[2024-01-24 13:01:18,787] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:18,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:18,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg37acef3a-6560-4431-b4fb-410765389dfc/dqc_reference
[2024-01-24 13:01:20,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,044] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,044] [INFO] Running command: gunzip -c /var/lib/cwl/stg1da3f8ac-63ca-4b8c-aa11-d7d7e72bcc5e/GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna.gz | prodigal -d GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/cds.fna -a GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:25,114] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:25,115] [INFO] Task started: HMMsearch
[2024-01-24 13:01:25,115] [INFO] Running command: hmmsearch --tblout GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37acef3a-6560-4431-b4fb-410765389dfc/dqc_reference/reference_markers.hmm GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:25,343] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:25,344] [INFO] Found 6/6 markers.
[2024-01-24 13:01:25,366] [INFO] Query marker FASTA was written to GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/markers.fasta
[2024-01-24 13:01:25,366] [INFO] Task started: Blastn
[2024-01-24 13:01:25,367] [INFO] Running command: blastn -query GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37acef3a-6560-4431-b4fb-410765389dfc/dqc_reference/reference_markers.fasta -out GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:25,955] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:25,959] [INFO] Selected 23 target genomes.
[2024-01-24 13:01:25,959] [INFO] Target genome list was writen to GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:25,967] [INFO] Task started: fastANI
[2024-01-24 13:01:25,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg1da3f8ac-63ca-4b8c-aa11-d7d7e72bcc5e/GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna.gz --refList GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/target_genomes.txt --output GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:35,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:35,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37acef3a-6560-4431-b4fb-410765389dfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:35,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37acef3a-6560-4431-b4fb-410765389dfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:35,742] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:35,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:35,742] [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 sulfureus	strain=ATCC 49903	GCA_000407025.1	1356	1356	type	True	100.0	762	764	95	conclusive
Enterococcus sulfureus	strain=ATCC 49903	GCA_000407605.1	1356	1356	type	True	99.987	756	764	95	conclusive
Enterococcus mediterraneensis	strain=Marseille-P4358	GCA_900604485.1	2364791	2364791	type	True	79.5073	101	764	95	below_threshold
Enterococcus casseliflavus	strain=NCTC12361	GCA_900447665.1	37734	37734	type	True	79.4339	112	764	95	below_threshold
Enterococcus faecalis	strain=ATCC 19433	GCA_000392875.1	1351	1351	type	True	79.0811	113	764	95	below_threshold
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	78.8991	101	764	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	78.8039	185	764	95	below_threshold
Enterococcus haemoperoxidus	strain=ATCC BAA-382	GCA_000407165.1	155618	155618	type	True	78.742	106	764	95	below_threshold
Enterococcus italicus	strain=DSM 15952	GCA_000185365.1	246144	246144	type	True	78.5434	160	764	95	below_threshold
Enterococcus casseliflavus	strain=NBRC 100478	GCA_001544095.1	37734	37734	type	True	78.484	105	764	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407285.1	1814218	41997	type	True	78.4624	177	764	95	below_threshold
Enterococcus italicus	strain=DSM 15952	GCA_001885995.1	246144	246144	type	True	78.4335	145	764	95	below_threshold
Enterococcus casseliflavus	strain=DSM 20680	GCA_001885845.1	37734	37734	type	True	78.4132	105	764	95	below_threshold
Enterococcus saccharolyticus	strain=DSM 20726	GCA_001886235.1	41997	41997	type	True	78.3336	179	764	95	below_threshold
Enterococcus alcedinis	strain=CCM 8433	GCA_014635985.1	1274384	1274384	type	True	77.9114	111	764	95	below_threshold
Enterococcus faecalis	strain=NBRC 100480	GCA_001544235.1	1351	1351	type	True	77.6525	107	764	95	below_threshold
Enterococcus ratti	strain=DSM 15687	GCA_001886195.1	150033	150033	type	True	77.6148	90	764	95	below_threshold
Enterococcus ureilyticus	strain=CCUG 48799	GCA_002806915.1	1131292	1131292	type	True	77.1229	103	764	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:35,744] [INFO] DFAST Taxonomy check result was written to GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:35,745] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:35,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:35,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37acef3a-6560-4431-b4fb-410765389dfc/dqc_reference/checkm_data
[2024-01-24 13:01:35,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:35,772] [INFO] Task started: CheckM
[2024-01-24 13:01:35,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/checkm_input GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/checkm_result
[2024-01-24 13:01:57,778] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:57,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:57,807] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:57,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:57,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/markers.fasta)
[2024-01-24 13:01:57,808] [INFO] Task started: Blastn
[2024-01-24 13:01:57,809] [INFO] Running command: blastn -query GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37acef3a-6560-4431-b4fb-410765389dfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:58,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:58,585] [INFO] Selected 22 target genomes.
[2024-01-24 13:01:58,586] [INFO] Target genome list was writen to GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:58,604] [INFO] Task started: fastANI
[2024-01-24 13:01:58,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg1da3f8ac-63ca-4b8c-aa11-d7d7e72bcc5e/GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna.gz --refList GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:09,253] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:09,283] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:09,283] [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_000407605.1	s__Enterococcus_G sulfureus	99.9882	756	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_G	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_900604485.1	s__Enterococcus_C mediterraneensis	79.3289	100	764	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_000392875.1	s__Enterococcus faecalis	78.9617	111	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.66	96.80	0.89	0.77	1902	-
GCF_011397115.1	s__Enterococcus_C saigonensis	78.8991	101	764	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_002197645.1	s__Enterococcus wangshanyuanii	78.8189	101	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002140715.1	s__Enterococcus sp002140715	78.7813	106	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000271405.2	s__Enterococcus_B hirae	78.6402	132	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.97	97.87	0.92	0.86	203	-
GCF_000415185.1	s__Enterococcus_B faecalis_A	78.5698	107	764	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_000185365.1	s__Enterococcus_G italicus	78.5434	160	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_G	95.0	98.35	97.28	0.93	0.86	7	-
GCF_000407505.1	s__Enterococcus_B phoeniculicola	78.5273	109	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.99	99.99	1.00	1.00	3	-
GCF_011038845.1	s__Enterococcus_B sp011038845	78.4966	91	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.61	99.61	0.98	0.98	2	-
GCF_001544095.1	s__Enterococcus_D casseliflavus	78.484	105	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	98.00	95.35	0.87	0.83	83	-
GCF_009933335.1	s__Enterococcus_F sp009933335	78.4814	143	764	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	78.4403	178	764	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_017316025.1	s__Enterococcus_C sp017316025	78.1903	98	764	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_017426705.1	s__Enterococcus_F sp017426705	78.1574	160	764	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_018917525.1	s__Enterococcus_A raffinosus_A	78.0284	82	764	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_005405265.1	s__Enterococcus_C songbeiensis	77.979	84	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.82	98.68	0.87	0.87	4	-
GCF_014635985.1	s__Enterococcus_I alcedinis	77.9254	111	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016909125.1	s__Enterococcus_I lemanii	77.8061	123	764	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_001886195.1	s__Enterococcus_B ratti	77.6493	89	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116505.1	s__Enterococcus_I avicola	77.5396	103	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:09,285] [INFO] GTDB search result was written to GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:09,285] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:09,290] [INFO] DFAST_QC result json was written to GCF_000407025.1_Ente_sulf_ATCC49903_V1_genomic.fna/dqc_result.json
[2024-01-24 13:02:09,290] [INFO] DFAST_QC completed!
[2024-01-24 13:02:09,290] [INFO] Total running time: 0h0m51s