[2024-01-24 14:30:47,327] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,329] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,329] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fb010ba-41f5-4c72-a64a-99d2c0f3be31/dqc_reference
[2024-01-24 14:30:48,546] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,547] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,547] [INFO] Running command: gunzip -c /var/lib/cwl/stg775b4420-c99e-4ca8-a785-c15cc364150f/GCF_900447935.1_43071_G02_genomic.fna.gz | prodigal -d GCF_900447935.1_43071_G02_genomic.fna/cds.fna -a GCF_900447935.1_43071_G02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:57,859] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:57,859] [INFO] Task started: HMMsearch
[2024-01-24 14:30:57,859] [INFO] Running command: hmmsearch --tblout GCF_900447935.1_43071_G02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fb010ba-41f5-4c72-a64a-99d2c0f3be31/dqc_reference/reference_markers.hmm GCF_900447935.1_43071_G02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:58,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:58,136] [INFO] Found 6/6 markers.
[2024-01-24 14:30:58,171] [INFO] Query marker FASTA was written to GCF_900447935.1_43071_G02_genomic.fna/markers.fasta
[2024-01-24 14:30:58,172] [INFO] Task started: Blastn
[2024-01-24 14:30:58,172] [INFO] Running command: blastn -query GCF_900447935.1_43071_G02_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fb010ba-41f5-4c72-a64a-99d2c0f3be31/dqc_reference/reference_markers.fasta -out GCF_900447935.1_43071_G02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:58,799] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:58,803] [INFO] Selected 11 target genomes.
[2024-01-24 14:30:58,804] [INFO] Target genome list was writen to GCF_900447935.1_43071_G02_genomic.fna/target_genomes.txt
[2024-01-24 14:30:58,811] [INFO] Task started: fastANI
[2024-01-24 14:30:58,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg775b4420-c99e-4ca8-a785-c15cc364150f/GCF_900447935.1_43071_G02_genomic.fna.gz --refList GCF_900447935.1_43071_G02_genomic.fna/target_genomes.txt --output GCF_900447935.1_43071_G02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:06,078] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:06,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fb010ba-41f5-4c72-a64a-99d2c0f3be31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:06,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fb010ba-41f5-4c72-a64a-99d2c0f3be31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:06,092] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:31:06,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:06,093] [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 gallinarum	strain=NCTC12359	GCA_900447935.1	1353	1353	suspected-type	True	100.0	1303	1306	95	conclusive
Enterococcus gallinarum	strain=NBRC 100675	GCA_001544275.1	1353	1353	suspected-type	True	99.938	1215	1306	95	conclusive
Enterococcus gallinarum	strain=DSM 24841	GCA_001886155.1	1353	1353	suspected-type	True	99.9199	1177	1306	95	conclusive
Enterococcus casseliflavus	strain=NBRC 100478	GCA_001544095.1	37734	37734	type	True	80.7479	406	1306	95	below_threshold
Enterococcus casseliflavus	strain=DSM 20680	GCA_001885845.1	37734	37734	type	True	80.6297	408	1306	95	below_threshold
Enterococcus mediterraneensis	strain=Marseille-P4358	GCA_900604485.1	2364791	2364791	type	True	79.6855	187	1306	95	below_threshold
Enterococcus wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	78.5983	122	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:06,095] [INFO] DFAST Taxonomy check result was written to GCF_900447935.1_43071_G02_genomic.fna/tc_result.tsv
[2024-01-24 14:31:06,096] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:06,096] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:06,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fb010ba-41f5-4c72-a64a-99d2c0f3be31/dqc_reference/checkm_data
[2024-01-24 14:31:06,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:06,139] [INFO] Task started: CheckM
[2024-01-24 14:31:06,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900447935.1_43071_G02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900447935.1_43071_G02_genomic.fna/checkm_input GCF_900447935.1_43071_G02_genomic.fna/checkm_result
[2024-01-24 14:31:42,311] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:42,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:42,341] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:42,342] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:42,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900447935.1_43071_G02_genomic.fna/markers.fasta)
[2024-01-24 14:31:42,342] [INFO] Task started: Blastn
[2024-01-24 14:31:42,342] [INFO] Running command: blastn -query GCF_900447935.1_43071_G02_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fb010ba-41f5-4c72-a64a-99d2c0f3be31/dqc_reference/reference_markers_gtdb.fasta -out GCF_900447935.1_43071_G02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:43,180] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:43,183] [INFO] Selected 15 target genomes.
[2024-01-24 14:31:43,184] [INFO] Target genome list was writen to GCF_900447935.1_43071_G02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:43,196] [INFO] Task started: fastANI
[2024-01-24 14:31:43,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg775b4420-c99e-4ca8-a785-c15cc364150f/GCF_900447935.1_43071_G02_genomic.fna.gz --refList GCF_900447935.1_43071_G02_genomic.fna/target_genomes_gtdb.txt --output GCF_900447935.1_43071_G02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:53,581] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:53,593] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:53,593] [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_001544275.1	s__Enterococcus_D gallinarum	99.938	1215	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.60	97.23	0.85	0.80	74	conclusive
GCF_001544095.1	s__Enterococcus_D casseliflavus	80.7328	407	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	98.00	95.35	0.87	0.83	83	-
GCF_002850555.1	s__Enterococcus_D sp002850555	80.3098	426	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.34	95.31	0.87	0.74	46	-
GCF_900604485.1	s__Enterococcus_C mediterraneensis	79.6833	187	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002140915.1	s__Enterococcus_D sp002140915	79.6238	337	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001297065.1	s__Enterococcus_D sp001297065	79.4922	349	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.01	96.72	0.90	0.84	5	-
GCF_003795145.1	s__Tetragenococcus koreensis	78.8643	87	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	99.21	98.98	0.92	0.90	7	-
GCF_000407285.1	s__Enterococcus_F saccharolyticus	78.72	141	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	99.99	99.99	1.00	1.00	3	-
GCF_002197645.1	s__Enterococcus wangshanyuanii	78.5983	122	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017315945.1	s__Enterococcus_B sp017315945	78.4344	150	1306	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_001544255.1	s__Enterococcus_B faecium	78.2953	148	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.30	98.03	0.91	0.72	2177	-
GCF_005405485.1	s__Enterococcus_A hulanensis	78.1127	117	1306	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_014635985.1	s__Enterococcus_I alcedinis	77.8732	83	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001730285.1	s__Enterococcus ureasiticus	77.7408	116	1306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:53,595] [INFO] GTDB search result was written to GCF_900447935.1_43071_G02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:53,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:53,599] [INFO] DFAST_QC result json was written to GCF_900447935.1_43071_G02_genomic.fna/dqc_result.json
[2024-01-24 14:31:53,599] [INFO] DFAST_QC completed!
[2024-01-24 14:31:53,599] [INFO] Total running time: 0h1m6s