[2024-01-25 20:07:20,486] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:20,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:20,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f20cbf0-668f-4886-8c22-64b0d841b7a5/dqc_reference
[2024-01-25 20:07:21,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:21,696] [INFO] Task started: Prodigal
[2024-01-25 20:07:21,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg060297fa-f8af-4cf6-a9f9-736f883491dc/GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna.gz | prodigal -d GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/cds.fna -a GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:32,083] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:32,084] [INFO] Task started: HMMsearch
[2024-01-25 20:07:32,084] [INFO] Running command: hmmsearch --tblout GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f20cbf0-668f-4886-8c22-64b0d841b7a5/dqc_reference/reference_markers.hmm GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:32,358] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:32,359] [INFO] Found 6/6 markers.
[2024-01-25 20:07:32,406] [INFO] Query marker FASTA was written to GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/markers.fasta
[2024-01-25 20:07:32,406] [INFO] Task started: Blastn
[2024-01-25 20:07:32,406] [INFO] Running command: blastn -query GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f20cbf0-668f-4886-8c22-64b0d841b7a5/dqc_reference/reference_markers.fasta -out GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:32,959] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:32,962] [INFO] Selected 17 target genomes.
[2024-01-25 20:07:32,962] [INFO] Target genome list was writen to GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/target_genomes.txt
[2024-01-25 20:07:32,972] [INFO] Task started: fastANI
[2024-01-25 20:07:32,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg060297fa-f8af-4cf6-a9f9-736f883491dc/GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna.gz --refList GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/target_genomes.txt --output GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:44,345] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:44,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f20cbf0-668f-4886-8c22-64b0d841b7a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:44,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f20cbf0-668f-4886-8c22-64b0d841b7a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:44,355] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:07:44,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:44,355] [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_000407485.1	160454	160454	type	True	100.0	1804	1806	95	conclusive
Enterococcus pallens	strain=ATCC BAA-351	GCA_000393975.1	160454	160454	type	True	99.9771	1792	1806	95	conclusive
Enterococcus pallens	strain=DSM 15690	GCA_001886075.1	160454	160454	type	True	99.9454	1669	1806	95	conclusive
Enterococcus florum	strain=Gos25-1	GCA_004309355.1	2480627	2480627	type	True	79.4422	377	1806	95	below_threshold
Enterococcus pseudoavium	strain=NBRC 100491	GCA_001544295.1	44007	44007	type	True	78.4917	219	1806	95	below_threshold
Enterococcus dongliensis	strain=63-4	GCA_005405225.1	2559925	2559925	type	True	78.393	165	1806	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	78.3612	276	1806	95	below_threshold
Enterococcus pingfangensis	strain=241-2-2	GCA_005405205.1	2559924	2559924	type	True	78.3541	173	1806	95	below_threshold
Enterococcus viikkiensis	strain=LMG 26075	GCA_005405345.1	930854	930854	type	True	78.1819	211	1806	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	78.1085	224	1806	95	below_threshold
Enterococcus wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	77.6576	117	1806	95	below_threshold
Enterococcus rotai	strain=LMG 26678	GCA_001465345.1	118060	118060	type	True	77.5998	101	1806	95	below_threshold
Enterococcus alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	77.2902	78	1806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:44,357] [INFO] DFAST Taxonomy check result was written to GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/tc_result.tsv
[2024-01-25 20:07:44,357] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:44,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:44,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f20cbf0-668f-4886-8c22-64b0d841b7a5/dqc_reference/checkm_data
[2024-01-25 20:07:44,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:44,408] [INFO] Task started: CheckM
[2024-01-25 20:07:44,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/checkm_input GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/checkm_result
[2024-01-25 20:08:18,518] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:18,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:18,539] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:18,539] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:18,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/markers.fasta)
[2024-01-25 20:08:18,540] [INFO] Task started: Blastn
[2024-01-25 20:08:18,540] [INFO] Running command: blastn -query GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f20cbf0-668f-4886-8c22-64b0d841b7a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:19,316] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:19,319] [INFO] Selected 16 target genomes.
[2024-01-25 20:08:19,320] [INFO] Target genome list was writen to GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:19,329] [INFO] Task started: fastANI
[2024-01-25 20:08:19,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg060297fa-f8af-4cf6-a9f9-736f883491dc/GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna.gz --refList GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/target_genomes_gtdb.txt --output GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:30,262] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:30,272] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:30,272] [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	100.0	1804	1806	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	84.5669	1173	1806	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	80.5997	718	1806	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	79.4613	375	1806	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	78.5821	287	1806	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_001544295.1	s__Enterococcus_A pseudoavium	78.5094	218	1806	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_005405225.1	s__Enterococcus_A dongliensis	78.393	165	1806	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	78.3541	173	1806	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	78.1845	212	1806	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	78.1535	202	1806	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_019218635.1	s__Enterococcus_A sp019218635	78.0925	225	1806	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_011397115.1	s__Enterococcus_C saigonensis	78.0072	114	1806	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_018917525.1	s__Enterococcus_A raffinosus_A	77.9899	278	1806	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	77.6746	115	1806	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	77.2902	78	1806	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 20:08:30,273] [INFO] GTDB search result was written to GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:30,274] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:30,277] [INFO] DFAST_QC result json was written to GCF_000407485.1_Ente_pall_BAA-351_V2_genomic.fna/dqc_result.json
[2024-01-25 20:08:30,277] [INFO] DFAST_QC completed!
[2024-01-25 20:08:30,277] [INFO] Total running time: 0h1m10s