[2023-06-27 13:42:40,035] [INFO] DFAST_QC pipeline started.
[2023-06-27 13:42:40,038] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 13:42:40,038] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e7ecac2-0543-48a2-8a14-8d3cc891f778/dqc_reference
[2023-06-27 13:42:42,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 13:42:42,295] [INFO] Task started: Prodigal
[2023-06-27 13:42:42,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg3aaddd96-9eba-4499-abde-28d50f2038ff/GCA_002359455.1_ASM235945v1_genomic.fna.gz | prodigal -d GCA_002359455.1_ASM235945v1_genomic.fna/cds.fna -a GCA_002359455.1_ASM235945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 13:42:49,200] [INFO] Task succeeded: Prodigal
[2023-06-27 13:42:49,201] [INFO] Task started: HMMsearch
[2023-06-27 13:42:49,201] [INFO] Running command: hmmsearch --tblout GCA_002359455.1_ASM235945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e7ecac2-0543-48a2-8a14-8d3cc891f778/dqc_reference/reference_markers.hmm GCA_002359455.1_ASM235945v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 13:42:49,443] [INFO] Task succeeded: HMMsearch
[2023-06-27 13:42:49,445] [INFO] Found 6/6 markers.
[2023-06-27 13:42:49,474] [INFO] Query marker FASTA was written to GCA_002359455.1_ASM235945v1_genomic.fna/markers.fasta
[2023-06-27 13:42:49,475] [INFO] Task started: Blastn
[2023-06-27 13:42:49,475] [INFO] Running command: blastn -query GCA_002359455.1_ASM235945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e7ecac2-0543-48a2-8a14-8d3cc891f778/dqc_reference/reference_markers.fasta -out GCA_002359455.1_ASM235945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:42:50,138] [INFO] Task succeeded: Blastn
[2023-06-27 13:42:50,142] [INFO] Selected 13 target genomes.
[2023-06-27 13:42:50,142] [INFO] Target genome list was writen to GCA_002359455.1_ASM235945v1_genomic.fna/target_genomes.txt
[2023-06-27 13:42:50,147] [INFO] Task started: fastANI
[2023-06-27 13:42:50,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aaddd96-9eba-4499-abde-28d50f2038ff/GCA_002359455.1_ASM235945v1_genomic.fna.gz --refList GCA_002359455.1_ASM235945v1_genomic.fna/target_genomes.txt --output GCA_002359455.1_ASM235945v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 13:42:57,816] [INFO] Task succeeded: fastANI
[2023-06-27 13:42:57,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e7ecac2-0543-48a2-8a14-8d3cc891f778/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 13:42:57,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e7ecac2-0543-48a2-8a14-8d3cc891f778/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 13:42:57,831] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-27 13:42:57,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 13:42:57,831] [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 casseliflavus	strain=FDAARGOS_1120	GCA_016727345.1	37734	37734	type	True	95.6522	819	911	95	conclusive
Enterococcus casseliflavus	strain=NBRC 100478	GCA_001544095.1	37734	37734	type	True	95.642	804	911	95	conclusive
Enterococcus casseliflavus	strain=DSM 20680	GCA_001885845.1	37734	37734	type	True	95.6205	812	911	95	conclusive
Enterococcus casseliflavus	strain=NCTC12361	GCA_900447665.1	37734	37734	type	True	95.5863	825	911	95	conclusive
Enterococcus gallinarum	strain=DSM 24841	GCA_001886155.1	1353	1353	suspected-type	True	79.4027	349	911	95	below_threshold
Enterococcus lactis	strain=CCM 8412	GCA_015751045.1	357441	357441	type	True	77.7625	97	911	95	below_threshold
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	77.4733	90	911	95	below_threshold
Enterococcus dispar	strain=DSM 6630	GCA_001886105.1	44009	44009	type	True	77.4453	82	911	95	below_threshold
Enterococcus saigonensis	strain=VE80	GCA_011397115.1	1805431	1805431	type	True	77.3507	70	911	95	below_threshold
Enterococcus larvae	strain=BWM-S5	GCA_017830045.1	2794352	2794352	type	True	76.8176	71	911	95	below_threshold
Enterococcus aquimarinus	strain=DSM 17690	GCA_001885765.1	328396	328396	type	True	76.8	75	911	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 13:42:57,833] [INFO] DFAST Taxonomy check result was written to GCA_002359455.1_ASM235945v1_genomic.fna/tc_result.tsv
[2023-06-27 13:42:57,834] [INFO] ===== Taxonomy check completed =====
[2023-06-27 13:42:57,834] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 13:42:57,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e7ecac2-0543-48a2-8a14-8d3cc891f778/dqc_reference/checkm_data
[2023-06-27 13:42:57,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 13:42:57,870] [INFO] Task started: CheckM
[2023-06-27 13:42:57,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002359455.1_ASM235945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002359455.1_ASM235945v1_genomic.fna/checkm_input GCA_002359455.1_ASM235945v1_genomic.fna/checkm_result
[2023-06-27 13:43:25,322] [INFO] Task succeeded: CheckM
[2023-06-27 13:43:25,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.08%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 13:43:25,345] [INFO] ===== Completeness check finished =====
[2023-06-27 13:43:25,346] [INFO] ===== Start GTDB Search =====
[2023-06-27 13:43:25,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002359455.1_ASM235945v1_genomic.fna/markers.fasta)
[2023-06-27 13:43:25,346] [INFO] Task started: Blastn
[2023-06-27 13:43:25,347] [INFO] Running command: blastn -query GCA_002359455.1_ASM235945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e7ecac2-0543-48a2-8a14-8d3cc891f778/dqc_reference/reference_markers_gtdb.fasta -out GCA_002359455.1_ASM235945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:43:26,304] [INFO] Task succeeded: Blastn
[2023-06-27 13:43:26,308] [INFO] Selected 10 target genomes.
[2023-06-27 13:43:26,308] [INFO] Target genome list was writen to GCA_002359455.1_ASM235945v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 13:43:26,317] [INFO] Task started: fastANI
[2023-06-27 13:43:26,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aaddd96-9eba-4499-abde-28d50f2038ff/GCA_002359455.1_ASM235945v1_genomic.fna.gz --refList GCA_002359455.1_ASM235945v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002359455.1_ASM235945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 13:43:32,778] [INFO] Task succeeded: fastANI
[2023-06-27 13:43:32,788] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-27 13:43:32,788] [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_001544095.1	s__Enterococcus_D casseliflavus	95.642	804	911	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	98.00	95.35	0.87	0.83	83	inconclusive
GCF_002850555.1	s__Enterococcus_D sp002850555	95.4652	847	911	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.34	95.31	0.87	0.74	46	inconclusive
GCF_002140915.1	s__Enterococcus_D sp002140915	79.9362	401	911	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_001297065.1	s__Enterococcus_D sp001297065	79.7559	421	911	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.01	96.72	0.90	0.84	5	-
GCF_001544275.1	s__Enterococcus_D gallinarum	79.3922	346	911	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_D	95.0	97.60	97.23	0.85	0.80	74	-
GCF_017426705.1	s__Enterococcus_F sp017426705	77.8069	107	911	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_013394305.1	s__Enterococcus_B pernyi	77.693	122	911	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	96.3614	98.21	97.00	0.90	0.84	22	-
GCF_017316305.1	s__Enterococcus_B sp017316305	77.6706	119	911	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	98.83	98.79	0.92	0.91	3	-
GCF_011397115.1	s__Enterococcus_C saigonensis	77.3507	70	911	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_017316025.1	s__Enterococcus_C sp017316025	77.3319	83	911	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 13:43:32,790] [INFO] GTDB search result was written to GCA_002359455.1_ASM235945v1_genomic.fna/result_gtdb.tsv
[2023-06-27 13:43:32,791] [INFO] ===== GTDB Search completed =====
[2023-06-27 13:43:32,794] [INFO] DFAST_QC result json was written to GCA_002359455.1_ASM235945v1_genomic.fna/dqc_result.json
[2023-06-27 13:43:32,794] [INFO] DFAST_QC completed!
[2023-06-27 13:43:32,794] [INFO] Total running time: 0h0m53s