[2024-01-24 13:40:28,543] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ed195b8-670d-4863-8a69-b87bdfc0edc9/dqc_reference
[2024-01-24 13:40:31,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,145] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,145] [INFO] Running command: gunzip -c /var/lib/cwl/stgee2a3e5e-f613-410a-aa14-0dad1caf60e3/GCF_001050095.1_Enterococcus_massiliensis_genomic.fna.gz | prodigal -d GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/cds.fna -a GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:37,778] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:37,778] [INFO] Task started: HMMsearch
[2024-01-24 13:40:37,779] [INFO] Running command: hmmsearch --tblout GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ed195b8-670d-4863-8a69-b87bdfc0edc9/dqc_reference/reference_markers.hmm GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:38,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:38,057] [INFO] Found 6/6 markers.
[2024-01-24 13:40:38,088] [INFO] Query marker FASTA was written to GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/markers.fasta
[2024-01-24 13:40:38,088] [INFO] Task started: Blastn
[2024-01-24 13:40:38,088] [INFO] Running command: blastn -query GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ed195b8-670d-4863-8a69-b87bdfc0edc9/dqc_reference/reference_markers.fasta -out GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:38,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:38,725] [INFO] Selected 28 target genomes.
[2024-01-24 13:40:38,726] [INFO] Target genome list was writen to GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/target_genomes.txt
[2024-01-24 13:40:38,736] [INFO] Task started: fastANI
[2024-01-24 13:40:38,736] [INFO] Running command: fastANI --query /var/lib/cwl/stgee2a3e5e-f613-410a-aa14-0dad1caf60e3/GCF_001050095.1_Enterococcus_massiliensis_genomic.fna.gz --refList GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/target_genomes.txt --output GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:51,210] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:51,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ed195b8-670d-4863-8a69-b87bdfc0edc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:51,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ed195b8-670d-4863-8a69-b87bdfc0edc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:51,230] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:40:51,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:40:51,230] [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 durans	strain=FDAARGOS 1437	GCA_019048325.1	53345	53345	type	True	80.4722	155	901	95	below_threshold
Enterococcus durans	strain=NBRC 100479	GCA_001544215.1	53345	53345	type	True	80.3151	151	901	95	below_threshold
Enterococcus mediterraneensis	strain=Marseille-P4358	GCA_900604485.1	2364791	2364791	type	True	79.9115	377	901	95	below_threshold
Enterococcus xiangfangensis	strain=11097	GCA_005405365.1	1296537	1296537	type	True	79.8649	135	901	95	below_threshold
Enterococcus thailandicus	strain=NBRC 101867	GCA_007989705.1	417368	417368	type	True	79.1805	157	901	95	below_threshold
Enterococcus casseliflavus	strain=FDAARGOS_1120	GCA_016727345.1	37734	37734	type	True	79.159	181	901	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	79.0768	137	901	95	below_threshold
Enterococcus thailandicus	strain=DSM 21767	GCA_001886265.1	417368	417368	type	True	79.0496	155	901	95	below_threshold
Enterococcus pingfangensis	strain=241-2-2	GCA_005405205.1	2559924	2559924	type	True	78.9939	122	901	95	below_threshold
Enterococcus casseliflavus	strain=NCTC12361	GCA_900447665.1	37734	37734	type	True	78.8526	176	901	95	below_threshold
Enterococcus casseliflavus	strain=NBRC 100478	GCA_001544095.1	37734	37734	type	True	78.7267	174	901	95	below_threshold
Enterococcus casseliflavus	strain=DSM 20680	GCA_001885845.1	37734	37734	type	True	78.7154	174	901	95	below_threshold
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000394035.1	154621	154621	type	True	78.5698	138	901	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	78.5167	138	901	95	below_threshold
Vagococcus zengguangii	strain=MN-17	GCA_005145005.1	2571750	2571750	type	True	78.4967	51	901	95	below_threshold
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000407505.1	154621	154621	type	True	78.4608	138	901	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000407425.1	1354	1354	type	True	78.4155	139	901	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000393835.1	1354	1354	type	True	78.3214	138	901	95	below_threshold
Enterococcus hirae	strain=DSM 20160	GCA_001885955.1	1354	1354	type	True	78.0498	139	901	95	below_threshold
Enterococcus canintestini	strain=DSM 21207	GCA_001885735.1	317010	317010	type	True	77.9674	142	901	95	below_threshold
Enterococcus wangshanyuanii	strain=MN05	GCA_002197645.1	2005703	2005703	type	True	77.8819	108	901	95	below_threshold
Enterococcus termitis	strain=LMG 8895	GCA_001730305.1	332950	332950	type	True	77.6341	103	901	95	below_threshold
Enterococcus termitis	strain=DSM 22803	GCA_001886275.1	332950	332950	type	True	77.6031	98	901	95	below_threshold
Enterococcus villorum	strain=NBRC 100699	GCA_007990225.1	112904	112904	type	True	77.4939	134	901	95	below_threshold
Enterococcus alishanensis	strain=ALS3	GCA_019218635.1	1303817	1303817	type	True	77.2662	111	901	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:51,232] [INFO] DFAST Taxonomy check result was written to GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/tc_result.tsv
[2024-01-24 13:40:51,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:51,233] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:51,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ed195b8-670d-4863-8a69-b87bdfc0edc9/dqc_reference/checkm_data
[2024-01-24 13:40:51,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:51,266] [INFO] Task started: CheckM
[2024-01-24 13:40:51,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/checkm_input GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/checkm_result
[2024-01-24 13:41:18,143] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:18,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:18,171] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:18,171] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:18,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/markers.fasta)
[2024-01-24 13:41:18,172] [INFO] Task started: Blastn
[2024-01-24 13:41:18,172] [INFO] Running command: blastn -query GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ed195b8-670d-4863-8a69-b87bdfc0edc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:18,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:18,992] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:18,993] [INFO] Target genome list was writen to GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:19,013] [INFO] Task started: fastANI
[2024-01-24 13:41:19,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgee2a3e5e-f613-410a-aa14-0dad1caf60e3/GCF_001050095.1_Enterococcus_massiliensis_genomic.fna.gz --refList GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/target_genomes_gtdb.txt --output GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:29,137] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:29,226] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:29,226] [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_005405265.1	s__Enterococcus_C songbeiensis	98.6807	638	901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	98.82	98.68	0.87	0.87	4	conclusive
GCF_001544215.1	s__Enterococcus_B durans	80.3541	150	901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.77	96.42	0.88	0.77	135	-
GCF_011397115.1	s__Enterococcus_C saigonensis	79.8752	159	901	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	79.8704	376	901	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_005405365.1	s__Enterococcus_A xiangfangensis	79.8649	135	901	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_002850555.1	s__Enterococcus_D sp002850555	79.0913	165	901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.34	95.31	0.87	0.74	46	-
GCF_001886265.1	s__Enterococcus_B thailandicus	79.0496	155	901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.46	99.20	0.93	0.90	6	-
GCF_005405205.1	s__Enterococcus_A pingfangensis	78.9939	122	901	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_009933175.1	s__Enterococcus_B sp009933175	78.921	131	901	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_002140915.1	s__Enterococcus_D sp002140915	78.7972	163	901	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_001544095.1	s__Enterococcus_D casseliflavus	78.7518	173	901	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_017315945.1	s__Enterococcus_B sp017315945	78.6222	137	901	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_011038845.1	s__Enterococcus_B sp011038845	78.1367	118	901	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_009933335.1	s__Enterococcus_F sp009933335	78.0626	128	901	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_001465345.1	s__Enterococcus rotai	77.9868	110	901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885735.1	s__Enterococcus_C canintestini	77.9424	143	901	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_009933135.1	s__Enterococcus_C sp009933135	77.7806	126	901	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_001730305.1	s__Enterococcus termitis	77.6659	102	901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007990225.1	s__Enterococcus_B villorum	77.5413	132	901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.96	97.46	0.94	0.89	6	-
GCF_000415185.1	s__Enterococcus_B faecalis_A	77.517	159	901	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	77.2861	75	901	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 13:41:29,228] [INFO] GTDB search result was written to GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:29,229] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:29,235] [INFO] DFAST_QC result json was written to GCF_001050095.1_Enterococcus_massiliensis_genomic.fna/dqc_result.json
[2024-01-24 13:41:29,235] [INFO] DFAST_QC completed!
[2024-01-24 13:41:29,236] [INFO] Total running time: 0h1m1s