[2024-01-24 12:40:08,015] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:08,016] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:08,017] [INFO] DQC Reference Directory: /var/lib/cwl/stg6226c190-1ea0-4f16-a989-1abcf91fbef3/dqc_reference
[2024-01-24 12:40:09,290] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,291] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,291] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8260e9a-8844-4118-995b-73609efb811f/GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna.gz | prodigal -d GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/cds.fna -a GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:14,323] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:14,323] [INFO] Task started: HMMsearch
[2024-01-24 12:40:14,323] [INFO] Running command: hmmsearch --tblout GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6226c190-1ea0-4f16-a989-1abcf91fbef3/dqc_reference/reference_markers.hmm GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:14,583] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:14,585] [INFO] Found 6/6 markers.
[2024-01-24 12:40:14,616] [INFO] Query marker FASTA was written to GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/markers.fasta
[2024-01-24 12:40:14,616] [INFO] Task started: Blastn
[2024-01-24 12:40:14,617] [INFO] Running command: blastn -query GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6226c190-1ea0-4f16-a989-1abcf91fbef3/dqc_reference/reference_markers.fasta -out GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:15,267] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:15,270] [INFO] Selected 13 target genomes.
[2024-01-24 12:40:15,270] [INFO] Target genome list was writen to GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:15,275] [INFO] Task started: fastANI
[2024-01-24 12:40:15,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8260e9a-8844-4118-995b-73609efb811f/GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna.gz --refList GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/target_genomes.txt --output GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:22,758] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:22,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6226c190-1ea0-4f16-a989-1abcf91fbef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:22,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6226c190-1ea0-4f16-a989-1abcf91fbef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:22,768] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:40:22,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:22,768] [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 columbae	strain=ATCC 51263	GCA_000406925.1	1355	1355	type	True	99.9958	851	856	95	conclusive
Enterococcus columbae	strain=ATCC 51263	GCA_000407225.1	1355	1355	type	True	99.9695	841	856	95	conclusive
Enterococcus columbae	strain=DSM 7374	GCA_000373065.1	1355	1355	type	True	99.9269	814	856	95	conclusive
Enterococcus columbae	strain=DSM 7374	GCA_001885835.1	1355	1355	type	True	99.8961	789	856	95	conclusive
Enterococcus cecorum	strain=ATCC 43198	GCA_000492155.1	44008	44008	type	True	80.7001	323	856	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	79.1837	162	856	95	below_threshold
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	77.9458	75	856	95	below_threshold
Enterococcus alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	77.8305	102	856	95	below_threshold
Vagococcus humatus	strain=JCM 31581	GCA_003950325.1	1889241	1889241	type	True	77.6621	68	856	95	below_threshold
Vagococcus allomyrinae	strain=BWB3-3	GCA_017829975.1	2794353	2794353	type	True	77.633	59	856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:22,770] [INFO] DFAST Taxonomy check result was written to GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:22,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:22,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:22,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6226c190-1ea0-4f16-a989-1abcf91fbef3/dqc_reference/checkm_data
[2024-01-24 12:40:22,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:22,811] [INFO] Task started: CheckM
[2024-01-24 12:40:22,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/checkm_input GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/checkm_result
[2024-01-24 12:40:45,118] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:45,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:45,144] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:45,144] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:45,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/markers.fasta)
[2024-01-24 12:40:45,145] [INFO] Task started: Blastn
[2024-01-24 12:40:45,146] [INFO] Running command: blastn -query GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6226c190-1ea0-4f16-a989-1abcf91fbef3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:45,941] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:45,945] [INFO] Selected 18 target genomes.
[2024-01-24 12:40:45,945] [INFO] Target genome list was writen to GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:45,955] [INFO] Task started: fastANI
[2024-01-24 12:40:45,955] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8260e9a-8844-4118-995b-73609efb811f/GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna.gz --refList GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:54,499] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:54,517] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:54,517] [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_000406925.1	s__Enterococcus_E columbae	99.9958	851	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	99.98	99.97	1.00	0.99	4	conclusive
GCF_000407565.1	s__Enterococcus_E cecorum	80.5059	325	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	97.77	96.06	0.87	0.77	49	-
GCA_019120335.1	s__Enterococcus_E stercoripullorum	80.0608	285	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197645.1	s__Enterococcus wangshanyuanii	79.0099	90	856	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	78.8467	89	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000407165.1	s__Enterococcus haemoperoxidus	78.7053	103	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.97	1.00	1.00	3	-
GCF_000407285.1	s__Enterococcus_F saccharolyticus	78.592	151	856	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_001544255.1	s__Enterococcus_B faecium	78.4994	77	856	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_001465345.1	s__Enterococcus rotai	78.4549	87	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744255.1	s__Carnobacterium divergens	78.3805	71	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.06	98.93	0.92	0.90	24	-
GCF_009933335.1	s__Enterococcus_F sp009933335	78.3389	132	856	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_017315945.1	s__Enterococcus_B sp017315945	78.1734	102	856	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_009933135.1	s__Enterococcus_C sp009933135	78.0709	58	856	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_014635985.1	s__Enterococcus_I alcedinis	77.7745	103	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001465115.1	s__Enterococcus silesiacus	77.7306	97	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016909125.1	s__Enterococcus_I lemanii	77.7186	128	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	98.21	98.21	0.88	0.88	2	-
GCA_019116505.1	s__Enterococcus_I avicola	77.7102	100	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003950325.1	s__Vagococcus_C humatus	77.6809	69	856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:54,519] [INFO] GTDB search result was written to GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:54,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:54,525] [INFO] DFAST_QC result json was written to GCF_000406925.1_Ente_colu_ATCC51263_V1_genomic.fna/dqc_result.json
[2024-01-24 12:40:54,525] [INFO] DFAST_QC completed!
[2024-01-24 12:40:54,526] [INFO] Total running time: 0h0m47s