[2024-01-24 12:37:37,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg566b68a9-446d-40fb-8bea-9b74e6a67972/dqc_reference
[2024-01-24 12:37:41,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,018] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,018] [INFO] Running command: gunzip -c /var/lib/cwl/stgd78bd7b1-1687-4a93-8146-10d07356cad0/GCF_001886115.1_ASM188611v1_genomic.fna.gz | prodigal -d GCF_001886115.1_ASM188611v1_genomic.fna/cds.fna -a GCF_001886115.1_ASM188611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:48,497] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:48,497] [INFO] Task started: HMMsearch
[2024-01-24 12:37:48,497] [INFO] Running command: hmmsearch --tblout GCF_001886115.1_ASM188611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg566b68a9-446d-40fb-8bea-9b74e6a67972/dqc_reference/reference_markers.hmm GCF_001886115.1_ASM188611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:48,764] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:48,766] [INFO] Found 6/6 markers.
[2024-01-24 12:37:48,804] [INFO] Query marker FASTA was written to GCF_001886115.1_ASM188611v1_genomic.fna/markers.fasta
[2024-01-24 12:37:48,804] [INFO] Task started: Blastn
[2024-01-24 12:37:48,805] [INFO] Running command: blastn -query GCF_001886115.1_ASM188611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg566b68a9-446d-40fb-8bea-9b74e6a67972/dqc_reference/reference_markers.fasta -out GCF_001886115.1_ASM188611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:49,407] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:49,411] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:49,411] [INFO] Target genome list was writen to GCF_001886115.1_ASM188611v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:49,441] [INFO] Task started: fastANI
[2024-01-24 12:37:49,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78bd7b1-1687-4a93-8146-10d07356cad0/GCF_001886115.1_ASM188611v1_genomic.fna.gz --refList GCF_001886115.1_ASM188611v1_genomic.fna/target_genomes.txt --output GCF_001886115.1_ASM188611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:59,755] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:59,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg566b68a9-446d-40fb-8bea-9b74e6a67972/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:59,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg566b68a9-446d-40fb-8bea-9b74e6a67972/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:59,770] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:37:59,770] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:59,771] [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 phoeniculicola	strain=DSM 14726	GCA_001886115.1	154621	154621	type	True	100.0	1250	1255	95	conclusive
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000407505.1	154621	154621	type	True	99.9957	1254	1255	95	conclusive
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000394035.1	154621	154621	type	True	99.9939	1255	1255	95	conclusive
Enterococcus thailandicus	strain=NBRC 101867	GCA_007989705.1	417368	417368	type	True	78.6892	186	1255	95	below_threshold
Enterococcus thailandicus	strain=DSM 21767	GCA_001886265.1	417368	417368	type	True	78.6648	185	1255	95	below_threshold
Enterococcus hirae	strain=DSM 20160	GCA_001885955.1	1354	1354	type	True	78.2626	130	1255	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	78.2234	133	1255	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_002813755.1	53346	53346	type	True	78.1224	128	1255	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_001886035.1	53346	53346	type	True	78.0908	124	1255	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	78.0687	141	1255	95	below_threshold
Enterococcus crotali	strain=ETRF1	GCA_000633635.1	1453587	1453587	type	True	78.0031	165	1255	95	below_threshold
Enterococcus wangshanyuanii	strain=CGMCC 1.15942	GCA_014644255.1	2005703	2005703	type	True	77.9902	137	1255	95	below_threshold
Enterococcus wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	77.8739	143	1255	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.4151	114	1255	95	below_threshold
Vagococcus martis	strain=D7T301	GCA_002026305.1	1768210	1768210	type	True	77.0458	79	1255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:59,772] [INFO] DFAST Taxonomy check result was written to GCF_001886115.1_ASM188611v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:59,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:59,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:59,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg566b68a9-446d-40fb-8bea-9b74e6a67972/dqc_reference/checkm_data
[2024-01-24 12:37:59,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:59,824] [INFO] Task started: CheckM
[2024-01-24 12:37:59,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001886115.1_ASM188611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001886115.1_ASM188611v1_genomic.fna/checkm_input GCF_001886115.1_ASM188611v1_genomic.fna/checkm_result
[2024-01-24 12:38:28,848] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:28,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:28,872] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:28,873] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:28,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001886115.1_ASM188611v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:28,874] [INFO] Task started: Blastn
[2024-01-24 12:38:28,874] [INFO] Running command: blastn -query GCF_001886115.1_ASM188611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg566b68a9-446d-40fb-8bea-9b74e6a67972/dqc_reference/reference_markers_gtdb.fasta -out GCF_001886115.1_ASM188611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:29,635] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:29,639] [INFO] Selected 23 target genomes.
[2024-01-24 12:38:29,639] [INFO] Target genome list was writen to GCF_001886115.1_ASM188611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:29,657] [INFO] Task started: fastANI
[2024-01-24 12:38:29,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78bd7b1-1687-4a93-8146-10d07356cad0/GCF_001886115.1_ASM188611v1_genomic.fna.gz --refList GCF_001886115.1_ASM188611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001886115.1_ASM188611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:42,639] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:42,662] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:42,663] [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_000407505.1	s__Enterococcus_B phoeniculicola	99.9957	1254	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_009933175.1	s__Enterococcus_B sp009933175	80.2949	451	1255	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_001886265.1	s__Enterococcus_B thailandicus	78.6648	185	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.46	99.20	0.93	0.90	6	-
GCF_013394305.1	s__Enterococcus_B pernyi	78.1779	123	1255	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_017377505.1	s__Enterococcus sp017377505	78.1437	151	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_002813755.1	s__Enterococcus_B mundtii	78.1224	128	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	99.56	98.27	0.96	0.86	24	-
GCA_000271405.2	s__Enterococcus_B hirae	78.0983	132	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.97	97.87	0.92	0.86	203	-
GCF_002174455.1	s__Enterococcus sp002174455	78.0967	140	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.86	99.86	0.99	0.99	2	-
GCF_007990225.1	s__Enterococcus_B villorum	78.0687	141	1255	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_000407145.1	s__Enterococcus caccae	78.0045	164	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_000633635.1	s__Enterococcus crotali	78.0031	165	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.61	98.61	0.93	0.93	2	-
GCF_003957375.1	s__Enterococcus_B mundtii_C	77.9926	132	1255	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_001742285.1	s__Enterococcus rivorum	77.9531	143	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000392875.1	s__Enterococcus faecalis	77.9359	139	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.66	96.80	0.89	0.77	1902	-
GCF_001730285.1	s__Enterococcus ureasiticus	77.9342	151	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCF_002140175.1	s__Enterococcus_B sp002140175	77.9234	137	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.33	99.33	0.96	0.96	2	-
GCF_002197645.1	s__Enterococcus wangshanyuanii	77.8979	142	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000407445.1	s__Enterococcus moraviensis	77.7	164	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001886195.1	s__Enterococcus_B ratti	77.4843	132	1255	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_002026305.1	s__Vagococcus martis	77.0458	79	1255	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:42,664] [INFO] GTDB search result was written to GCF_001886115.1_ASM188611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:42,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:42,669] [INFO] DFAST_QC result json was written to GCF_001886115.1_ASM188611v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:42,670] [INFO] DFAST_QC completed!
[2024-01-24 12:38:42,670] [INFO] Total running time: 0h1m5s