[2024-01-25 19:34:21,046] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:21,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:21,047] [INFO] DQC Reference Directory: /var/lib/cwl/stg834dbb12-3fea-420d-b167-bdb2492fd03c/dqc_reference
[2024-01-25 19:34:22,156] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,156] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,157] [INFO] Running command: gunzip -c /var/lib/cwl/stg133a6555-6052-4104-9287-0a7dd3ba9477/GCF_016908995.1_ASM1690899v1_genomic.fna.gz | prodigal -d GCF_016908995.1_ASM1690899v1_genomic.fna/cds.fna -a GCF_016908995.1_ASM1690899v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:28,130] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:28,130] [INFO] Task started: HMMsearch
[2024-01-25 19:34:28,130] [INFO] Running command: hmmsearch --tblout GCF_016908995.1_ASM1690899v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg834dbb12-3fea-420d-b167-bdb2492fd03c/dqc_reference/reference_markers.hmm GCF_016908995.1_ASM1690899v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:28,336] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:28,337] [INFO] Found 6/6 markers.
[2024-01-25 19:34:28,365] [INFO] Query marker FASTA was written to GCF_016908995.1_ASM1690899v1_genomic.fna/markers.fasta
[2024-01-25 19:34:28,365] [INFO] Task started: Blastn
[2024-01-25 19:34:28,365] [INFO] Running command: blastn -query GCF_016908995.1_ASM1690899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834dbb12-3fea-420d-b167-bdb2492fd03c/dqc_reference/reference_markers.fasta -out GCF_016908995.1_ASM1690899v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:28,935] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:28,938] [INFO] Selected 15 target genomes.
[2024-01-25 19:34:28,938] [INFO] Target genome list was writen to GCF_016908995.1_ASM1690899v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:28,943] [INFO] Task started: fastANI
[2024-01-25 19:34:28,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg133a6555-6052-4104-9287-0a7dd3ba9477/GCF_016908995.1_ASM1690899v1_genomic.fna.gz --refList GCF_016908995.1_ASM1690899v1_genomic.fna/target_genomes.txt --output GCF_016908995.1_ASM1690899v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:39,098] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:39,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg834dbb12-3fea-420d-b167-bdb2492fd03c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:39,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg834dbb12-3fea-420d-b167-bdb2492fd03c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:39,107] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:34:39,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:34:39,108] [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 ureilyticus	strain=LMG 26676	GCA_001730315.1	1131292	1131292	type	True	99.9825	1129	1135	95	conclusive
Enterococcus ureilyticus	strain=CCUG 48799	GCA_002806915.1	1131292	1131292	type	True	99.9706	1122	1135	95	conclusive
Enterococcus plantarum	strain=LMG 26214	GCA_001730295.1	1077675	1077675	type	True	84.3736	714	1135	95	below_threshold
Enterococcus rotai	strain=LMG 26678	GCA_001465345.1	118060	118060	type	True	83.9265	764	1135	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	83.7607	759	1135	95	below_threshold
Enterococcus ureasiticus	strain=DSM 23328	GCA_001730285.1	903984	903984	type	True	83.7432	757	1135	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000393995.1	155618	155618	type	True	83.6848	757	1135	95	below_threshold
Enterococcus silesiacus	strain=DSM 22801	GCA_001886225.1	332949	332949	type	True	83.6423	766	1135	95	below_threshold
Enterococcus crotali	strain=ETRF1	GCA_000633635.1	1453587	1453587	type	True	83.1553	806	1135	95	below_threshold
Enterococcus caccae	strain=ATCC BAA-1240	GCA_000407145.1	317735	317735	type	True	82.8479	730	1135	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	78.4095	207	1135	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	77.6842	125	1135	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	77.5774	122	1135	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.4764	102	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:39,109] [INFO] DFAST Taxonomy check result was written to GCF_016908995.1_ASM1690899v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:39,109] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:39,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:39,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg834dbb12-3fea-420d-b167-bdb2492fd03c/dqc_reference/checkm_data
[2024-01-25 19:34:39,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:39,146] [INFO] Task started: CheckM
[2024-01-25 19:34:39,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908995.1_ASM1690899v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908995.1_ASM1690899v1_genomic.fna/checkm_input GCF_016908995.1_ASM1690899v1_genomic.fna/checkm_result
[2024-01-25 19:35:01,864] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:01,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:01,885] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:01,885] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:01,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908995.1_ASM1690899v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:01,887] [INFO] Task started: Blastn
[2024-01-25 19:35:01,887] [INFO] Running command: blastn -query GCF_016908995.1_ASM1690899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834dbb12-3fea-420d-b167-bdb2492fd03c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908995.1_ASM1690899v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:02,647] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:02,653] [INFO] Selected 11 target genomes.
[2024-01-25 19:35:02,653] [INFO] Target genome list was writen to GCF_016908995.1_ASM1690899v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:02,658] [INFO] Task started: fastANI
[2024-01-25 19:35:02,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg133a6555-6052-4104-9287-0a7dd3ba9477/GCF_016908995.1_ASM1690899v1_genomic.fna.gz --refList GCF_016908995.1_ASM1690899v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908995.1_ASM1690899v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:11,737] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:11,744] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:11,745] [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_001730315.1	s__Enterococcus ureilyticus	99.9825	1129	1135	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	conclusive
GCF_001730295.1	s__Enterococcus plantarum	84.3624	715	1135	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_001465345.1	s__Enterococcus rotai	83.9406	762	1135	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	83.773	758	1135	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.97	1.00	1.00	3	-
GCF_001730285.1	s__Enterococcus ureasiticus	83.7432	757	1135	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCA_001465115.1	s__Enterococcus silesiacus	83.6263	782	1135	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000633635.1	s__Enterococcus crotali	83.1821	802	1135	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.61	98.61	0.93	0.93	2	-
GCF_002141365.1	s__Enterococcus sp002141365	82.9588	790	1135	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	82.8883	754	1135	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCF_000407145.1	s__Enterococcus caccae	82.8615	729	1135	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_001730365.1	s__Enterococcus quebecensis	81.8291	622	1135	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:11,746] [INFO] GTDB search result was written to GCF_016908995.1_ASM1690899v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:11,746] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:11,749] [INFO] DFAST_QC result json was written to GCF_016908995.1_ASM1690899v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:11,749] [INFO] DFAST_QC completed!
[2024-01-25 19:35:11,749] [INFO] Total running time: 0h0m51s