[2023-06-13 06:33:41,824] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:33:41,827] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:33:41,828] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4eb79c1-498f-4711-8fd5-4e871aa5e9bf/dqc_reference
[2023-06-13 06:33:43,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:33:43,361] [INFO] Task started: Prodigal
[2023-06-13 06:33:43,362] [INFO] Running command: gunzip -c /var/lib/cwl/stga1904fd4-c0e9-4538-b00c-09479d5b9925/GCA_022649545.1_ASM2264954v1_genomic.fna.gz | prodigal -d GCA_022649545.1_ASM2264954v1_genomic.fna/cds.fna -a GCA_022649545.1_ASM2264954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:33:46,820] [INFO] Task succeeded: Prodigal
[2023-06-13 06:33:46,821] [INFO] Task started: HMMsearch
[2023-06-13 06:33:46,821] [INFO] Running command: hmmsearch --tblout GCA_022649545.1_ASM2264954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4eb79c1-498f-4711-8fd5-4e871aa5e9bf/dqc_reference/reference_markers.hmm GCA_022649545.1_ASM2264954v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:33:47,020] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:33:47,022] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga1904fd4-c0e9-4538-b00c-09479d5b9925/GCA_022649545.1_ASM2264954v1_genomic.fna.gz]
[2023-06-13 06:33:47,044] [INFO] Query marker FASTA was written to GCA_022649545.1_ASM2264954v1_genomic.fna/markers.fasta
[2023-06-13 06:33:47,044] [INFO] Task started: Blastn
[2023-06-13 06:33:47,045] [INFO] Running command: blastn -query GCA_022649545.1_ASM2264954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4eb79c1-498f-4711-8fd5-4e871aa5e9bf/dqc_reference/reference_markers.fasta -out GCA_022649545.1_ASM2264954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:33:47,691] [INFO] Task succeeded: Blastn
[2023-06-13 06:33:47,695] [INFO] Selected 11 target genomes.
[2023-06-13 06:33:47,695] [INFO] Target genome list was writen to GCA_022649545.1_ASM2264954v1_genomic.fna/target_genomes.txt
[2023-06-13 06:33:47,775] [INFO] Task started: fastANI
[2023-06-13 06:33:47,775] [INFO] Running command: fastANI --query /var/lib/cwl/stga1904fd4-c0e9-4538-b00c-09479d5b9925/GCA_022649545.1_ASM2264954v1_genomic.fna.gz --refList GCA_022649545.1_ASM2264954v1_genomic.fna/target_genomes.txt --output GCA_022649545.1_ASM2264954v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:33:51,196] [INFO] Task succeeded: fastANI
[2023-06-13 06:33:51,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4eb79c1-498f-4711-8fd5-4e871aa5e9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:33:51,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4eb79c1-498f-4711-8fd5-4e871aa5e9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:33:51,204] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2023-06-13 06:33:51,204] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 06:33:51,204] [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 mesenteroides subsp. jonggajibkimchii	strain=DRC1506	GCA_001886915.1	2026657	1245	type	True	99.583	467	505	95	conclusive
Leuconostoc mesenteroides subsp. mesenteroides	strain=NBRC 100496	GCA_007990165.1	33967	1245	type	True	99.0451	469	505	95	conclusive
Leuconostoc mesenteroides subsp. dextranicum	strain=NBRC 100495	GCA_007990145.1	33966	1245	type	True	99.0126	409	505	95	conclusive
Leuconostoc mesenteroides	strain=NCTC12954	GCA_900461615.1	1245	1245	type	True	98.9979	478	505	95	conclusive
Leuconostoc mesenteroides subsp. mesenteroides	strain=ATCC 8293	GCA_000014445.1	33967	1245	type	True	98.9969	478	505	95	conclusive
Leuconostoc mesenteroides subsp. cremoris	strain=ATCC 19254	GCA_000160595.1	33965	1245	type	True	98.2043	381	505	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 06:33:51,206] [INFO] DFAST Taxonomy check result was written to GCA_022649545.1_ASM2264954v1_genomic.fna/tc_result.tsv
[2023-06-13 06:33:51,207] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:33:51,207] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:33:51,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4eb79c1-498f-4711-8fd5-4e871aa5e9bf/dqc_reference/checkm_data
[2023-06-13 06:33:51,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:33:51,225] [INFO] Task started: CheckM
[2023-06-13 06:33:51,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022649545.1_ASM2264954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022649545.1_ASM2264954v1_genomic.fna/checkm_input GCA_022649545.1_ASM2264954v1_genomic.fna/checkm_result
[2023-06-13 06:34:10,758] [INFO] Task succeeded: CheckM
[2023-06-13 06:34:10,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:34:10,777] [INFO] ===== Completeness check finished =====
[2023-06-13 06:34:10,777] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:34:10,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022649545.1_ASM2264954v1_genomic.fna/markers.fasta)
[2023-06-13 06:34:10,778] [INFO] Task started: Blastn
[2023-06-13 06:34:10,778] [INFO] Running command: blastn -query GCA_022649545.1_ASM2264954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4eb79c1-498f-4711-8fd5-4e871aa5e9bf/dqc_reference/reference_markers_gtdb.fasta -out GCA_022649545.1_ASM2264954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:34:11,558] [INFO] Task succeeded: Blastn
[2023-06-13 06:34:11,562] [INFO] Selected 10 target genomes.
[2023-06-13 06:34:11,562] [INFO] Target genome list was writen to GCA_022649545.1_ASM2264954v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:34:11,572] [INFO] Task started: fastANI
[2023-06-13 06:34:11,573] [INFO] Running command: fastANI --query /var/lib/cwl/stga1904fd4-c0e9-4538-b00c-09479d5b9925/GCA_022649545.1_ASM2264954v1_genomic.fna.gz --refList GCA_022649545.1_ASM2264954v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022649545.1_ASM2264954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:34:15,688] [INFO] Task succeeded: fastANI
[2023-06-13 06:34:15,700] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:34:15,701] [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_000014445.1	s__Leuconostoc mesenteroides	98.9969	478	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.82	97.34	0.92	0.82	89	conclusive
GCF_001891125.1	s__Leuconostoc suionicum	94.2267	460	505	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	90.9262	401	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_008107645.1	s__Leuconostoc litchii	81.7069	309	505	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	80.1939	99	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.86	96.88	0.92	0.91	7	-
GCF_000092505.1	s__Leuconostoc kimchii	79.7165	125	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_014634805.1	s__Leuconostoc falkenbergense	79.4684	161	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.11	96.75	0.91	0.87	34	-
GCF_014207505.1	s__Leuconostoc carnosum	79.3462	140	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	-
GCF_016908715.1	s__Leuconostoc rapi	79.1354	125	505	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 06:34:15,703] [INFO] GTDB search result was written to GCA_022649545.1_ASM2264954v1_genomic.fna/result_gtdb.tsv
[2023-06-13 06:34:15,703] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:34:15,706] [INFO] DFAST_QC result json was written to GCA_022649545.1_ASM2264954v1_genomic.fna/dqc_result.json
[2023-06-13 06:34:15,707] [INFO] DFAST_QC completed!
[2023-06-13 06:34:15,707] [INFO] Total running time: 0h0m34s