[2024-01-25 20:08:05,775] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:08:05,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:08:05,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fc34347-996a-4c5e-a2e3-9948d191df44/dqc_reference
[2024-01-25 20:08:06,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:08:06,876] [INFO] Task started: Prodigal
[2024-01-25 20:08:06,876] [INFO] Running command: gunzip -c /var/lib/cwl/stga034f94d-62db-4a14-ac0e-020c6374fd7d/GCF_014634745.1_ASM1463474v1_genomic.fna.gz | prodigal -d GCF_014634745.1_ASM1463474v1_genomic.fna/cds.fna -a GCF_014634745.1_ASM1463474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:11,198] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:11,198] [INFO] Task started: HMMsearch
[2024-01-25 20:08:11,198] [INFO] Running command: hmmsearch --tblout GCF_014634745.1_ASM1463474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fc34347-996a-4c5e-a2e3-9948d191df44/dqc_reference/reference_markers.hmm GCF_014634745.1_ASM1463474v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:11,389] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:11,390] [INFO] Found 6/6 markers.
[2024-01-25 20:08:11,409] [INFO] Query marker FASTA was written to GCF_014634745.1_ASM1463474v1_genomic.fna/markers.fasta
[2024-01-25 20:08:11,410] [INFO] Task started: Blastn
[2024-01-25 20:08:11,410] [INFO] Running command: blastn -query GCF_014634745.1_ASM1463474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc34347-996a-4c5e-a2e3-9948d191df44/dqc_reference/reference_markers.fasta -out GCF_014634745.1_ASM1463474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:11,948] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:11,951] [INFO] Selected 14 target genomes.
[2024-01-25 20:08:11,951] [INFO] Target genome list was writen to GCF_014634745.1_ASM1463474v1_genomic.fna/target_genomes.txt
[2024-01-25 20:08:11,956] [INFO] Task started: fastANI
[2024-01-25 20:08:11,956] [INFO] Running command: fastANI --query /var/lib/cwl/stga034f94d-62db-4a14-ac0e-020c6374fd7d/GCF_014634745.1_ASM1463474v1_genomic.fna.gz --refList GCF_014634745.1_ASM1463474v1_genomic.fna/target_genomes.txt --output GCF_014634745.1_ASM1463474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:17,747] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:17,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fc34347-996a-4c5e-a2e3-9948d191df44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:17,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fc34347-996a-4c5e-a2e3-9948d191df44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:17,758] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:08:17,758] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:17,758] [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=LMG 11482	GCA_014634745.1	33968	33968	suspected-type	True	100.0	685	687	95	conclusive
Leuconostoc pseudomesenteroides	strain=NCDO 768	GCA_012396745.1	33968	33968	suspected-type	True	99.9819	670	687	95	conclusive
Leuconostoc pseudomesenteroides	strain=FDAARGOS_1003	GCA_016127255.1	33968	33968	suspected-type	True	99.9655	666	687	95	conclusive
Leuconostoc falkenbergense	strain=LMG 10779	GCA_014634805.1	2766470	2766470	type	True	92.3394	518	687	95	below_threshold
Leuconostoc suionicum	strain=DSM 20241	GCA_001891125.1	1511761	1511761	type	True	79.9556	214	687	95	below_threshold
Leuconostoc mesenteroides subsp. mesenteroides	strain=NBRC 100496	GCA_007990165.1	33967	1245	type	True	79.9529	215	687	95	below_threshold
Leuconostoc mesenteroides subsp. jonggajibkimchii	strain=DRC1506	GCA_001886915.1	2026657	1245	type	True	79.7384	210	687	95	below_threshold
Leuconostoc gelidum subsp. gelidum	strain=KCTC 3527	GCA_000166715.2	1607839	1244	type	True	79.0218	168	687	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	78.8032	165	687	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	78.7785	161	687	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:17,759] [INFO] DFAST Taxonomy check result was written to GCF_014634745.1_ASM1463474v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:17,760] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:17,760] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:17,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fc34347-996a-4c5e-a2e3-9948d191df44/dqc_reference/checkm_data
[2024-01-25 20:08:17,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:17,783] [INFO] Task started: CheckM
[2024-01-25 20:08:17,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014634745.1_ASM1463474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014634745.1_ASM1463474v1_genomic.fna/checkm_input GCF_014634745.1_ASM1463474v1_genomic.fna/checkm_result
[2024-01-25 20:08:36,808] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:36,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:36,823] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:36,823] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:36,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014634745.1_ASM1463474v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:36,824] [INFO] Task started: Blastn
[2024-01-25 20:08:36,824] [INFO] Running command: blastn -query GCF_014634745.1_ASM1463474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc34347-996a-4c5e-a2e3-9948d191df44/dqc_reference/reference_markers_gtdb.fasta -out GCF_014634745.1_ASM1463474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:37,571] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:37,574] [INFO] Selected 15 target genomes.
[2024-01-25 20:08:37,574] [INFO] Target genome list was writen to GCF_014634745.1_ASM1463474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:37,584] [INFO] Task started: fastANI
[2024-01-25 20:08:37,585] [INFO] Running command: fastANI --query /var/lib/cwl/stga034f94d-62db-4a14-ac0e-020c6374fd7d/GCF_014634745.1_ASM1463474v1_genomic.fna.gz --refList GCF_014634745.1_ASM1463474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014634745.1_ASM1463474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:44,058] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:44,066] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:44,066] [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	100.0	685	687	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	92.3056	519	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.11	96.75	0.91	0.87	34	-
GCF_000014445.1	s__Leuconostoc mesenteroides	80.2027	221	687	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	79.9919	220	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001891125.1	s__Leuconostoc suionicum	79.9303	215	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.16	97.05	0.94	0.91	7	-
GCF_012396485.1	s__Leuconostoc holzapfelii	79.6487	141	687	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	79.261	146	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.95	98.13	0.88	0.76	13	-
GCF_001047135.2	s__Fructobacillus tropaeoli	79.0557	52	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	97.33	96.88	0.89	0.88	3	-
GCF_000166715.1	s__Leuconostoc gelidum	79.0218	168	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
GCF_004354555.1	s__Leuconostoc citreum	78.9782	157	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.02	98.68	0.92	0.88	33	-
GCF_016908715.1	s__Leuconostoc rapi	78.6441	168	687	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	78.3299	109	687	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc_B	95.0	99.89	99.83	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:44,068] [INFO] GTDB search result was written to GCF_014634745.1_ASM1463474v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:44,068] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:44,071] [INFO] DFAST_QC result json was written to GCF_014634745.1_ASM1463474v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:44,071] [INFO] DFAST_QC completed!
[2024-01-25 20:08:44,071] [INFO] Total running time: 0h0m38s