_reference
[2024-01-24 13:37:06,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,573] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,573] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c7c6eb5-530e-4f8a-9fd9-5e49d2de0876/GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna.gz | prodigal -d GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/cds.fna -a GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:17,207] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:17,208] [INFO] Task started: HMMsearch
[2024-01-24 13:37:17,208] [INFO] Running command: hmmsearch --tblout GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg313a4b98-521a-4fc6-8bd4-a8f166fbd4f7/dqc_reference/reference_markers.hmm GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:17,528] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:17,530] [INFO] Found 6/6 markers.
[2024-01-24 13:37:17,595] [INFO] Query marker FASTA was written to GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/markers.fasta
[2024-01-24 13:37:17,595] [INFO] Task started: Blastn
[2024-01-24 13:37:17,596] [INFO] Running command: blastn -query GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg313a4b98-521a-4fc6-8bd4-a8f166fbd4f7/dqc_reference/reference_markers.fasta -out GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:18,258] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:18,261] [INFO] Selected 15 target genomes.
[2024-01-24 13:37:18,261] [INFO] Target genome list was writen to GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/target_genomes.txt
[2024-01-24 13:37:18,273] [INFO] Task started: fastANI
[2024-01-24 13:37:18,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c7c6eb5-530e-4f8a-9fd9-5e49d2de0876/GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna.gz --refList GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/target_genomes.txt --output GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:28,471] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:28,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg313a4b98-521a-4fc6-8bd4-a8f166fbd4f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:28,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg313a4b98-521a-4fc6-8bd4-a8f166fbd4f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:28,480] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:37:28,481] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:28,481] [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 gilvus	strain=ATCC BAA-350	GCA_000407545.1	160453	160453	type	True	100.0	1390	1391	95	conclusive
Enterococcus gilvus	strain=ATCC BAA-350	GCA_000394615.1	160453	160453	type	True	99.9821	1369	1391	95	conclusive
Enterococcus gilvus	strain=DSM 15689	GCA_001885915.1	160453	160453	type	True	99.9588	1330	1391	95	conclusive
Enterococcus malodoratus	strain=ATCC 43197	GCA_000407185.1	71451	71451	type	True	81.6779	700	1391	95	below_threshold
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	81.6118	685	1391	95	below_threshold
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	81.412	685	1391	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	81.3091	624	1391	95	below_threshold
Enterococcus avium	strain=ATCC 14025	GCA_000407245.1	33945	33945	type	True	81.2493	631	1391	95	below_threshold
Enterococcus hermanniensis	strain=DSM 17122	GCA_001885945.1	249189	249189	type	True	80.0048	400	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:28,482] [INFO] DFAST Taxonomy check result was written to GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/tc_result.tsv
[2024-01-24 13:37:28,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:28,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:28,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg313a4b98-521a-4fc6-8bd4-a8f166fbd4f7/dqc_reference/checkm_data
[2024-01-24 13:37:28,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:28,529] [INFO] Task started: CheckM
[2024-01-24 13:37:28,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/checkm_input GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/checkm_result
[2024-01-24 13:38:05,989] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:05,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:06,009] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:06,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:06,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/markers.fasta)
[2024-01-24 13:38:06,010] [INFO] Task started: Blastn
[2024-01-24 13:38:06,011] [INFO] Running command: blastn -query GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg313a4b98-521a-4fc6-8bd4-a8f166fbd4f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:06,898] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:06,901] [INFO] Selected 12 target genomes.
[2024-01-24 13:38:06,901] [INFO] Target genome list was writen to GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:06,917] [INFO] Task started: fastANI
[2024-01-24 13:38:06,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c7c6eb5-530e-4f8a-9fd9-5e49d2de0876/GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna.gz --refList GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/target_genomes_gtdb.txt --output GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:16,759] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:16,775] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:16,776] [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_000407545.1	s__Enterococcus_A gilvus	100.0	1390	1391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.79	97.90	0.91	0.83	8	conclusive
GCF_000407185.1	s__Enterococcus_A malodoratus	81.7064	701	1391	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_005405485.1	s__Enterococcus_A hulanensis	81.4219	684	1391	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_018917525.1	s__Enterococcus_A raffinosus_A	81.3826	631	1391	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	81.3749	642	1391	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	81.1173	443	1391	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_005405205.1	s__Enterococcus_A pingfangensis	81.1042	393	1391	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_001886185.1	s__Enterococcus_A raffinosus	81.1002	632	1391	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_017315985.1	s__Enterococcus_A sp017315985	81.0584	645	1391	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_001885945.1	s__Enterococcus_A hermanniensis	80.0048	400	1391	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 13:38:16,782] [INFO] GTDB search result was written to GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:16,783] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:16,787] [INFO] DFAST_QC result json was written to GCF_000407545.1_Ente_gilf_BAA-350_PQ1_CCUG_45553_V2_genomic.fna/dqc_result.json
[2024-01-24 13:38:16,787] [INFO] DFAST_QC completed!
[2024-01-24 13:38:16,787] [INFO] Total running time: 0h1m12s