[2024-01-24 12:53:54,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:54,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:54,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d7508f6-c15f-4efc-8c54-1bf4f01c7587/dqc_reference
[2024-01-24 12:53:56,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:56,103] [INFO] Task started: Prodigal
[2024-01-24 12:53:56,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg281f16d7-a4ea-41de-be05-1e4f37b54028/GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna.gz | prodigal -d GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/cds.fna -a GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:01,988] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:01,989] [INFO] Task started: HMMsearch
[2024-01-24 12:54:01,989] [INFO] Running command: hmmsearch --tblout GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d7508f6-c15f-4efc-8c54-1bf4f01c7587/dqc_reference/reference_markers.hmm GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:02,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:02,287] [INFO] Found 6/6 markers.
[2024-01-24 12:54:02,311] [INFO] Query marker FASTA was written to GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/markers.fasta
[2024-01-24 12:54:02,312] [INFO] Task started: Blastn
[2024-01-24 12:54:02,312] [INFO] Running command: blastn -query GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7508f6-c15f-4efc-8c54-1bf4f01c7587/dqc_reference/reference_markers.fasta -out GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:02,882] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:02,887] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:02,887] [INFO] Target genome list was writen to GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:02,931] [INFO] Task started: fastANI
[2024-01-24 12:54:02,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg281f16d7-a4ea-41de-be05-1e4f37b54028/GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna.gz --refList GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/target_genomes.txt --output GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:08,732] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:08,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d7508f6-c15f-4efc-8c54-1bf4f01c7587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:08,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d7508f6-c15f-4efc-8c54-1bf4f01c7587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:08,749] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:54:08,749] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:08,749] [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 dispar	strain=ATCC 51266	GCA_000406945.1	44009	44009	type	True	99.9966	935	939	95	conclusive
Enterococcus dispar	strain=ATCC 51266	GCA_000407585.1	44009	44009	type	True	99.9857	934	939	95	conclusive
Enterococcus dispar	strain=DSM 6630	GCA_001886105.1	44009	44009	type	True	99.958	884	939	95	conclusive
Enterococcus canintestini	strain=DSM 21207	GCA_001885735.1	317010	317010	type	True	86.3014	679	939	95	below_threshold
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	83.1598	623	939	95	below_threshold
Enterococcus mediterraneensis	strain=Marseille-P4358	GCA_900604485.1	2364791	2364791	type	True	80.1536	147	939	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	78.6022	121	939	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	78.364	107	939	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:08,751] [INFO] DFAST Taxonomy check result was written to GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:08,753] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:08,754] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:08,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d7508f6-c15f-4efc-8c54-1bf4f01c7587/dqc_reference/checkm_data
[2024-01-24 12:54:08,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:08,785] [INFO] Task started: CheckM
[2024-01-24 12:54:08,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/checkm_input GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/checkm_result
[2024-01-24 12:54:32,692] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:32,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:32,711] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:32,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:32,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/markers.fasta)
[2024-01-24 12:54:32,712] [INFO] Task started: Blastn
[2024-01-24 12:54:32,712] [INFO] Running command: blastn -query GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7508f6-c15f-4efc-8c54-1bf4f01c7587/dqc_reference/reference_markers_gtdb.fasta -out GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:33,488] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:33,492] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:33,492] [INFO] Target genome list was writen to GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:33,507] [INFO] Task started: fastANI
[2024-01-24 12:54:33,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg281f16d7-a4ea-41de-be05-1e4f37b54028/GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna.gz --refList GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:39,967] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:39,979] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:39,979] [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_000406945.1	s__Enterococcus_C dispar	99.9966	935	939	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	99.61	99.21	0.95	0.90	5	conclusive
GCF_001885735.1	s__Enterococcus_C canintestini	86.2826	680	939	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.44	98.44	0.92	0.92	2	-
GCF_017316025.1	s__Enterococcus_C sp017316025	83.603	654	939	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_011397115.1	s__Enterococcus_C saigonensis	83.1423	623	939	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_900604485.1	s__Enterococcus_C mediterraneensis	79.9259	145	939	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_017315945.1	s__Enterococcus_B sp017315945	79.8852	147	939	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_001544375.1	s__Enterococcus_H canis	79.1043	111	939	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_H	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002140915.1	s__Enterococcus_D sp002140915	79.0123	116	939	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909125.1	s__Enterococcus_I lemanii	78.171	126	939	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_017316125.1	s__Enterococcus_B sp017316125	78.0691	138	939	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_009933335.1	s__Enterococcus_F sp009933335	77.7855	139	939	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_017426705.1	s__Enterococcus_F sp017426705	77.5653	162	939	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:39,981] [INFO] GTDB search result was written to GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:39,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:39,985] [INFO] DFAST_QC result json was written to GCF_000406945.1_Ente_disp_ATCC51266_V1_genomic.fna/dqc_result.json
[2024-01-24 12:54:39,985] [INFO] DFAST_QC completed!
[2024-01-24 12:54:39,986] [INFO] Total running time: 0h0m45s