[2024-01-24 13:13:25,446] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:25,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:25,457] [INFO] DQC Reference Directory: /var/lib/cwl/stg2721a30b-50b5-4894-ae6a-6a0d954ff71f/dqc_reference
[2024-01-24 13:13:26,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:26,922] [INFO] Task started: Prodigal
[2024-01-24 13:13:26,923] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb0d20ad-27ae-426a-bc02-927b9db08470/GCF_017830045.1_ASM1783004v1_genomic.fna.gz | prodigal -d GCF_017830045.1_ASM1783004v1_genomic.fna/cds.fna -a GCF_017830045.1_ASM1783004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:37,035] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:37,035] [INFO] Task started: HMMsearch
[2024-01-24 13:13:37,035] [INFO] Running command: hmmsearch --tblout GCF_017830045.1_ASM1783004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2721a30b-50b5-4894-ae6a-6a0d954ff71f/dqc_reference/reference_markers.hmm GCF_017830045.1_ASM1783004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:37,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:37,356] [INFO] Found 6/6 markers.
[2024-01-24 13:13:37,395] [INFO] Query marker FASTA was written to GCF_017830045.1_ASM1783004v1_genomic.fna/markers.fasta
[2024-01-24 13:13:37,396] [INFO] Task started: Blastn
[2024-01-24 13:13:37,396] [INFO] Running command: blastn -query GCF_017830045.1_ASM1783004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2721a30b-50b5-4894-ae6a-6a0d954ff71f/dqc_reference/reference_markers.fasta -out GCF_017830045.1_ASM1783004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:38,063] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:38,066] [INFO] Selected 22 target genomes.
[2024-01-24 13:13:38,066] [INFO] Target genome list was writen to GCF_017830045.1_ASM1783004v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:38,091] [INFO] Task started: fastANI
[2024-01-24 13:13:38,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb0d20ad-27ae-426a-bc02-927b9db08470/GCF_017830045.1_ASM1783004v1_genomic.fna.gz --refList GCF_017830045.1_ASM1783004v1_genomic.fna/target_genomes.txt --output GCF_017830045.1_ASM1783004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:50,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:50,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2721a30b-50b5-4894-ae6a-6a0d954ff71f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:50,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2721a30b-50b5-4894-ae6a-6a0d954ff71f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:50,907] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:50,907] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:50,908] [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 larvae	strain=BWM-S5	GCA_017830045.1	2794352	2794352	type	True	100.0	1375	1375	95	conclusive
Enterococcus wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	78.2283	201	1375	95	below_threshold
Enterococcus wangshanyuanii	strain=CGMCC 1.15942	GCA_014644255.1	2005703	2005703	type	True	78.1901	199	1375	95	below_threshold
Enterococcus caccae	strain=ATCC BAA-1240	GCA_000407145.1	317735	317735	type	True	78.1379	190	1375	95	below_threshold
Enterococcus caccae	strain=ATCC BAA-1240	GCA_000394055.1	317735	317735	type	True	78.1098	190	1375	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	78.1089	192	1375	95	below_threshold
Enterococcus caccae	strain=DSM 19114	GCA_001885825.1	317735	317735	type	True	78.0237	191	1375	95	below_threshold
Enterococcus crotali	strain=ETRF1	GCA_000633635.1	1453587	1453587	type	True	78.018	190	1375	95	below_threshold
Enterococcus ureasiticus	strain=DSM 23328	GCA_001730285.1	903984	903984	type	True	78.0146	179	1375	95	below_threshold
Enterococcus moraviensis	strain=DSM 15919	GCA_001886065.1	155617	155617	type	True	78.007	190	1375	95	below_threshold
Enterococcus silesiacus	strain=DSM 22801	GCA_001886225.1	332949	332949	type	True	77.8156	195	1375	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_002813755.1	53346	53346	type	True	77.7964	98	1375	95	below_threshold
Enterococcus mundtii	strain=NBRC 100490	GCA_007990125.1	53346	53346	type	True	77.7382	93	1375	95	below_threshold
Enterococcus faecalis	strain=ATCC 19433	GCA_000392875.1	1351	1351	type	True	77.6393	129	1375	95	below_threshold
Enterococcus faecalis	strain=PartL-Efaecalis-RM8376	GCA_022869705.1	1351	1351	type	True	77.5762	125	1375	95	below_threshold
Enterococcus mundtii	strain=DSM 4838	GCA_001886035.1	53346	53346	type	True	77.4765	94	1375	95	below_threshold
Enterococcus faecalis	strain=NBRC 100480	GCA_001544235.1	1351	1351	type	True	77.4038	132	1375	95	below_threshold
Enterococcus faecalis	strain=NCTC 775	GCA_015311765.1	1351	1351	type	True	77.2799	129	1375	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:50,910] [INFO] DFAST Taxonomy check result was written to GCF_017830045.1_ASM1783004v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:50,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:50,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:50,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2721a30b-50b5-4894-ae6a-6a0d954ff71f/dqc_reference/checkm_data
[2024-01-24 13:13:50,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:50,953] [INFO] Task started: CheckM
[2024-01-24 13:13:50,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017830045.1_ASM1783004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017830045.1_ASM1783004v1_genomic.fna/checkm_input GCF_017830045.1_ASM1783004v1_genomic.fna/checkm_result
[2024-01-24 13:14:26,566] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:26,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:26,590] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:26,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:26,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017830045.1_ASM1783004v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:26,591] [INFO] Task started: Blastn
[2024-01-24 13:14:26,591] [INFO] Running command: blastn -query GCF_017830045.1_ASM1783004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2721a30b-50b5-4894-ae6a-6a0d954ff71f/dqc_reference/reference_markers_gtdb.fasta -out GCF_017830045.1_ASM1783004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:27,390] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:27,393] [INFO] Selected 14 target genomes.
[2024-01-24 13:14:27,394] [INFO] Target genome list was writen to GCF_017830045.1_ASM1783004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:27,472] [INFO] Task started: fastANI
[2024-01-24 13:14:27,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb0d20ad-27ae-426a-bc02-927b9db08470/GCF_017830045.1_ASM1783004v1_genomic.fna.gz --refList GCF_017830045.1_ASM1783004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017830045.1_ASM1783004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:37,263] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:37,274] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:37,274] [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_017830045.1	s__Enterococcus sp017830045	100.0	1375	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016745255.1	s__Enterococcus sp016745255	81.8447	829	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002140975.1	s__Enterococcus sp002140975	80.9644	784	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745275.1	s__Enterococcus sp016745275	78.3195	359	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197645.1	s__Enterococcus wangshanyuanii	78.2283	201	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001742285.1	s__Enterococcus rivorum	78.133	136	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000407145.1	s__Enterococcus caccae	78.1195	191	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.98	1.00	1.00	4	-
GCF_001730285.1	s__Enterococcus ureasiticus	78.035	178	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	96.19	96.18	0.80	0.79	3	-
GCF_000633635.1	s__Enterococcus crotali	78.018	190	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.61	98.61	0.93	0.93	2	-
GCF_002813755.1	s__Enterococcus_B mundtii	77.7964	98	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	99.56	98.27	0.96	0.86	24	-
GCF_000392875.1	s__Enterococcus faecalis	77.6393	129	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.66	96.80	0.89	0.77	1902	-
GCF_002947535.1	s__Enterococcus_B mundtii_B	77.5129	90	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	97.82	97.77	0.91	0.90	3	-
GCF_017316305.1	s__Enterococcus_B sp017316305	77.3167	96	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.83	98.79	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:37,279] [INFO] GTDB search result was written to GCF_017830045.1_ASM1783004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:37,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:37,284] [INFO] DFAST_QC result json was written to GCF_017830045.1_ASM1783004v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:37,284] [INFO] DFAST_QC completed!
[2024-01-24 13:14:37,284] [INFO] Total running time: 0h1m12s