[2024-01-24 13:01:10,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:10,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:10,043] [INFO] DQC Reference Directory: /var/lib/cwl/stg04c89702-5e80-4185-a784-3ea0f89b3a37/dqc_reference
[2024-01-24 13:01:11,254] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:11,255] [INFO] Task started: Prodigal
[2024-01-24 13:01:11,255] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfc36e2c-e2ca-49d3-981d-70c1cade3dce/GCF_019656035.1_ASM1965603v1_genomic.fna.gz | prodigal -d GCF_019656035.1_ASM1965603v1_genomic.fna/cds.fna -a GCF_019656035.1_ASM1965603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:15,474] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:15,475] [INFO] Task started: HMMsearch
[2024-01-24 13:01:15,475] [INFO] Running command: hmmsearch --tblout GCF_019656035.1_ASM1965603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04c89702-5e80-4185-a784-3ea0f89b3a37/dqc_reference/reference_markers.hmm GCF_019656035.1_ASM1965603v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:15,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:15,758] [INFO] Found 6/6 markers.
[2024-01-24 13:01:15,776] [INFO] Query marker FASTA was written to GCF_019656035.1_ASM1965603v1_genomic.fna/markers.fasta
[2024-01-24 13:01:15,776] [INFO] Task started: Blastn
[2024-01-24 13:01:15,776] [INFO] Running command: blastn -query GCF_019656035.1_ASM1965603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04c89702-5e80-4185-a784-3ea0f89b3a37/dqc_reference/reference_markers.fasta -out GCF_019656035.1_ASM1965603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:16,364] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:16,368] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:16,368] [INFO] Target genome list was writen to GCF_019656035.1_ASM1965603v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:16,406] [INFO] Task started: fastANI
[2024-01-24 13:01:16,406] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfc36e2c-e2ca-49d3-981d-70c1cade3dce/GCF_019656035.1_ASM1965603v1_genomic.fna.gz --refList GCF_019656035.1_ASM1965603v1_genomic.fna/target_genomes.txt --output GCF_019656035.1_ASM1965603v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:21,273] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:21,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04c89702-5e80-4185-a784-3ea0f89b3a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:21,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04c89702-5e80-4185-a784-3ea0f89b3a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:21,288] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:21,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:21,289] [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 lactis	strain=JCM 6123	GCA_019656035.1	1246	1246	type	True	100.0	506	509	95	conclusive
Leuconostoc lactis	strain=JCM 6123	GCA_014651235.1	1246	1246	type	True	99.9968	501	509	95	conclusive
Leuconostoc holzapfelii	strain=CCUG 54536	GCA_012396485.1	434464	434464	type	True	82.9218	347	509	95	below_threshold
Leuconostoc holzapfelii	strain=JCM 16942	GCA_019655995.1	434464	434464	type	True	82.8945	349	509	95	below_threshold
Leuconostoc kimchii	strain=IMSNU 11154	GCA_000092505.1	136609	136609	type	True	80.4422	177	509	95	below_threshold
Leuconostoc citreum	strain=ATCC 49370	GCA_004354555.1	33964	33964	type	True	79.8366	181	509	95	below_threshold
Leuconostoc inhae	strain=DSM 15101	GCA_019656015.1	178001	178001	suspected-type	True	79.7383	173	509	95	below_threshold
Convivina intestini	strain=DSM 28795	GCA_003096575.1	1505726	1505726	type	True	78.6358	64	509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:21,292] [INFO] DFAST Taxonomy check result was written to GCF_019656035.1_ASM1965603v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:21,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:21,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:21,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04c89702-5e80-4185-a784-3ea0f89b3a37/dqc_reference/checkm_data
[2024-01-24 13:01:21,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:21,325] [INFO] Task started: CheckM
[2024-01-24 13:01:21,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019656035.1_ASM1965603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019656035.1_ASM1965603v1_genomic.fna/checkm_input GCF_019656035.1_ASM1965603v1_genomic.fna/checkm_result
[2024-01-24 13:01:41,364] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:41,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:41,387] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:41,387] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:41,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019656035.1_ASM1965603v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:41,388] [INFO] Task started: Blastn
[2024-01-24 13:01:41,388] [INFO] Running command: blastn -query GCF_019656035.1_ASM1965603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04c89702-5e80-4185-a784-3ea0f89b3a37/dqc_reference/reference_markers_gtdb.fasta -out GCF_019656035.1_ASM1965603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:42,195] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:42,200] [INFO] Selected 10 target genomes.
[2024-01-24 13:01:42,201] [INFO] Target genome list was writen to GCF_019656035.1_ASM1965603v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:42,208] [INFO] Task started: fastANI
[2024-01-24 13:01:42,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfc36e2c-e2ca-49d3-981d-70c1cade3dce/GCF_019656035.1_ASM1965603v1_genomic.fna.gz --refList GCF_019656035.1_ASM1965603v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019656035.1_ASM1965603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:01:45,579] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:45,589] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:01:45,589] [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_014651235.1	s__Leuconostoc lactis	99.9968	501	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.49	96.95	0.90	0.86	22	conclusive
GCF_007954625.1	s__Leuconostoc lactis_A	94.7445	471	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.86	96.88	0.92	0.91	7	-
GCA_900554745.1	s__Leuconostoc sp900554745	87.622	278	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396485.1	s__Leuconostoc holzapfelii	82.9218	347	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	80.5176	118	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000092505.1	s__Leuconostoc kimchii	80.4331	177	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_004354555.1	s__Leuconostoc citreum	79.8688	180	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.02	98.68	0.92	0.88	33	-
GCF_014207505.1	s__Leuconostoc carnosum	79.8132	155	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	-
GCF_003096575.1	s__Convivina intestini	78.6003	64	509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Convivina	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:01:45,591] [INFO] GTDB search result was written to GCF_019656035.1_ASM1965603v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:01:45,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:01:45,595] [INFO] DFAST_QC result json was written to GCF_019656035.1_ASM1965603v1_genomic.fna/dqc_result.json
[2024-01-24 13:01:45,595] [INFO] DFAST_QC completed!
[2024-01-24 13:01:45,595] [INFO] Total running time: 0h0m36s