[2024-01-24 12:15:20,804] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,806] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,806] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4fbb212-4f0a-43f0-8b3f-5c40ccdb8f0c/dqc_reference
[2024-01-24 12:15:22,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:22,177] [INFO] Task started: Prodigal
[2024-01-24 12:15:22,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg8087ad60-56f7-44d8-97ac-d9e059af63ca/GCF_030161455.1_ASM3016145v1_genomic.fna.gz | prodigal -d GCF_030161455.1_ASM3016145v1_genomic.fna/cds.fna -a GCF_030161455.1_ASM3016145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:26,598] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:26,598] [INFO] Task started: HMMsearch
[2024-01-24 12:15:26,598] [INFO] Running command: hmmsearch --tblout GCF_030161455.1_ASM3016145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4fbb212-4f0a-43f0-8b3f-5c40ccdb8f0c/dqc_reference/reference_markers.hmm GCF_030161455.1_ASM3016145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:26,840] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:26,842] [INFO] Found 6/6 markers.
[2024-01-24 12:15:26,864] [INFO] Query marker FASTA was written to GCF_030161455.1_ASM3016145v1_genomic.fna/markers.fasta
[2024-01-24 12:15:26,865] [INFO] Task started: Blastn
[2024-01-24 12:15:26,865] [INFO] Running command: blastn -query GCF_030161455.1_ASM3016145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4fbb212-4f0a-43f0-8b3f-5c40ccdb8f0c/dqc_reference/reference_markers.fasta -out GCF_030161455.1_ASM3016145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:27,488] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:27,495] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:27,495] [INFO] Target genome list was writen to GCF_030161455.1_ASM3016145v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:27,500] [INFO] Task started: fastANI
[2024-01-24 12:15:27,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg8087ad60-56f7-44d8-97ac-d9e059af63ca/GCF_030161455.1_ASM3016145v1_genomic.fna.gz --refList GCF_030161455.1_ASM3016145v1_genomic.fna/target_genomes.txt --output GCF_030161455.1_ASM3016145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:30,810] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:30,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4fbb212-4f0a-43f0-8b3f-5c40ccdb8f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:30,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4fbb212-4f0a-43f0-8b3f-5c40ccdb8f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:30,817] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:30,817] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:30,817] [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 gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	99.9994	633	640	95	conclusive
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	99.9986	639	640	95	conclusive
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_020089505.1	1607837	1244	type	True	94.5792	566	640	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_019655935.1	1607837	1244	type	True	94.5467	567	640	95	below_threshold
Leuconostoc gelidum subsp. gelidum	strain=KCTC 3527	GCA_000166715.2	1607839	1244	type	True	94.0289	559	640	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:30,819] [INFO] DFAST Taxonomy check result was written to GCF_030161455.1_ASM3016145v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:30,819] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:30,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:30,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4fbb212-4f0a-43f0-8b3f-5c40ccdb8f0c/dqc_reference/checkm_data
[2024-01-24 12:15:30,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:30,847] [INFO] Task started: CheckM
[2024-01-24 12:15:30,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161455.1_ASM3016145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161455.1_ASM3016145v1_genomic.fna/checkm_input GCF_030161455.1_ASM3016145v1_genomic.fna/checkm_result
[2024-01-24 12:15:50,868] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:50,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:50,887] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:50,888] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:50,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161455.1_ASM3016145v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:50,889] [INFO] Task started: Blastn
[2024-01-24 12:15:50,889] [INFO] Running command: blastn -query GCF_030161455.1_ASM3016145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4fbb212-4f0a-43f0-8b3f-5c40ccdb8f0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161455.1_ASM3016145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:51,647] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:51,650] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:51,650] [INFO] Target genome list was writen to GCF_030161455.1_ASM3016145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:51,660] [INFO] Task started: fastANI
[2024-01-24 12:15:51,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg8087ad60-56f7-44d8-97ac-d9e059af63ca/GCF_030161455.1_ASM3016145v1_genomic.fna.gz --refList GCF_030161455.1_ASM3016145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161455.1_ASM3016145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:56,451] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:56,462] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:56,462] [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
GCA_000166735.2	s__Leuconostoc inhae	99.3646	489	640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.95	98.13	0.88	0.76	13	conclusive
GCF_000166715.1	s__Leuconostoc gelidum	94.0289	559	640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
GCF_000092505.1	s__Leuconostoc kimchii	80.0842	321	640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_016908715.1	s__Leuconostoc rapi	79.9749	337	640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207505.1	s__Leuconostoc carnosum	79.868	265	640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.31	98.70	0.92	0.87	17	-
GCF_004354555.1	s__Leuconostoc citreum	79.1617	215	640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.02	98.68	0.92	0.88	33	-
GCF_012396485.1	s__Leuconostoc holzapfelii	78.8471	174	640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014634745.1	s__Leuconostoc pseudomesenteroides	78.6068	165	640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.98	96.85	0.90	0.84	11	-
GCF_007954625.1	s__Leuconostoc lactis_A	78.5077	197	640	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.86	96.88	0.92	0.91	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:56,464] [INFO] GTDB search result was written to GCF_030161455.1_ASM3016145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:56,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:56,468] [INFO] DFAST_QC result json was written to GCF_030161455.1_ASM3016145v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:56,468] [INFO] DFAST_QC completed!
[2024-01-24 12:15:56,468] [INFO] Total running time: 0h0m36s