[2024-01-24 12:14:34,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg47db3b7a-61ef-4930-9b3e-13ddcdd59575/dqc_reference
[2024-01-24 12:14:35,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,247] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,248] [INFO] Running command: gunzip -c /var/lib/cwl/stg25d6dc65-4f29-46d3-baa1-086ca9c4416d/GCF_012396485.1_ASM1239648v1_genomic.fna.gz | prodigal -d GCF_012396485.1_ASM1239648v1_genomic.fna/cds.fna -a GCF_012396485.1_ASM1239648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:39,597] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:39,597] [INFO] Task started: HMMsearch
[2024-01-24 12:14:39,597] [INFO] Running command: hmmsearch --tblout GCF_012396485.1_ASM1239648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47db3b7a-61ef-4930-9b3e-13ddcdd59575/dqc_reference/reference_markers.hmm GCF_012396485.1_ASM1239648v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:39,828] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:39,829] [INFO] Found 6/6 markers.
[2024-01-24 12:14:39,846] [INFO] Query marker FASTA was written to GCF_012396485.1_ASM1239648v1_genomic.fna/markers.fasta
[2024-01-24 12:14:39,846] [INFO] Task started: Blastn
[2024-01-24 12:14:39,846] [INFO] Running command: blastn -query GCF_012396485.1_ASM1239648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47db3b7a-61ef-4930-9b3e-13ddcdd59575/dqc_reference/reference_markers.fasta -out GCF_012396485.1_ASM1239648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:40,419] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:40,424] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:40,424] [INFO] Target genome list was writen to GCF_012396485.1_ASM1239648v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:40,492] [INFO] Task started: fastANI
[2024-01-24 12:14:40,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg25d6dc65-4f29-46d3-baa1-086ca9c4416d/GCF_012396485.1_ASM1239648v1_genomic.fna.gz --refList GCF_012396485.1_ASM1239648v1_genomic.fna/target_genomes.txt --output GCF_012396485.1_ASM1239648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:45,180] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:45,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47db3b7a-61ef-4930-9b3e-13ddcdd59575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:45,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47db3b7a-61ef-4930-9b3e-13ddcdd59575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:45,188] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:45,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:45,188] [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 holzapfelii	strain=CCUG 54536	GCA_012396485.1	434464	434464	type	True	100.0	574	576	95	conclusive
Leuconostoc holzapfelii	strain=JCM 16942	GCA_019655995.1	434464	434464	type	True	99.9931	565	576	95	conclusive
Leuconostoc lactis	strain=JCM 6123	GCA_019656035.1	1246	1246	type	True	83.0202	349	576	95	below_threshold
Leuconostoc lactis	strain=JCM 6123	GCA_014651235.1	1246	1246	type	True	82.9748	350	576	95	below_threshold
Leuconostoc citreum	strain=ATCC 49370	GCA_004354555.1	33964	33964	type	True	79.9183	193	576	95	below_threshold
Leuconostoc miyukkimchii	strain=JCM 17445	GCA_019656055.1	910540	910540	type	True	79.5433	181	576	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	79.3286	168	576	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	79.3086	173	576	95	below_threshold
Fructobacillus parabroussonetiae	strain=S1-1	GCA_018437265.1	2713174	2713174	type	True	78.8796	54	576	95	below_threshold
Leuconostoc carnosum	strain=JCM 9695	GCA_019655915.1	1252	1252	type	True	78.8482	177	576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:45,190] [INFO] DFAST Taxonomy check result was written to GCF_012396485.1_ASM1239648v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:45,190] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:45,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:45,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47db3b7a-61ef-4930-9b3e-13ddcdd59575/dqc_reference/checkm_data
[2024-01-24 12:14:45,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:45,216] [INFO] Task started: CheckM
[2024-01-24 12:14:45,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396485.1_ASM1239648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396485.1_ASM1239648v1_genomic.fna/checkm_input GCF_012396485.1_ASM1239648v1_genomic.fna/checkm_result
[2024-01-24 12:15:04,042] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:04,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:04,058] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:04,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:04,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396485.1_ASM1239648v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:04,059] [INFO] Task started: Blastn
[2024-01-24 12:15:04,059] [INFO] Running command: blastn -query GCF_012396485.1_ASM1239648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47db3b7a-61ef-4930-9b3e-13ddcdd59575/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396485.1_ASM1239648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:04,834] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:04,837] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:04,837] [INFO] Target genome list was writen to GCF_012396485.1_ASM1239648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:04,860] [INFO] Task started: fastANI
[2024-01-24 12:15:04,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg25d6dc65-4f29-46d3-baa1-086ca9c4416d/GCF_012396485.1_ASM1239648v1_genomic.fna.gz --refList GCF_012396485.1_ASM1239648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396485.1_ASM1239648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:09,261] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:09,269] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:09,269] [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_012396485.1	s__Leuconostoc holzapfelii	100.0	574	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900554745.1	s__Leuconostoc sp900554745	84.7556	231	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954625.1	s__Leuconostoc lactis_A	83.2993	372	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.86	96.88	0.92	0.91	7	-
GCF_014651235.1	s__Leuconostoc lactis	82.9748	350	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.49	96.95	0.90	0.86	22	-
GCF_004354555.1	s__Leuconostoc citreum	79.9631	193	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.02	98.68	0.92	0.88	33	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	79.7037	121	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014634745.1	s__Leuconostoc pseudomesenteroides	79.6405	138	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.98	96.85	0.90	0.84	11	-
GCF_016908715.1	s__Leuconostoc rapi	79.544	171	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207505.1	s__Leuconostoc carnosum	79.0647	184	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	-
GCF_008107645.1	s__Leuconostoc litchii	78.9667	117	576	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:09,270] [INFO] GTDB search result was written to GCF_012396485.1_ASM1239648v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:09,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:09,273] [INFO] DFAST_QC result json was written to GCF_012396485.1_ASM1239648v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:09,274] [INFO] DFAST_QC completed!
[2024-01-24 12:15:09,274] [INFO] Total running time: 0h0m35s