[2024-01-24 13:13:03,180] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:03,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:03,182] [INFO] DQC Reference Directory: /var/lib/cwl/stg46545126-5846-41a2-8726-e1d6db8f157f/dqc_reference
[2024-01-24 13:13:04,403] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:04,404] [INFO] Task started: Prodigal
[2024-01-24 13:13:04,404] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e87e95a-bbd1-447c-8dc3-a235d9a6dda6/GCF_012396745.1_ASM1239674v1_genomic.fna.gz | prodigal -d GCF_012396745.1_ASM1239674v1_genomic.fna/cds.fna -a GCF_012396745.1_ASM1239674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:09,439] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:09,440] [INFO] Task started: HMMsearch
[2024-01-24 13:13:09,440] [INFO] Running command: hmmsearch --tblout GCF_012396745.1_ASM1239674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46545126-5846-41a2-8726-e1d6db8f157f/dqc_reference/reference_markers.hmm GCF_012396745.1_ASM1239674v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:09,672] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:09,673] [INFO] Found 6/6 markers.
[2024-01-24 13:13:09,700] [INFO] Query marker FASTA was written to GCF_012396745.1_ASM1239674v1_genomic.fna/markers.fasta
[2024-01-24 13:13:09,701] [INFO] Task started: Blastn
[2024-01-24 13:13:09,701] [INFO] Running command: blastn -query GCF_012396745.1_ASM1239674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46545126-5846-41a2-8726-e1d6db8f157f/dqc_reference/reference_markers.fasta -out GCF_012396745.1_ASM1239674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:10,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:10,281] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:10,282] [INFO] Target genome list was writen to GCF_012396745.1_ASM1239674v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:10,351] [INFO] Task started: fastANI
[2024-01-24 13:13:10,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e87e95a-bbd1-447c-8dc3-a235d9a6dda6/GCF_012396745.1_ASM1239674v1_genomic.fna.gz --refList GCF_012396745.1_ASM1239674v1_genomic.fna/target_genomes.txt --output GCF_012396745.1_ASM1239674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:15,868] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:15,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46545126-5846-41a2-8726-e1d6db8f157f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:15,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46545126-5846-41a2-8726-e1d6db8f157f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:15,885] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:13:15,885] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:15,886] [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 pseudomesenteroides	strain=NCDO 768	GCA_012396745.1	33968	33968	suspected-type	True	100.0	696	698	95	conclusive
Leuconostoc pseudomesenteroides	strain=FDAARGOS_1003	GCA_016127255.1	33968	33968	suspected-type	True	99.9809	672	698	95	conclusive
Leuconostoc pseudomesenteroides	strain=LMG 11482	GCA_014634745.1	33968	33968	suspected-type	True	99.9736	677	698	95	conclusive
Leuconostoc falkenbergense	strain=LMG 10779	GCA_014634805.1	2766470	2766470	type	True	92.4631	520	698	95	below_threshold
Leuconostoc suionicum	strain=DSM 20241	GCA_001891125.1	1511761	1511761	type	True	80.3986	206	698	95	below_threshold
Leuconostoc mesenteroides subsp. mesenteroides	strain=NBRC 100496	GCA_007990165.1	33967	1245	type	True	79.9282	220	698	95	below_threshold
Leuconostoc mesenteroides subsp. jonggajibkimchii	strain=DRC1506	GCA_001886915.1	2026657	1245	type	True	79.6641	219	698	95	below_threshold
Leuconostoc gelidum subsp. gelidum	strain=KCTC 3527	GCA_000166715.2	1607839	1244	type	True	79.2193	161	698	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	78.815	163	698	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	78.721	169	698	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:15,887] [INFO] DFAST Taxonomy check result was written to GCF_012396745.1_ASM1239674v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:15,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:15,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:15,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46545126-5846-41a2-8726-e1d6db8f157f/dqc_reference/checkm_data
[2024-01-24 13:13:15,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:15,913] [INFO] Task started: CheckM
[2024-01-24 13:13:15,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396745.1_ASM1239674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396745.1_ASM1239674v1_genomic.fna/checkm_input GCF_012396745.1_ASM1239674v1_genomic.fna/checkm_result
[2024-01-24 13:13:38,204] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:38,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:38,227] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:38,227] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:38,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396745.1_ASM1239674v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:38,228] [INFO] Task started: Blastn
[2024-01-24 13:13:38,228] [INFO] Running command: blastn -query GCF_012396745.1_ASM1239674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46545126-5846-41a2-8726-e1d6db8f157f/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396745.1_ASM1239674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:39,060] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:39,064] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:39,064] [INFO] Target genome list was writen to GCF_012396745.1_ASM1239674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:39,217] [INFO] Task started: fastANI
[2024-01-24 13:13:39,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e87e95a-bbd1-447c-8dc3-a235d9a6dda6/GCF_012396745.1_ASM1239674v1_genomic.fna.gz --refList GCF_012396745.1_ASM1239674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396745.1_ASM1239674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:45,486] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:45,503] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:45,503] [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_014634745.1	s__Leuconostoc pseudomesenteroides	99.9736	677	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.98	96.85	0.90	0.84	11	conclusive
GCF_014634805.1	s__Leuconostoc falkenbergense	92.4631	520	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.11	96.75	0.91	0.87	34	-
GCF_001891125.1	s__Leuconostoc suionicum	80.3986	206	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.16	97.05	0.94	0.91	7	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	80.1946	221	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000014445.1	s__Leuconostoc mesenteroides	79.9739	226	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.82	97.34	0.92	0.82	89	-
GCF_012396485.1	s__Leuconostoc holzapfelii	79.5306	144	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004354555.1	s__Leuconostoc citreum	79.3646	142	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.02	98.68	0.92	0.88	33	-
GCF_000166715.1	s__Leuconostoc gelidum	79.2193	161	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
GCF_001047135.2	s__Fructobacillus tropaeoli	79.2001	51	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	97.33	96.88	0.89	0.88	3	-
GCA_000166735.2	s__Leuconostoc inhae	78.9428	147	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.95	98.13	0.88	0.76	13	-
GCF_016908715.1	s__Leuconostoc rapi	78.8272	162	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165675.1	s__Leuconostoc_B fallax	78.5335	102	698	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc_B	95.0	99.89	99.83	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:45,505] [INFO] GTDB search result was written to GCF_012396745.1_ASM1239674v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:45,505] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:45,508] [INFO] DFAST_QC result json was written to GCF_012396745.1_ASM1239674v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:45,509] [INFO] DFAST_QC completed!
[2024-01-24 13:13:45,509] [INFO] Total running time: 0h0m42s