[2024-01-24 11:12:58,167] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,169] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b9432aa-db5d-4f38-b329-d8a43f96c7fd/dqc_reference
[2024-01-24 11:12:59,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,577] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg32e4d7d8-122c-43a8-8c2a-c6604da14e09/GCF_001886145.1_ASM188614v1_genomic.fna.gz | prodigal -d GCF_001886145.1_ASM188614v1_genomic.fna/cds.fna -a GCF_001886145.1_ASM188614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:05,798] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:05,799] [INFO] Task started: HMMsearch
[2024-01-24 11:13:05,799] [INFO] Running command: hmmsearch --tblout GCF_001886145.1_ASM188614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b9432aa-db5d-4f38-b329-d8a43f96c7fd/dqc_reference/reference_markers.hmm GCF_001886145.1_ASM188614v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:06,125] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:06,126] [INFO] Found 6/6 markers.
[2024-01-24 11:13:06,157] [INFO] Query marker FASTA was written to GCF_001886145.1_ASM188614v1_genomic.fna/markers.fasta
[2024-01-24 11:13:06,158] [INFO] Task started: Blastn
[2024-01-24 11:13:06,158] [INFO] Running command: blastn -query GCF_001886145.1_ASM188614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b9432aa-db5d-4f38-b329-d8a43f96c7fd/dqc_reference/reference_markers.fasta -out GCF_001886145.1_ASM188614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:06,760] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:06,767] [INFO] Selected 17 target genomes.
[2024-01-24 11:13:06,768] [INFO] Target genome list was writen to GCF_001886145.1_ASM188614v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:06,774] [INFO] Task started: fastANI
[2024-01-24 11:13:06,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg32e4d7d8-122c-43a8-8c2a-c6604da14e09/GCF_001886145.1_ASM188614v1_genomic.fna.gz --refList GCF_001886145.1_ASM188614v1_genomic.fna/target_genomes.txt --output GCF_001886145.1_ASM188614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:17,868] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:17,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b9432aa-db5d-4f38-b329-d8a43f96c7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:17,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b9432aa-db5d-4f38-b329-d8a43f96c7fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:17,881] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:17,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:17,882] [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 quebecensis	strain=DSM 23327	GCA_001886145.1	903983	903983	type	True	100.0	1026	1027	95	conclusive
Enterococcus quebecensis	strain=LMG 26306	GCA_001730365.1	903983	903983	type	True	99.9893	1026	1027	95	conclusive
Enterococcus ureasiticus	strain=DSM 23328	GCA_001730285.1	903984	903984	type	True	82.723	729	1027	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000393995.1	155618	155618	type	True	82.4923	709	1027	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	82.4491	699	1027	95	below_threshold
Enterococcus crotali	strain=ETRF1	GCA_000633635.1	1453587	1453587	type	True	82.241	664	1027	95	below_threshold
Enterococcus plantarum	strain=LMG 26214	GCA_001730295.1	1077675	1077675	type	True	82.2403	622	1027	95	below_threshold
Enterococcus rotai	strain=LMG 26678	GCA_001465345.1	118060	118060	type	True	82.1791	636	1027	95	below_threshold
Enterococcus silesiacus	strain=DSM 22801	GCA_001886225.1	332949	332949	type	True	82.1485	658	1027	95	below_threshold
Enterococcus moraviensis	strain=DSM 15919	GCA_001886065.1	155617	155617	type	True	81.8644	639	1027	95	below_threshold
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000394015.1	155617	155617	type	True	81.8638	654	1027	95	below_threshold
Enterococcus moraviensis	strain=ATCC BAA-383	GCA_000407445.1	155617	155617	type	True	81.8158	663	1027	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.2421	226	1027	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	77.7087	137	1027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:17,883] [INFO] DFAST Taxonomy check result was written to GCF_001886145.1_ASM188614v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:17,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:17,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:17,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b9432aa-db5d-4f38-b329-d8a43f96c7fd/dqc_reference/checkm_data
[2024-01-24 11:13:17,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:17,929] [INFO] Task started: CheckM
[2024-01-24 11:13:17,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001886145.1_ASM188614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001886145.1_ASM188614v1_genomic.fna/checkm_input GCF_001886145.1_ASM188614v1_genomic.fna/checkm_result
[2024-01-24 11:13:43,883] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:43,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:43,908] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:43,908] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:43,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001886145.1_ASM188614v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:43,909] [INFO] Task started: Blastn
[2024-01-24 11:13:43,909] [INFO] Running command: blastn -query GCF_001886145.1_ASM188614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b9432aa-db5d-4f38-b329-d8a43f96c7fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_001886145.1_ASM188614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:44,661] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:44,664] [INFO] Selected 12 target genomes.
[2024-01-24 11:13:44,664] [INFO] Target genome list was writen to GCF_001886145.1_ASM188614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:44,672] [INFO] Task started: fastANI
[2024-01-24 11:13:44,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg32e4d7d8-122c-43a8-8c2a-c6604da14e09/GCF_001886145.1_ASM188614v1_genomic.fna.gz --refList GCF_001886145.1_ASM188614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001886145.1_ASM188614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:53,653] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:53,669] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:53,670] [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_001730365.1	s__Enterococcus quebecensis	99.9893	1026	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_017377505.1	s__Enterococcus sp017377505	83.1071	721	1027	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	82.6917	732	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCF_002141365.1	s__Enterococcus sp002141365	82.4759	709	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407165.1	s__Enterococcus haemoperoxidus	82.4572	698	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.97	1.00	1.00	3	-
GCF_000407145.1	s__Enterococcus caccae	82.2943	675	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_001730295.1	s__Enterococcus plantarum	82.2403	622	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_000633635.1	s__Enterococcus crotali	82.2296	665	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.61	98.61	0.93	0.93	2	-
GCF_001465345.1	s__Enterococcus rotai	82.1786	636	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148425.1	s__Enterococcus sp002148425	82.0881	652	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCF_002140715.1	s__Enterococcus sp002140715	82.0083	669	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407445.1	s__Enterococcus moraviensis	81.8223	663	1027	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:53,672] [INFO] GTDB search result was written to GCF_001886145.1_ASM188614v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:53,672] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:53,676] [INFO] DFAST_QC result json was written to GCF_001886145.1_ASM188614v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:53,676] [INFO] DFAST_QC completed!
[2024-01-24 11:13:53,676] [INFO] Total running time: 0h0m56s