[2024-01-25 18:55:35,809] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:35,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:35,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ba05105-ecbb-420c-a052-66f6fe97e9b8/dqc_reference
[2024-01-25 18:55:36,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:36,952] [INFO] Task started: Prodigal
[2024-01-25 18:55:36,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bed8152-f1ec-445e-a802-6f40f6c66d0a/GCF_003795145.1_ASM379514v1_genomic.fna.gz | prodigal -d GCF_003795145.1_ASM379514v1_genomic.fna/cds.fna -a GCF_003795145.1_ASM379514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:41,968] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:41,969] [INFO] Task started: HMMsearch
[2024-01-25 18:55:41,969] [INFO] Running command: hmmsearch --tblout GCF_003795145.1_ASM379514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ba05105-ecbb-420c-a052-66f6fe97e9b8/dqc_reference/reference_markers.hmm GCF_003795145.1_ASM379514v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:42,215] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:42,216] [INFO] Found 6/6 markers.
[2024-01-25 18:55:42,240] [INFO] Query marker FASTA was written to GCF_003795145.1_ASM379514v1_genomic.fna/markers.fasta
[2024-01-25 18:55:42,240] [INFO] Task started: Blastn
[2024-01-25 18:55:42,241] [INFO] Running command: blastn -query GCF_003795145.1_ASM379514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ba05105-ecbb-420c-a052-66f6fe97e9b8/dqc_reference/reference_markers.fasta -out GCF_003795145.1_ASM379514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:42,783] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:42,786] [INFO] Selected 14 target genomes.
[2024-01-25 18:55:42,787] [INFO] Target genome list was writen to GCF_003795145.1_ASM379514v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:42,802] [INFO] Task started: fastANI
[2024-01-25 18:55:42,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bed8152-f1ec-445e-a802-6f40f6c66d0a/GCF_003795145.1_ASM379514v1_genomic.fna.gz --refList GCF_003795145.1_ASM379514v1_genomic.fna/target_genomes.txt --output GCF_003795145.1_ASM379514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:50,358] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:50,359] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ba05105-ecbb-420c-a052-66f6fe97e9b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:50,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ba05105-ecbb-420c-a052-66f6fe97e9b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:50,366] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:50,366] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:50,366] [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
Tetragenococcus koreensis	strain=KCTC 3924	GCA_003795145.1	290335	290335	type	True	100.0	908	909	95	conclusive
Tetragenococcus halophilus subsp. halophilus	strain=DSM 20339	GCA_003841405.1	1513897	51669	type	True	81.0117	519	909	95	below_threshold
Tetragenococcus halophilus subsp. flandriensis	strain=DSM 23766	GCA_002922845.1	1513898	51669	type	True	80.7472	445	909	95	below_threshold
Tetragenococcus solitarius	strain=NBRC 100494	GCA_001544195.1	71453	71453	type	True	80.7137	494	909	95	below_threshold
Tetragenococcus muriaticus	strain=DSM 15685	GCA_000423785.1	64642	64642	type	True	80.0047	401	909	95	below_threshold
Enterococcus saccharolyticus subsp. saccharolyticus	strain=ATCC 43076	GCA_000407005.1	1814218	41997	type	True	78.1417	142	909	95	below_threshold
Vagococcus humatus	strain=JCM 31581	GCA_003950325.1	1889241	1889241	type	True	76.8926	56	909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:50,367] [INFO] DFAST Taxonomy check result was written to GCF_003795145.1_ASM379514v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:50,368] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:50,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:50,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ba05105-ecbb-420c-a052-66f6fe97e9b8/dqc_reference/checkm_data
[2024-01-25 18:55:50,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:50,410] [INFO] Task started: CheckM
[2024-01-25 18:55:50,410] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003795145.1_ASM379514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003795145.1_ASM379514v1_genomic.fna/checkm_input GCF_003795145.1_ASM379514v1_genomic.fna/checkm_result
[2024-01-25 18:56:10,560] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:10,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:10,588] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:10,589] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:10,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003795145.1_ASM379514v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:10,589] [INFO] Task started: Blastn
[2024-01-25 18:56:10,589] [INFO] Running command: blastn -query GCF_003795145.1_ASM379514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ba05105-ecbb-420c-a052-66f6fe97e9b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003795145.1_ASM379514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:11,365] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:11,369] [INFO] Selected 12 target genomes.
[2024-01-25 18:56:11,370] [INFO] Target genome list was writen to GCF_003795145.1_ASM379514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:11,388] [INFO] Task started: fastANI
[2024-01-25 18:56:11,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bed8152-f1ec-445e-a802-6f40f6c66d0a/GCF_003795145.1_ASM379514v1_genomic.fna.gz --refList GCF_003795145.1_ASM379514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003795145.1_ASM379514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:17,385] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:17,392] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:17,392] [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_003795145.1	s__Tetragenococcus koreensis	100.0	908	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	99.21	98.98	0.92	0.90	7	conclusive
GCF_003795125.1	s__Tetragenococcus osmophilus	81.1154	431	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003841405.1	s__Tetragenococcus halophilus	81.0708	517	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	97.86	96.17	0.89	0.79	30	-
GCF_001544195.1	s__Tetragenococcus solitarius	80.7196	493	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423785.1	s__Tetragenococcus muriaticus	80.0242	397	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	98.93	98.87	0.88	0.86	3	-
GCF_017316025.1	s__Enterococcus_C sp017316025	77.9733	89	909	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_000407285.1	s__Enterococcus_F saccharolyticus	77.7312	137	909	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_003950325.1	s__Vagococcus_C humatus	76.8926	56	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017377505.1	s__Enterococcus sp017377505	76.8442	62	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:17,394] [INFO] GTDB search result was written to GCF_003795145.1_ASM379514v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:17,395] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:17,420] [INFO] DFAST_QC result json was written to GCF_003795145.1_ASM379514v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:17,420] [INFO] DFAST_QC completed!
[2024-01-25 18:56:17,421] [INFO] Total running time: 0h0m42s