[2024-01-25 19:47:21,388] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:21,389] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:21,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ee110f2-1135-42c3-b0a6-b09efe01eee9/dqc_reference
[2024-01-25 19:47:22,572] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:22,572] [INFO] Task started: Prodigal
[2024-01-25 19:47:22,573] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f49fa3c-bc21-4e58-b93b-d3ada4d0f5e9/GCF_947055815.1_DSM_20682_assembly_genomic.fna.gz | prodigal -d GCF_947055815.1_DSM_20682_assembly_genomic.fna/cds.fna -a GCF_947055815.1_DSM_20682_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:26,716] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:26,716] [INFO] Task started: HMMsearch
[2024-01-25 19:47:26,716] [INFO] Running command: hmmsearch --tblout GCF_947055815.1_DSM_20682_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ee110f2-1135-42c3-b0a6-b09efe01eee9/dqc_reference/reference_markers.hmm GCF_947055815.1_DSM_20682_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:26,999] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:27,000] [INFO] Found 6/6 markers.
[2024-01-25 19:47:27,032] [INFO] Query marker FASTA was written to GCF_947055815.1_DSM_20682_assembly_genomic.fna/markers.fasta
[2024-01-25 19:47:27,032] [INFO] Task started: Blastn
[2024-01-25 19:47:27,032] [INFO] Running command: blastn -query GCF_947055815.1_DSM_20682_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ee110f2-1135-42c3-b0a6-b09efe01eee9/dqc_reference/reference_markers.fasta -out GCF_947055815.1_DSM_20682_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:27,608] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:27,611] [INFO] Selected 10 target genomes.
[2024-01-25 19:47:27,612] [INFO] Target genome list was writen to GCF_947055815.1_DSM_20682_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:47:27,629] [INFO] Task started: fastANI
[2024-01-25 19:47:27,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f49fa3c-bc21-4e58-b93b-d3ada4d0f5e9/GCF_947055815.1_DSM_20682_assembly_genomic.fna.gz --refList GCF_947055815.1_DSM_20682_assembly_genomic.fna/target_genomes.txt --output GCF_947055815.1_DSM_20682_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:33,440] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:33,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ee110f2-1135-42c3-b0a6-b09efe01eee9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:33,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ee110f2-1135-42c3-b0a6-b09efe01eee9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:33,447] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:47:33,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:33,447] [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 cecorum	strain=NCTC12421	GCA_900474605.1	44008	44008	type	True	99.9976	765	768	95	conclusive
Enterococcus cecorum	strain=ATCC 43198	GCA_000492155.1	44008	44008	type	True	99.997	763	768	95	conclusive
Enterococcus cecorum	strain=ATCC 43198	GCA_000407565.1	44008	44008	type	True	99.9936	762	768	95	conclusive
Enterococcus cecorum	strain=DSM 20682	GCA_000379745.1	44008	44008	type	True	99.9695	749	768	95	conclusive
Enterococcus cecorum	strain=DSM 20682	GCA_001885885.1	44008	44008	type	True	99.9493	722	768	95	conclusive
Enterococcus hirae	strain=ATCC 9790	GCA_000271405.2	1354	1354	type	True	78.9326	92	768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:33,448] [INFO] DFAST Taxonomy check result was written to GCF_947055815.1_DSM_20682_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:47:33,449] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:33,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:33,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ee110f2-1135-42c3-b0a6-b09efe01eee9/dqc_reference/checkm_data
[2024-01-25 19:47:33,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:33,478] [INFO] Task started: CheckM
[2024-01-25 19:47:33,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_947055815.1_DSM_20682_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_947055815.1_DSM_20682_assembly_genomic.fna/checkm_input GCF_947055815.1_DSM_20682_assembly_genomic.fna/checkm_result
[2024-01-25 19:47:52,029] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:52,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:52,056] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:52,057] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:52,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_947055815.1_DSM_20682_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:47:52,057] [INFO] Task started: Blastn
[2024-01-25 19:47:52,057] [INFO] Running command: blastn -query GCF_947055815.1_DSM_20682_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ee110f2-1135-42c3-b0a6-b09efe01eee9/dqc_reference/reference_markers_gtdb.fasta -out GCF_947055815.1_DSM_20682_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:52,853] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:52,856] [INFO] Selected 19 target genomes.
[2024-01-25 19:47:52,856] [INFO] Target genome list was writen to GCF_947055815.1_DSM_20682_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:52,879] [INFO] Task started: fastANI
[2024-01-25 19:47:52,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f49fa3c-bc21-4e58-b93b-d3ada4d0f5e9/GCF_947055815.1_DSM_20682_assembly_genomic.fna.gz --refList GCF_947055815.1_DSM_20682_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_947055815.1_DSM_20682_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:01,920] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:01,930] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:01,931] [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_000407565.1	s__Enterococcus_E cecorum	99.9936	762	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	97.77	96.06	0.87	0.77	49	conclusive
GCA_019120335.1	s__Enterococcus_E stercoripullorum	94.9503	574	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000406925.1	s__Enterococcus_E columbae	80.6134	334	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E	95.0	99.98	99.97	1.00	0.99	4	-
GCF_002140715.1	s__Enterococcus sp002140715	78.8451	78	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000407445.1	s__Enterococcus moraviensis	78.4246	83	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000407505.1	s__Enterococcus_B phoeniculicola	78.3472	95	768	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_001886265.1	s__Enterococcus_B thailandicus	78.15	98	768	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_001730365.1	s__Enterococcus quebecensis	78.0205	78	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003950315.1	s__Vagococcus bubulae	77.9199	66	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017426705.1	s__Enterococcus_F sp017426705	77.9129	148	768	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_009933335.1	s__Enterococcus_F sp009933335	77.8943	126	768	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_003987495.1	s__Vagococcus_D salmoninarum	77.8846	54	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D	95.0	98.18	98.18	0.88	0.88	2	-
GCF_001544255.1	s__Enterococcus_B faecium	77.7859	83	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.30	98.03	0.91	0.72	2177	-
GCF_017316025.1	s__Enterococcus_C sp017316025	77.7569	97	768	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_016908885.1	s__Enterococcus_C diestrammenae	77.5557	68	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	97.93	97.75	0.91	0.88	3	-
GCF_001886195.1	s__Enterococcus_B ratti	77.4837	78	768	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_000423785.1	s__Tetragenococcus muriaticus	76.7747	51	768	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	98.93	98.87	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:01,932] [INFO] GTDB search result was written to GCF_947055815.1_DSM_20682_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:01,933] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:01,935] [INFO] DFAST_QC result json was written to GCF_947055815.1_DSM_20682_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:48:01,935] [INFO] DFAST_QC completed!
[2024-01-25 19:48:01,936] [INFO] Total running time: 0h0m41s