[2024-01-24 12:40:35,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:35,388] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:35,388] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd5610ef-5879-429d-9877-5b3389f75fd7/dqc_reference
[2024-01-24 12:40:36,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:36,693] [INFO] Task started: Prodigal
[2024-01-24 12:40:36,693] [INFO] Running command: gunzip -c /var/lib/cwl/stg924aca24-1de9-4d77-9df3-b49e3407e706/GCF_008326545.1_ASM832654v1_genomic.fna.gz | prodigal -d GCF_008326545.1_ASM832654v1_genomic.fna/cds.fna -a GCF_008326545.1_ASM832654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:40,810] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:40,811] [INFO] Task started: HMMsearch
[2024-01-24 12:40:40,811] [INFO] Running command: hmmsearch --tblout GCF_008326545.1_ASM832654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd5610ef-5879-429d-9877-5b3389f75fd7/dqc_reference/reference_markers.hmm GCF_008326545.1_ASM832654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:41,013] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:41,015] [INFO] Found 6/6 markers.
[2024-01-24 12:40:41,035] [INFO] Query marker FASTA was written to GCF_008326545.1_ASM832654v1_genomic.fna/markers.fasta
[2024-01-24 12:40:41,035] [INFO] Task started: Blastn
[2024-01-24 12:40:41,035] [INFO] Running command: blastn -query GCF_008326545.1_ASM832654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd5610ef-5879-429d-9877-5b3389f75fd7/dqc_reference/reference_markers.fasta -out GCF_008326545.1_ASM832654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:41,615] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:41,622] [INFO] Selected 22 target genomes.
[2024-01-24 12:40:41,623] [INFO] Target genome list was writen to GCF_008326545.1_ASM832654v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:41,640] [INFO] Task started: fastANI
[2024-01-24 12:40:41,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg924aca24-1de9-4d77-9df3-b49e3407e706/GCF_008326545.1_ASM832654v1_genomic.fna.gz --refList GCF_008326545.1_ASM832654v1_genomic.fna/target_genomes.txt --output GCF_008326545.1_ASM832654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:48,298] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:48,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd5610ef-5879-429d-9877-5b3389f75fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:48,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd5610ef-5879-429d-9877-5b3389f75fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:48,322] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:48,322] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:48,323] [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 citreum	strain=ATCC 49370	GCA_004354555.1	33964	33964	type	True	99.9985	594	597	95	conclusive
Leuconostoc holzapfelii	strain=JCM 16942	GCA_019655995.1	434464	434464	type	True	79.855	194	597	95	below_threshold
Leuconostoc holzapfelii	strain=CCUG 54536	GCA_012396485.1	434464	434464	type	True	79.8254	193	597	95	below_threshold
Leuconostoc lactis	strain=JCM 6123	GCA_019656035.1	1246	1246	type	True	79.7003	188	597	95	below_threshold
Leuconostoc lactis	strain=JCM 6123	GCA_014651235.1	1246	1246	type	True	79.6643	188	597	95	below_threshold
Leuconostoc miyukkimchii	strain=JCM 17445	GCA_019656055.1	910540	910540	type	True	79.6494	200	597	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	79.3374	211	597	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	79.2924	210	597	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_019655935.1	1607837	1244	type	True	79.2667	212	597	95	below_threshold
Leuconostoc gelidum subsp. gelidum	strain=KCTC 3527	GCA_000166715.2	1607839	1244	type	True	79.2401	210	597	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_020089505.1	1607837	1244	type	True	79.1756	218	597	95	below_threshold
Leuconostoc inhae	strain=DSM 15101	GCA_019656015.1	178001	178001	suspected-type	True	79.0454	218	597	95	below_threshold
Leuconostoc kimchii	strain=IMSNU 11154	GCA_000092505.1	136609	136609	type	True	79.0326	227	597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:48,324] [INFO] DFAST Taxonomy check result was written to GCF_008326545.1_ASM832654v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:48,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:48,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:48,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd5610ef-5879-429d-9877-5b3389f75fd7/dqc_reference/checkm_data
[2024-01-24 12:40:48,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:48,346] [INFO] Task started: CheckM
[2024-01-24 12:40:48,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008326545.1_ASM832654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008326545.1_ASM832654v1_genomic.fna/checkm_input GCF_008326545.1_ASM832654v1_genomic.fna/checkm_result
[2024-01-24 12:41:08,086] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:08,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:08,109] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:08,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:08,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008326545.1_ASM832654v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:08,110] [INFO] Task started: Blastn
[2024-01-24 12:41:08,110] [INFO] Running command: blastn -query GCF_008326545.1_ASM832654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd5610ef-5879-429d-9877-5b3389f75fd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_008326545.1_ASM832654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:08,916] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:08,921] [INFO] Selected 14 target genomes.
[2024-01-24 12:41:08,921] [INFO] Target genome list was writen to GCF_008326545.1_ASM832654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:08,942] [INFO] Task started: fastANI
[2024-01-24 12:41:08,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg924aca24-1de9-4d77-9df3-b49e3407e706/GCF_008326545.1_ASM832654v1_genomic.fna.gz --refList GCF_008326545.1_ASM832654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008326545.1_ASM832654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:13,212] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:13,226] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:13,226] [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_004354555.1	s__Leuconostoc citreum	99.9985	594	597	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.02	98.68	0.92	0.88	33	conclusive
GCF_012396485.1	s__Leuconostoc holzapfelii	79.8102	194	597	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	79.7364	191	597	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	79.6634	187	597	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.49	96.95	0.90	0.86	22	-
GCA_000166735.2	s__Leuconostoc inhae	79.5323	178	597	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.95	98.13	0.88	0.76	13	-
GCF_000166715.1	s__Leuconostoc gelidum	79.2401	210	597	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
GCF_016908715.1	s__Leuconostoc rapi	79.1562	233	597	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	79.0326	227	597	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCA_900554745.1	s__Leuconostoc sp900554745	78.6984	117	597	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 12:41:13,228] [INFO] GTDB search result was written to GCF_008326545.1_ASM832654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:13,228] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:13,232] [INFO] DFAST_QC result json was written to GCF_008326545.1_ASM832654v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:13,232] [INFO] DFAST_QC completed!
[2024-01-24 12:41:13,232] [INFO] Total running time: 0h0m38s