[2024-01-24 11:12:54,995] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:54,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:54,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fbc0f33-7397-4fce-b36f-db73d40c53db/dqc_reference
[2024-01-24 11:12:56,268] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:56,269] [INFO] Task started: Prodigal
[2024-01-24 11:12:56,269] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf7ff4da-9e31-4bde-88d5-7a4cfb0d131d/GCF_003950325.1_ASM395032v1_genomic.fna.gz | prodigal -d GCF_003950325.1_ASM395032v1_genomic.fna/cds.fna -a GCF_003950325.1_ASM395032v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:59,958] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:59,958] [INFO] Task started: HMMsearch
[2024-01-24 11:12:59,958] [INFO] Running command: hmmsearch --tblout GCF_003950325.1_ASM395032v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fbc0f33-7397-4fce-b36f-db73d40c53db/dqc_reference/reference_markers.hmm GCF_003950325.1_ASM395032v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:00,244] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:00,245] [INFO] Found 6/6 markers.
[2024-01-24 11:13:00,264] [INFO] Query marker FASTA was written to GCF_003950325.1_ASM395032v1_genomic.fna/markers.fasta
[2024-01-24 11:13:00,265] [INFO] Task started: Blastn
[2024-01-24 11:13:00,265] [INFO] Running command: blastn -query GCF_003950325.1_ASM395032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fbc0f33-7397-4fce-b36f-db73d40c53db/dqc_reference/reference_markers.fasta -out GCF_003950325.1_ASM395032v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:00,967] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:00,970] [INFO] Selected 25 target genomes.
[2024-01-24 11:13:00,970] [INFO] Target genome list was writen to GCF_003950325.1_ASM395032v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:01,111] [INFO] Task started: fastANI
[2024-01-24 11:13:01,111] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf7ff4da-9e31-4bde-88d5-7a4cfb0d131d/GCF_003950325.1_ASM395032v1_genomic.fna.gz --refList GCF_003950325.1_ASM395032v1_genomic.fna/target_genomes.txt --output GCF_003950325.1_ASM395032v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:11,169] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:11,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fbc0f33-7397-4fce-b36f-db73d40c53db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:11,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fbc0f33-7397-4fce-b36f-db73d40c53db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:11,186] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:11,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:11,186] [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
Vagococcus humatus	strain=JCM 31581	GCA_003950325.1	1889241	1889241	type	True	100.0	694	695	95	conclusive
Vagococcus teuberi	strain=DSM 21459	GCA_001870205.1	519472	519472	type	True	78.2074	96	695	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	78.0893	87	695	95	below_threshold
Vagococcus coleopterorum	strain=HDW17A	GCA_011303955.1	2714946	2714946	type	True	78.0823	76	695	95	below_threshold
Vagococcus lutrae	strain=CCUG 39187	GCA_003987555.1	81947	81947	type	True	78.0384	85	695	95	below_threshold
Vagococcus fluvialis	strain=NCDO 2497	GCA_003987575.1	2738	2738	type	True	77.8341	114	695	95	below_threshold
Vagococcus carniphilus	strain=ATCC BAA-640	GCA_014397115.1	218144	218144	type	True	77.8169	120	695	95	below_threshold
Enterococcus dispar	strain=ATCC 51266	GCA_000407585.1	44009	44009	type	True	77.816	59	695	95	below_threshold
Vagococcus fluvialis	strain=DSM 5731	GCA_003337315.1	2738	2738	type	True	77.7726	117	695	95	below_threshold
Vagococcus penaei	strain=CD276	GCA_001998885.1	633807	633807	type	True	77.7202	81	695	95	below_threshold
Vagococcus penaei	strain=LMG 24833	GCA_003987515.1	633807	633807	type	True	77.6684	80	695	95	below_threshold
Enterococcus dispar	strain=ATCC 51266	GCA_000406945.1	44009	44009	type	True	77.6048	57	695	95	below_threshold
Vagococcus salmoninarum	strain=NCFB 2777	GCA_003987495.1	2739	2739	type	True	77.5046	112	695	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.4778	77	695	95	below_threshold
Enterococcus dispar	strain=DSM 6630	GCA_001886105.1	44009	44009	type	True	77.3223	55	695	95	below_threshold
Vagococcus bubulae	strain=SS1994	GCA_003950315.1	1977868	1977868	type	True	77.3042	109	695	95	below_threshold
Carnobacterium divergens	strain=66	GCA_000744255.1	2748	2748	type	True	77.2548	64	695	95	below_threshold
Carnobacterium divergens	strain=NCTC13772	GCA_900446755.1	2748	2748	type	True	77.1991	66	695	95	below_threshold
Carnobacterium divergens	strain=DSM 20623	GCA_001437085.1	2748	2748	type	True	76.9516	63	695	95	below_threshold
Enterococcus quebecensis	strain=DSM 23327	GCA_001886145.1	903983	903983	type	True	76.6373	76	695	95	below_threshold
Carnobacterium maltaromaticum	strain=DSM 20342	GCA_001437315.1	2751	2751	type	True	76.3991	71	695	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:11,189] [INFO] DFAST Taxonomy check result was written to GCF_003950325.1_ASM395032v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:11,190] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:11,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:11,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fbc0f33-7397-4fce-b36f-db73d40c53db/dqc_reference/checkm_data
[2024-01-24 11:13:11,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:11,216] [INFO] Task started: CheckM
[2024-01-24 11:13:11,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003950325.1_ASM395032v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003950325.1_ASM395032v1_genomic.fna/checkm_input GCF_003950325.1_ASM395032v1_genomic.fna/checkm_result
[2024-01-24 11:13:30,528] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:30,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:30,543] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:30,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:30,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003950325.1_ASM395032v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:30,544] [INFO] Task started: Blastn
[2024-01-24 11:13:30,545] [INFO] Running command: blastn -query GCF_003950325.1_ASM395032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fbc0f33-7397-4fce-b36f-db73d40c53db/dqc_reference/reference_markers_gtdb.fasta -out GCF_003950325.1_ASM395032v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:31,456] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:31,461] [INFO] Selected 28 target genomes.
[2024-01-24 11:13:31,461] [INFO] Target genome list was writen to GCF_003950325.1_ASM395032v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:31,507] [INFO] Task started: fastANI
[2024-01-24 11:13:31,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf7ff4da-9e31-4bde-88d5-7a4cfb0d131d/GCF_003950325.1_ASM395032v1_genomic.fna.gz --refList GCF_003950325.1_ASM395032v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003950325.1_ASM395032v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:44,251] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:44,269] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:44,270] [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_003950325.1	s__Vagococcus_C humatus	100.0	694	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017315945.1	s__Enterococcus_B sp017315945	79.6766	70	695	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_016909125.1	s__Enterococcus_I lemanii	78.7633	76	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	98.21	98.21	0.88	0.88	2	-
GCF_001870205.1	s__Vagococcus teuberi	78.295	97	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.6178	98.63	98.63	0.90	0.90	3	-
GCF_011303955.1	s__Vagococcus_D coleopterorum	78.0418	75	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397115.1	s__Vagococcus carniphilus	77.8169	120	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003337315.1	s__Vagococcus fluvialis	77.8002	116	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	98.30	97.38	0.91	0.88	13	-
GCF_000407565.1	s__Enterococcus_E cecorum	77.7609	68	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	97.77	96.06	0.87	0.77	49	-
GCF_000406945.1	s__Enterococcus_C dispar	77.7388	58	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	99.61	99.21	0.95	0.90	5	-
GCF_017316025.1	s__Enterococcus_C sp017316025	77.7334	58	695	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_001998885.1	s__Vagococcus penaei	77.7202	81	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003462485.1	s__Vagococcus sp003462485	77.6287	91	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987495.1	s__Vagococcus_D salmoninarum	77.5046	112	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	98.18	98.18	0.88	0.88	2	-
GCF_019218635.1	s__Enterococcus_A sp019218635	77.4778	77	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017426705.1	s__Enterococcus_F sp017426705	77.3956	82	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017316125.1	s__Enterococcus_B sp017316125	77.3026	70	695	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_000744255.1	s__Carnobacterium divergens	77.2966	63	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.06	98.93	0.92	0.90	24	-
GCF_002140715.1	s__Enterococcus sp002140715	77.282	76	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003950315.1	s__Vagococcus bubulae	77.2784	110	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407285.1	s__Enterococcus_F saccharolyticus	77.2486	79	695	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_001730365.1	s__Enterococcus quebecensis	77.058	75	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003795125.1	s__Tetragenococcus osmophilus	76.9257	53	695	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:44,271] [INFO] GTDB search result was written to GCF_003950325.1_ASM395032v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:44,272] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:44,277] [INFO] DFAST_QC result json was written to GCF_003950325.1_ASM395032v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:44,277] [INFO] DFAST_QC completed!
[2024-01-24 11:13:44,277] [INFO] Total running time: 0h0m49s