[2023-06-13 04:12:52,625] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:12:52,629] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:12:52,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b764134-c815-4655-8d83-36631909cabd/dqc_reference
[2023-06-13 04:12:54,170] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:12:54,172] [INFO] Task started: Prodigal
[2023-06-13 04:12:54,172] [INFO] Running command: gunzip -c /var/lib/cwl/stged3ed052-7148-4076-8499-61a8deeb37af/GCA_022654615.1_ASM2265461v1_genomic.fna.gz | prodigal -d GCA_022654615.1_ASM2265461v1_genomic.fna/cds.fna -a GCA_022654615.1_ASM2265461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:12:57,656] [INFO] Task succeeded: Prodigal
[2023-06-13 04:12:57,656] [INFO] Task started: HMMsearch
[2023-06-13 04:12:57,656] [INFO] Running command: hmmsearch --tblout GCA_022654615.1_ASM2265461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b764134-c815-4655-8d83-36631909cabd/dqc_reference/reference_markers.hmm GCA_022654615.1_ASM2265461v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:12:57,869] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:12:57,870] [WARNING] Found 4/6 markers. [/var/lib/cwl/stged3ed052-7148-4076-8499-61a8deeb37af/GCA_022654615.1_ASM2265461v1_genomic.fna.gz]
[2023-06-13 04:12:57,907] [INFO] Query marker FASTA was written to GCA_022654615.1_ASM2265461v1_genomic.fna/markers.fasta
[2023-06-13 04:12:57,907] [INFO] Task started: Blastn
[2023-06-13 04:12:57,907] [INFO] Running command: blastn -query GCA_022654615.1_ASM2265461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b764134-c815-4655-8d83-36631909cabd/dqc_reference/reference_markers.fasta -out GCA_022654615.1_ASM2265461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:12:58,444] [INFO] Task succeeded: Blastn
[2023-06-13 04:12:58,448] [INFO] Selected 7 target genomes.
[2023-06-13 04:12:58,449] [INFO] Target genome list was writen to GCA_022654615.1_ASM2265461v1_genomic.fna/target_genomes.txt
[2023-06-13 04:12:58,452] [INFO] Task started: fastANI
[2023-06-13 04:12:58,452] [INFO] Running command: fastANI --query /var/lib/cwl/stged3ed052-7148-4076-8499-61a8deeb37af/GCA_022654615.1_ASM2265461v1_genomic.fna.gz --refList GCA_022654615.1_ASM2265461v1_genomic.fna/target_genomes.txt --output GCA_022654615.1_ASM2265461v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:13:01,182] [INFO] Task succeeded: fastANI
[2023-06-13 04:13:01,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b764134-c815-4655-8d83-36631909cabd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:13:01,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b764134-c815-4655-8d83-36631909cabd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:13:01,194] [INFO] Found 7 fastANI hits (7 hits with ANI > threshold)
[2023-06-13 04:13:01,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 04:13:01,194] [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
Leuconostoc mesenteroides subsp. mesenteroides	strain=NBRC 100496	GCA_007990165.1	33967	1245	type	True	99.2077	486	526	95	conclusive
Leuconostoc mesenteroides subsp. mesenteroides	strain=ATCC 8293	GCA_000014445.1	33967	1245	type	True	99.1869	492	526	95	conclusive
Leuconostoc mesenteroides	strain=NCTC12954	GCA_900461615.1	1245	1245	type	True	99.1842	493	526	95	conclusive
Leuconostoc mesenteroides subsp. dextranicum	strain=NBRC 100495	GCA_007990145.1	33966	1245	type	True	98.9241	416	526	95	conclusive
Leuconostoc mesenteroides subsp. jonggajibkimchii	strain=DRC1506	GCA_001886915.1	2026657	1245	type	True	98.7392	476	526	95	conclusive
Leuconostoc mesenteroides subsp. dextranicum	strain=DSM 20484	GCA_001047695.1	33966	1245	type	True	98.6312	439	526	95	conclusive
Leuconostoc mesenteroides subsp. cremoris	strain=ATCC 19254	GCA_000160595.1	33965	1245	type	True	97.9287	399	526	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 04:13:01,210] [INFO] DFAST Taxonomy check result was written to GCA_022654615.1_ASM2265461v1_genomic.fna/tc_result.tsv
[2023-06-13 04:13:01,211] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:13:01,211] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:13:01,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b764134-c815-4655-8d83-36631909cabd/dqc_reference/checkm_data
[2023-06-13 04:13:01,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:13:01,232] [INFO] Task started: CheckM
[2023-06-13 04:13:01,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022654615.1_ASM2265461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022654615.1_ASM2265461v1_genomic.fna/checkm_input GCA_022654615.1_ASM2265461v1_genomic.fna/checkm_result
[2023-06-13 04:13:19,959] [INFO] Task succeeded: CheckM
[2023-06-13 04:13:19,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:13:19,981] [INFO] ===== Completeness check finished =====
[2023-06-13 04:13:19,982] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:13:19,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022654615.1_ASM2265461v1_genomic.fna/markers.fasta)
[2023-06-13 04:13:19,983] [INFO] Task started: Blastn
[2023-06-13 04:13:19,983] [INFO] Running command: blastn -query GCA_022654615.1_ASM2265461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b764134-c815-4655-8d83-36631909cabd/dqc_reference/reference_markers_gtdb.fasta -out GCA_022654615.1_ASM2265461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:13:20,482] [INFO] Task succeeded: Blastn
[2023-06-13 04:13:20,487] [INFO] Selected 9 target genomes.
[2023-06-13 04:13:20,487] [INFO] Target genome list was writen to GCA_022654615.1_ASM2265461v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:13:20,494] [INFO] Task started: fastANI
[2023-06-13 04:13:20,494] [INFO] Running command: fastANI --query /var/lib/cwl/stged3ed052-7148-4076-8499-61a8deeb37af/GCA_022654615.1_ASM2265461v1_genomic.fna.gz --refList GCA_022654615.1_ASM2265461v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022654615.1_ASM2265461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:13:24,161] [INFO] Task succeeded: fastANI
[2023-06-13 04:13:24,168] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 04:13:24,169] [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_000014445.1	s__Leuconostoc mesenteroides	99.1869	492	526	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.82	97.34	0.92	0.82	89	conclusive
GCF_001891125.1	s__Leuconostoc suionicum	93.982	472	526	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.16	97.05	0.94	0.91	7	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	90.6322	425	526	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_008107645.1	s__Leuconostoc litchii	81.8116	327	526	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014634805.1	s__Leuconostoc falkenbergense	80.0012	170	526	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.11	96.75	0.91	0.87	34	-
GCF_007954625.1	s__Leuconostoc lactis_A	79.5864	100	526	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.86	96.88	0.92	0.91	7	-
GCF_000092505.1	s__Leuconostoc kimchii	79.4027	138	526	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-06-13 04:13:24,171] [INFO] GTDB search result was written to GCA_022654615.1_ASM2265461v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:13:24,171] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:13:24,174] [INFO] DFAST_QC result json was written to GCA_022654615.1_ASM2265461v1_genomic.fna/dqc_result.json
[2023-06-13 04:13:24,174] [INFO] DFAST_QC completed!
[2023-06-13 04:13:24,174] [INFO] Total running time: 0h0m32s