[2024-01-24 13:31:44,341] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,344] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbd61c19-f47b-404d-a550-7e305f25e839/dqc_reference
[2024-01-24 13:31:45,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,612] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg198bba25-c2ab-4a53-9189-b9643a784f91/GCF_014651235.1_ASM1465123v1_genomic.fna.gz | prodigal -d GCF_014651235.1_ASM1465123v1_genomic.fna/cds.fna -a GCF_014651235.1_ASM1465123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:49,858] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:49,859] [INFO] Task started: HMMsearch
[2024-01-24 13:31:49,859] [INFO] Running command: hmmsearch --tblout GCF_014651235.1_ASM1465123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbd61c19-f47b-404d-a550-7e305f25e839/dqc_reference/reference_markers.hmm GCF_014651235.1_ASM1465123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:50,060] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:50,062] [INFO] Found 6/6 markers.
[2024-01-24 13:31:50,086] [INFO] Query marker FASTA was written to GCF_014651235.1_ASM1465123v1_genomic.fna/markers.fasta
[2024-01-24 13:31:50,086] [INFO] Task started: Blastn
[2024-01-24 13:31:50,086] [INFO] Running command: blastn -query GCF_014651235.1_ASM1465123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd61c19-f47b-404d-a550-7e305f25e839/dqc_reference/reference_markers.fasta -out GCF_014651235.1_ASM1465123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:50,675] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:50,679] [INFO] Selected 16 target genomes.
[2024-01-24 13:31:50,679] [INFO] Target genome list was writen to GCF_014651235.1_ASM1465123v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:50,701] [INFO] Task started: fastANI
[2024-01-24 13:31:50,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg198bba25-c2ab-4a53-9189-b9643a784f91/GCF_014651235.1_ASM1465123v1_genomic.fna.gz --refList GCF_014651235.1_ASM1465123v1_genomic.fna/target_genomes.txt --output GCF_014651235.1_ASM1465123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:55,648] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:55,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbd61c19-f47b-404d-a550-7e305f25e839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:55,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbd61c19-f47b-404d-a550-7e305f25e839/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:55,659] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:55,659] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:55,659] [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_014651235.1	1246	1246	type	True	100.0	516	519	95	conclusive
Leuconostoc lactis	strain=JCM 6123	GCA_019656035.1	1246	1246	type	True	99.9948	504	519	95	conclusive
Leuconostoc holzapfelii	strain=CCUG 54536	GCA_012396485.1	434464	434464	type	True	82.9772	346	519	95	below_threshold
Leuconostoc holzapfelii	strain=JCM 16942	GCA_019655995.1	434464	434464	type	True	82.896	350	519	95	below_threshold
Leuconostoc kimchii	strain=IMSNU 11154	GCA_000092505.1	136609	136609	type	True	80.4992	187	519	95	below_threshold
Leuconostoc citreum	strain=ATCC 49370	GCA_004354555.1	33964	33964	type	True	80.1084	176	519	95	below_threshold
Leuconostoc inhae	strain=DSM 15101	GCA_019656015.1	178001	178001	suspected-type	True	79.1994	183	519	95	below_threshold
Convivina intestini	strain=DSM 28795	GCA_003096575.1	1505726	1505726	type	True	78.3501	64	519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:55,661] [INFO] DFAST Taxonomy check result was written to GCF_014651235.1_ASM1465123v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:55,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:55,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:55,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbd61c19-f47b-404d-a550-7e305f25e839/dqc_reference/checkm_data
[2024-01-24 13:31:55,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:55,686] [INFO] Task started: CheckM
[2024-01-24 13:31:55,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651235.1_ASM1465123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651235.1_ASM1465123v1_genomic.fna/checkm_input GCF_014651235.1_ASM1465123v1_genomic.fna/checkm_result
[2024-01-24 13:32:16,318] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:16,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:16,346] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:16,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:16,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651235.1_ASM1465123v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:16,347] [INFO] Task started: Blastn
[2024-01-24 13:32:16,347] [INFO] Running command: blastn -query GCF_014651235.1_ASM1465123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd61c19-f47b-404d-a550-7e305f25e839/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651235.1_ASM1465123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:17,154] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:17,159] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:17,159] [INFO] Target genome list was writen to GCF_014651235.1_ASM1465123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:17,169] [INFO] Task started: fastANI
[2024-01-24 13:32:17,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg198bba25-c2ab-4a53-9189-b9643a784f91/GCF_014651235.1_ASM1465123v1_genomic.fna.gz --refList GCF_014651235.1_ASM1465123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651235.1_ASM1465123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:21,293] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:21,309] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:21,309] [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	100.0	516	519	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	94.6879	478	519	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	87.7189	279	519	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	82.9832	345	519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092505.1	s__Leuconostoc kimchii	80.5134	186	519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	80.3608	129	519	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004354555.1	s__Leuconostoc citreum	80.1157	175	519	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	79.7396	162	519	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	78.3501	64	519	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 13:32:21,311] [INFO] GTDB search result was written to GCF_014651235.1_ASM1465123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:21,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:21,315] [INFO] DFAST_QC result json was written to GCF_014651235.1_ASM1465123v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:21,315] [INFO] DFAST_QC completed!
[2024-01-24 13:32:21,315] [INFO] Total running time: 0h0m37s