[2024-01-24 14:14:00,271] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,273] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,273] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ec46e74-3188-4102-bb78-90f389764118/dqc_reference
[2024-01-24 14:14:01,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:01,591] [INFO] Task started: Prodigal
[2024-01-24 14:14:01,591] [INFO] Running command: gunzip -c /var/lib/cwl/stg10282626-3abe-4a38-a619-49fcabbf6e9d/GCF_017874975.1_ASM1787497v1_genomic.fna.gz | prodigal -d GCF_017874975.1_ASM1787497v1_genomic.fna/cds.fna -a GCF_017874975.1_ASM1787497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:07,316] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:07,317] [INFO] Task started: HMMsearch
[2024-01-24 14:14:07,317] [INFO] Running command: hmmsearch --tblout GCF_017874975.1_ASM1787497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ec46e74-3188-4102-bb78-90f389764118/dqc_reference/reference_markers.hmm GCF_017874975.1_ASM1787497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:07,717] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:07,720] [INFO] Found 6/6 markers.
[2024-01-24 14:14:07,761] [INFO] Query marker FASTA was written to GCF_017874975.1_ASM1787497v1_genomic.fna/markers.fasta
[2024-01-24 14:14:07,762] [INFO] Task started: Blastn
[2024-01-24 14:14:07,762] [INFO] Running command: blastn -query GCF_017874975.1_ASM1787497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ec46e74-3188-4102-bb78-90f389764118/dqc_reference/reference_markers.fasta -out GCF_017874975.1_ASM1787497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:08,822] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:08,825] [INFO] Selected 26 target genomes.
[2024-01-24 14:14:08,826] [INFO] Target genome list was writen to GCF_017874975.1_ASM1787497v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:08,836] [INFO] Task started: fastANI
[2024-01-24 14:14:08,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg10282626-3abe-4a38-a619-49fcabbf6e9d/GCF_017874975.1_ASM1787497v1_genomic.fna.gz --refList GCF_017874975.1_ASM1787497v1_genomic.fna/target_genomes.txt --output GCF_017874975.1_ASM1787497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:24,147] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:24,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ec46e74-3188-4102-bb78-90f389764118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:24,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ec46e74-3188-4102-bb78-90f389764118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:24,169] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:24,170] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:24,170] [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 alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	99.9961	870	881	95	conclusive
Enterococcus aquimarinus	strain=DSM 17690	GCA_001885765.1	328396	328396	type	True	79.0464	287	881	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	78.3481	189	881	95	below_threshold
Enterococcus saccharolyticus	strain=DSM 20726	GCA_001886235.1	41997	41997	type	True	78.176	190	881	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407285.1	1814218	41997	type	True	78.147	190	881	95	below_threshold
Enterococcus mediterraneensis	strain=Marseille-P4358	GCA_900604485.1	2364791	2364791	type	True	78.0426	73	881	95	below_threshold
Enterococcus thailandicus	strain=NBRC 101867	GCA_007989705.1	417368	417368	type	True	77.9541	100	881	95	below_threshold
Enterococcus faecalis	strain=ATCC 19433	GCA_000392875.1	1351	1351	type	True	77.9366	106	881	95	below_threshold
Enterococcus thailandicus	strain=DSM 21767	GCA_001886265.1	417368	417368	type	True	77.9173	98	881	95	below_threshold
Enterococcus silesiacus	strain=DSM 22801	GCA_001886225.1	332949	332949	type	True	77.8785	90	881	95	below_threshold
Enterococcus sulfureus	strain=ATCC 49903	GCA_000407025.1	1356	1356	type	True	77.8464	112	881	95	below_threshold
Enterococcus crotali	strain=ETRF1	GCA_000633635.1	1453587	1453587	type	True	77.8158	99	881	95	below_threshold
Enterococcus faecalis	strain=NBRC 100480	GCA_001544235.1	1351	1351	type	True	77.811	107	881	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_002813755.1	53346	53346	type	True	77.791	90	881	95	below_threshold
Enterococcus rivorum	strain=LMG 25899	GCA_001742285.1	762845	762845	type	True	77.7893	89	881	95	below_threshold
Enterococcus plantarum	strain=LMG 26214	GCA_001730295.1	1077675	1077675	type	True	77.674	91	881	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	77.6606	102	881	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000393995.1	155618	155618	type	True	77.6044	104	881	95	below_threshold
Vagococcus salmoninarum	strain=NCFB 2777	GCA_003987495.1	2739	2739	type	True	77.4735	61	881	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	77.451	70	881	95	below_threshold
Enterococcus ratti	strain=DSM 15687	GCA_001886195.1	150033	150033	type	True	77.0447	73	881	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	76.9378	91	881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:24,174] [INFO] DFAST Taxonomy check result was written to GCF_017874975.1_ASM1787497v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:24,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:24,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:24,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ec46e74-3188-4102-bb78-90f389764118/dqc_reference/checkm_data
[2024-01-24 14:14:24,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:24,229] [INFO] Task started: CheckM
[2024-01-24 14:14:24,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874975.1_ASM1787497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874975.1_ASM1787497v1_genomic.fna/checkm_input GCF_017874975.1_ASM1787497v1_genomic.fna/checkm_result
[2024-01-24 14:14:50,929] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:50,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:50,956] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:50,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:50,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874975.1_ASM1787497v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:50,957] [INFO] Task started: Blastn
[2024-01-24 14:14:50,957] [INFO] Running command: blastn -query GCF_017874975.1_ASM1787497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ec46e74-3188-4102-bb78-90f389764118/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874975.1_ASM1787497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:51,745] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:51,749] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:51,749] [INFO] Target genome list was writen to GCF_017874975.1_ASM1787497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:51,767] [INFO] Task started: fastANI
[2024-01-24 14:14:51,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg10282626-3abe-4a38-a619-49fcabbf6e9d/GCF_017874975.1_ASM1787497v1_genomic.fna.gz --refList GCF_017874975.1_ASM1787497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874975.1_ASM1787497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:00,826] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:00,848] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:00,848] [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_014635985.1	s__Enterococcus_I alcedinis	99.9961	870	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_019116505.1	s__Enterococcus_I avicola	82.3228	380	881	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_001885765.1	s__Enterococcus_I aquimarinus	79.0464	287	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	98.10	98.04	0.96	0.95	6	-
GCF_016909125.1	s__Enterococcus_I lemanii	78.4228	275	881	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_017426705.1	s__Enterococcus_F sp017426705	78.2972	194	881	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_000407285.1	s__Enterococcus_F saccharolyticus	78.1534	189	881	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_900604485.1	s__Enterococcus_C mediterraneensis	78.0426	73	881	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_002174455.1	s__Enterococcus sp002174455	77.9451	83	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.86	99.86	0.99	0.99	2	-
GCF_000407605.1	s__Enterococcus_G sulfureus	77.9426	119	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_G	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001886265.1	s__Enterococcus_B thailandicus	77.9173	98	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.46	99.20	0.93	0.90	6	-
GCA_001465115.1	s__Enterococcus silesiacus	77.8882	89	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000407445.1	s__Enterococcus moraviensis	77.8173	103	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_009933335.1	s__Enterococcus_F sp009933335	77.7461	191	881	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_002148425.1	s__Enterococcus sp002148425	77.729	94	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCF_001730295.1	s__Enterococcus plantarum	77.6813	90	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.57	98.46	0.89	0.88	4	-
GCF_005405265.1	s__Enterococcus_C songbeiensis	77.4657	70	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.82	98.68	0.87	0.87	4	-
GCA_019115705.1	s__Tetragenococcus pullicola	77.1911	81	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886195.1	s__Enterococcus_B ratti	77.0447	73	881	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_019218635.1	s__Enterococcus_A sp019218635	76.9367	91	881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:00,850] [INFO] GTDB search result was written to GCF_017874975.1_ASM1787497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:00,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:00,856] [INFO] DFAST_QC result json was written to GCF_017874975.1_ASM1787497v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:00,857] [INFO] DFAST_QC completed!
[2024-01-24 14:15:00,857] [INFO] Total running time: 0h1m1s