[2024-01-24 11:35:06,815] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:06,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:06,818] [INFO] DQC Reference Directory: /var/lib/cwl/stgd87fb15c-cfdf-4c58-aa98-c3ba96a33dfd/dqc_reference
[2024-01-24 11:35:08,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:08,094] [INFO] Task started: Prodigal
[2024-01-24 11:35:08,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg15b9e5a9-0f57-4e50-8088-e8bd18c8eddd/GCF_002813755.1_ASM281375v1_genomic.fna.gz | prodigal -d GCF_002813755.1_ASM281375v1_genomic.fna/cds.fna -a GCF_002813755.1_ASM281375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:16,059] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:16,059] [INFO] Task started: HMMsearch
[2024-01-24 11:35:16,060] [INFO] Running command: hmmsearch --tblout GCF_002813755.1_ASM281375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd87fb15c-cfdf-4c58-aa98-c3ba96a33dfd/dqc_reference/reference_markers.hmm GCF_002813755.1_ASM281375v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:16,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:16,312] [INFO] Found 6/6 markers.
[2024-01-24 11:35:16,342] [INFO] Query marker FASTA was written to GCF_002813755.1_ASM281375v1_genomic.fna/markers.fasta
[2024-01-24 11:35:16,342] [INFO] Task started: Blastn
[2024-01-24 11:35:16,342] [INFO] Running command: blastn -query GCF_002813755.1_ASM281375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd87fb15c-cfdf-4c58-aa98-c3ba96a33dfd/dqc_reference/reference_markers.fasta -out GCF_002813755.1_ASM281375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:16,936] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:16,939] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:16,939] [INFO] Target genome list was writen to GCF_002813755.1_ASM281375v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:16,961] [INFO] Task started: fastANI
[2024-01-24 11:35:16,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg15b9e5a9-0f57-4e50-8088-e8bd18c8eddd/GCF_002813755.1_ASM281375v1_genomic.fna.gz --refList GCF_002813755.1_ASM281375v1_genomic.fna/target_genomes.txt --output GCF_002813755.1_ASM281375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:24,431] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:24,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd87fb15c-cfdf-4c58-aa98-c3ba96a33dfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:24,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd87fb15c-cfdf-4c58-aa98-c3ba96a33dfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:24,442] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:35:24,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:24,442] [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 mundtii	strain=DSM 4838	GCA_002813755.1	53346	53346	type	True	100.0	1165	1168	95	conclusive
Enterococcus mundtii	strain=DSM 4838	GCA_001886035.1	53346	53346	type	True	99.959	1090	1168	95	conclusive
Enterococcus mundtii	strain=NBRC 100490	GCA_007990125.1	53346	53346	type	True	99.9423	1093	1168	95	conclusive
Enterococcus durans	strain=FDAARGOS 1437	GCA_019048325.1	53345	53345	type	True	80.4778	390	1168	95	below_threshold
Enterococcus faecium	strain=NCTC7171	GCA_900447735.1	1352	1352	type	True	80.2564	359	1168	95	below_threshold
Enterococcus durans	strain=NBRC 100479	GCA_001544215.1	53345	53345	type	True	80.1669	369	1168	95	below_threshold
Enterococcus faecium	strain=NBRC 100486	GCA_001544255.1	1352	1352	type	True	79.6504	341	1168	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	79.5735	346	1168	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	79.5571	363	1168	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	79.1182	65	1168	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.8654	135	1168	95	below_threshold
Enterococcus larvae	strain=BWM-S5	GCA_017830045.1	2794352	2794352	type	True	78.1952	98	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:24,444] [INFO] DFAST Taxonomy check result was written to GCF_002813755.1_ASM281375v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:24,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:24,444] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:24,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd87fb15c-cfdf-4c58-aa98-c3ba96a33dfd/dqc_reference/checkm_data
[2024-01-24 11:35:24,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:24,480] [INFO] Task started: CheckM
[2024-01-24 11:35:24,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002813755.1_ASM281375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002813755.1_ASM281375v1_genomic.fna/checkm_input GCF_002813755.1_ASM281375v1_genomic.fna/checkm_result
[2024-01-24 11:35:55,378] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:55,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:55,400] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:55,400] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:55,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002813755.1_ASM281375v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:55,401] [INFO] Task started: Blastn
[2024-01-24 11:35:55,401] [INFO] Running command: blastn -query GCF_002813755.1_ASM281375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd87fb15c-cfdf-4c58-aa98-c3ba96a33dfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002813755.1_ASM281375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:56,208] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:56,213] [INFO] Selected 5 target genomes.
[2024-01-24 11:35:56,213] [INFO] Target genome list was writen to GCF_002813755.1_ASM281375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:56,219] [INFO] Task started: fastANI
[2024-01-24 11:35:56,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg15b9e5a9-0f57-4e50-8088-e8bd18c8eddd/GCF_002813755.1_ASM281375v1_genomic.fna.gz --refList GCF_002813755.1_ASM281375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002813755.1_ASM281375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:01,031] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:01,036] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:01,037] [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_002813755.1	s__Enterococcus_B mundtii	100.0	1165	1168	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	99.56	98.27	0.96	0.86	24	conclusive
GCF_013394305.1	s__Enterococcus_B pernyi	96.32	932	1168	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	98.21	97.00	0.90	0.84	22	-
GCF_003957375.1	s__Enterococcus_B mundtii_C	95.3241	857	1168	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.247	99.65	99.65	0.94	0.94	2	-
GCF_002947535.1	s__Enterococcus_B mundtii_B	94.3174	926	1168	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	97.82	97.77	0.91	0.90	3	-
GCF_017316305.1	s__Enterococcus_B sp017316305	87.5492	873	1168	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.83	98.79	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:01,039] [INFO] GTDB search result was written to GCF_002813755.1_ASM281375v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:01,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:01,043] [INFO] DFAST_QC result json was written to GCF_002813755.1_ASM281375v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:01,043] [INFO] DFAST_QC completed!
[2024-01-24 11:36:01,043] [INFO] Total running time: 0h0m54s