[2024-01-25 17:46:05,615] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:05,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:05,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d09a82e-6885-4536-8564-b17e6efbaca9/dqc_reference
[2024-01-25 17:46:06,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:06,798] [INFO] Task started: Prodigal
[2024-01-25 17:46:06,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg19d0533d-7588-46ef-9d9a-65c735eca012/GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna.gz | prodigal -d GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/cds.fna -a GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:17,416] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:17,416] [INFO] Task started: HMMsearch
[2024-01-25 17:46:17,416] [INFO] Running command: hmmsearch --tblout GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d09a82e-6885-4536-8564-b17e6efbaca9/dqc_reference/reference_markers.hmm GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:17,727] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:17,728] [INFO] Found 6/6 markers.
[2024-01-25 17:46:17,774] [INFO] Query marker FASTA was written to GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/markers.fasta
[2024-01-25 17:46:17,774] [INFO] Task started: Blastn
[2024-01-25 17:46:17,774] [INFO] Running command: blastn -query GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d09a82e-6885-4536-8564-b17e6efbaca9/dqc_reference/reference_markers.fasta -out GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:18,363] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:18,365] [INFO] Selected 17 target genomes.
[2024-01-25 17:46:18,366] [INFO] Target genome list was writen to GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:18,379] [INFO] Task started: fastANI
[2024-01-25 17:46:18,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg19d0533d-7588-46ef-9d9a-65c735eca012/GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna.gz --refList GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/target_genomes.txt --output GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:30,487] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:30,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d09a82e-6885-4536-8564-b17e6efbaca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:30,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d09a82e-6885-4536-8564-b17e6efbaca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:30,496] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:46:30,496] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:30,496] [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 pallens	strain=ATCC BAA-351	GCA_000393975.1	160454	160454	type	True	99.9982	1808	1823	95	conclusive
Enterococcus pallens	strain=ATCC BAA-351	GCA_000407485.1	160454	160454	type	True	99.9813	1792	1823	95	conclusive
Enterococcus pallens	strain=DSM 15690	GCA_001886075.1	160454	160454	type	True	99.9504	1667	1823	95	conclusive
Enterococcus florum	strain=Gos25-1	GCA_004309355.1	2480627	2480627	type	True	79.4476	370	1823	95	below_threshold
Enterococcus pseudoavium	strain=NBRC 100491	GCA_001544295.1	44007	44007	type	True	78.786	208	1823	95	below_threshold
Enterococcus dongliensis	strain=63-4	GCA_005405225.1	2559925	2559925	type	True	78.5165	171	1823	95	below_threshold
Enterococcus pingfangensis	strain=241-2-2	GCA_005405205.1	2559924	2559924	type	True	78.482	167	1823	95	below_threshold
Enterococcus viikkiensis	strain=LMG 26075	GCA_005405345.1	930854	930854	type	True	78.4597	211	1823	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	78.3289	287	1823	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	78.1257	228	1823	95	below_threshold
Enterococcus wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	78.0039	112	1823	95	below_threshold
Enterococcus alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	77.905	71	1823	95	below_threshold
Enterococcus rotai	strain=LMG 26678	GCA_001465345.1	118060	118060	type	True	77.8251	103	1823	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:30,497] [INFO] DFAST Taxonomy check result was written to GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:30,498] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:30,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:30,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d09a82e-6885-4536-8564-b17e6efbaca9/dqc_reference/checkm_data
[2024-01-25 17:46:30,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:30,551] [INFO] Task started: CheckM
[2024-01-25 17:46:30,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/checkm_input GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/checkm_result
[2024-01-25 17:47:04,535] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:04,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:04,561] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:04,561] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:04,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/markers.fasta)
[2024-01-25 17:47:04,561] [INFO] Task started: Blastn
[2024-01-25 17:47:04,561] [INFO] Running command: blastn -query GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d09a82e-6885-4536-8564-b17e6efbaca9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:05,329] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:05,337] [INFO] Selected 16 target genomes.
[2024-01-25 17:47:05,337] [INFO] Target genome list was writen to GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:05,348] [INFO] Task started: fastANI
[2024-01-25 17:47:05,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg19d0533d-7588-46ef-9d9a-65c735eca012/GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna.gz --refList GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:16,843] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:16,853] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:16,853] [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_000407485.1	s__Enterococcus_A pallens	99.9815	1792	1823	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.99	99.98	1.00	0.99	3	conclusive
GCF_017377655.1	s__Enterococcus_A sp017377655	84.4976	1192	1823	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_017377575.1	s__Enterococcus_A sp017377575	80.7398	708	1823	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_004309355.1	s__Enterococcus_A florum	79.4336	371	1823	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_001544295.1	s__Enterococcus_A pseudoavium	78.786	208	1823	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_000406965.1	s__Enterococcus_A avium	78.6726	296	1823	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.01	97.91	0.91	0.78	43	-
GCF_011397115.1	s__Enterococcus_C saigonensis	78.6686	110	1823	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_005405225.1	s__Enterococcus_A dongliensis	78.5165	171	1823	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_005405205.1	s__Enterococcus_A pingfangensis	78.482	167	1823	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_005405345.1	s__Enterococcus_A viikkiensis	78.4597	211	1823	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_005405365.1	s__Enterococcus_A xiangfangensis	78.4234	199	1823	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.65	99.31	0.96	0.92	3	-
GCF_018917525.1	s__Enterococcus_A raffinosus_A	78.1985	270	1823	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_019218635.1	s__Enterococcus_A sp019218635	78.1413	227	1823	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_002197645.1	s__Enterococcus wangshanyuanii	78.0051	112	1823	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014635985.1	s__Enterococcus_I alcedinis	77.905	71	1823	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:16,855] [INFO] GTDB search result was written to GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:16,855] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:16,859] [INFO] DFAST_QC result json was written to GCF_000393975.1_Ente_pall_BAA-351_V1_genomic.fna/dqc_result.json
[2024-01-25 17:47:16,859] [INFO] DFAST_QC completed!
[2024-01-25 17:47:16,859] [INFO] Total running time: 0h1m11s