[2024-01-24 12:40:50,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:50,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:50,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg2360e7de-750f-4383-9664-f3a59c5e45aa/dqc_reference
[2024-01-24 12:40:51,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:51,977] [INFO] Task started: Prodigal
[2024-01-24 12:40:51,978] [INFO] Running command: gunzip -c /var/lib/cwl/stge294f61f-3d97-4d87-ace4-ce174903b946/GCF_004354645.1_ASM435464v1_genomic.fna.gz | prodigal -d GCF_004354645.1_ASM435464v1_genomic.fna/cds.fna -a GCF_004354645.1_ASM435464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:55,588] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:55,589] [INFO] Task started: HMMsearch
[2024-01-24 12:40:55,589] [INFO] Running command: hmmsearch --tblout GCF_004354645.1_ASM435464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2360e7de-750f-4383-9664-f3a59c5e45aa/dqc_reference/reference_markers.hmm GCF_004354645.1_ASM435464v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:55,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:55,794] [INFO] Found 6/6 markers.
[2024-01-24 12:40:55,812] [INFO] Query marker FASTA was written to GCF_004354645.1_ASM435464v1_genomic.fna/markers.fasta
[2024-01-24 12:40:55,813] [INFO] Task started: Blastn
[2024-01-24 12:40:55,813] [INFO] Running command: blastn -query GCF_004354645.1_ASM435464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2360e7de-750f-4383-9664-f3a59c5e45aa/dqc_reference/reference_markers.fasta -out GCF_004354645.1_ASM435464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:56,382] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:56,386] [INFO] Selected 22 target genomes.
[2024-01-24 12:40:56,386] [INFO] Target genome list was writen to GCF_004354645.1_ASM435464v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:56,393] [INFO] Task started: fastANI
[2024-01-24 12:40:56,393] [INFO] Running command: fastANI --query /var/lib/cwl/stge294f61f-3d97-4d87-ace4-ce174903b946/GCF_004354645.1_ASM435464v1_genomic.fna.gz --refList GCF_004354645.1_ASM435464v1_genomic.fna/target_genomes.txt --output GCF_004354645.1_ASM435464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:02,979] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:02,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2360e7de-750f-4383-9664-f3a59c5e45aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:02,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2360e7de-750f-4383-9664-f3a59c5e45aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:02,997] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:41:02,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:02,998] [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 fallax	strain=ATCC 700006	GCA_004354645.1	1251	1251	type	True	100.0	542	544	95	conclusive
Leuconostoc fallax	strain=KCTC 3537	GCA_000165675.2	1251	1251	type	True	99.8994	527	544	95	conclusive
Leuconostoc pseudomesenteroides	strain=FDAARGOS_1003	GCA_016127255.1	33968	33968	suspected-type	True	79.5669	102	544	95	below_threshold
Leuconostoc mesenteroides	strain=NCTC12954	GCA_900461615.1	1245	1245	type	True	79.4483	118	544	95	below_threshold
Leuconostoc mesenteroides subsp. jonggajibkimchii	strain=DRC1506	GCA_001886915.1	2026657	1245	type	True	79.2569	114	544	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	79.1953	125	544	95	below_threshold
Leuconostoc kimchii	strain=IMSNU 11154	GCA_000092505.1	136609	136609	type	True	78.7442	123	544	95	below_threshold
Leuconostoc pseudomesenteroides	strain=NCDO 768	GCA_012396745.1	33968	33968	suspected-type	True	78.7016	101	544	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	78.4816	120	544	95	below_threshold
Leuconostoc mesenteroides subsp. mesenteroides	strain=NBRC 100496	GCA_007990165.1	33967	1245	type	True	78.1837	113	544	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_020089505.1	1607837	1244	type	True	78.1789	106	544	95	below_threshold
Leuconostoc litchii	strain=MB7	GCA_008107645.1	1981069	1981069	type	True	78.1583	116	544	95	below_threshold
Leuconostoc inhae	strain=DSM 15101	GCA_019656015.1	178001	178001	suspected-type	True	78.0256	118	544	95	below_threshold
Leuconostoc rapi	strain=DSM 27776	GCA_016908715.1	1406906	1406906	type	True	77.9869	118	544	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_019655935.1	1607837	1244	type	True	77.8611	103	544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:02,999] [INFO] DFAST Taxonomy check result was written to GCF_004354645.1_ASM435464v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:03,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:03,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:03,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2360e7de-750f-4383-9664-f3a59c5e45aa/dqc_reference/checkm_data
[2024-01-24 12:41:03,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:03,024] [INFO] Task started: CheckM
[2024-01-24 12:41:03,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354645.1_ASM435464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354645.1_ASM435464v1_genomic.fna/checkm_input GCF_004354645.1_ASM435464v1_genomic.fna/checkm_result
[2024-01-24 12:41:21,192] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:21,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:21,215] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:21,215] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:21,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354645.1_ASM435464v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:21,216] [INFO] Task started: Blastn
[2024-01-24 12:41:21,216] [INFO] Running command: blastn -query GCF_004354645.1_ASM435464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2360e7de-750f-4383-9664-f3a59c5e45aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354645.1_ASM435464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:21,975] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:21,990] [INFO] Selected 21 target genomes.
[2024-01-24 12:41:21,990] [INFO] Target genome list was writen to GCF_004354645.1_ASM435464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:22,006] [INFO] Task started: fastANI
[2024-01-24 12:41:22,006] [INFO] Running command: fastANI --query /var/lib/cwl/stge294f61f-3d97-4d87-ace4-ce174903b946/GCF_004354645.1_ASM435464v1_genomic.fna.gz --refList GCF_004354645.1_ASM435464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354645.1_ASM435464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:28,802] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:28,817] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:28,817] [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_000165675.1	s__Leuconostoc_B fallax	99.8994	527	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc_B	95.0	99.89	99.83	0.97	0.96	3	conclusive
GCF_004354555.1	s__Leuconostoc citreum	79.3525	106	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.02	98.68	0.92	0.88	33	-
GCF_000014445.1	s__Leuconostoc mesenteroides	79.3419	115	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.82	97.34	0.92	0.82	89	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	79.0167	114	544	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	78.866	124	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_014207505.1	s__Leuconostoc carnosum	78.8533	118	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	-
GCF_014634745.1	s__Leuconostoc pseudomesenteroides	78.6648	96	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.98	96.85	0.90	0.84	11	-
GCF_012396485.1	s__Leuconostoc holzapfelii	78.3585	98	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107645.1	s__Leuconostoc litchii	78.1461	117	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908715.1	s__Leuconostoc rapi	77.9976	117	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000166735.2	s__Leuconostoc inhae	77.9532	93	544	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	77.7788	106	544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:28,819] [INFO] GTDB search result was written to GCF_004354645.1_ASM435464v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:28,820] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:28,824] [INFO] DFAST_QC result json was written to GCF_004354645.1_ASM435464v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:28,824] [INFO] DFAST_QC completed!
[2024-01-24 12:41:28,824] [INFO] Total running time: 0h0m38s