[2024-01-24 12:47:06,874] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:06,876] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:06,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg8856cb03-3338-4e96-b26c-ac06506fab41/dqc_reference
[2024-01-24 12:47:08,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:08,084] [INFO] Task started: Prodigal
[2024-01-24 12:47:08,085] [INFO] Running command: gunzip -c /var/lib/cwl/stga0f021b4-d062-43bf-87b1-da39d9f5f5d3/GCF_007991295.1_ASM799129v1_genomic.fna.gz | prodigal -d GCF_007991295.1_ASM799129v1_genomic.fna/cds.fna -a GCF_007991295.1_ASM799129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:12,744] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:12,744] [INFO] Task started: HMMsearch
[2024-01-24 12:47:12,744] [INFO] Running command: hmmsearch --tblout GCF_007991295.1_ASM799129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8856cb03-3338-4e96-b26c-ac06506fab41/dqc_reference/reference_markers.hmm GCF_007991295.1_ASM799129v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:12,988] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:12,989] [INFO] Found 6/6 markers.
[2024-01-24 12:47:13,026] [INFO] Query marker FASTA was written to GCF_007991295.1_ASM799129v1_genomic.fna/markers.fasta
[2024-01-24 12:47:13,027] [INFO] Task started: Blastn
[2024-01-24 12:47:13,027] [INFO] Running command: blastn -query GCF_007991295.1_ASM799129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8856cb03-3338-4e96-b26c-ac06506fab41/dqc_reference/reference_markers.fasta -out GCF_007991295.1_ASM799129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:13,690] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:13,694] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:13,694] [INFO] Target genome list was writen to GCF_007991295.1_ASM799129v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:13,784] [INFO] Task started: fastANI
[2024-01-24 12:47:13,784] [INFO] Running command: fastANI --query /var/lib/cwl/stga0f021b4-d062-43bf-87b1-da39d9f5f5d3/GCF_007991295.1_ASM799129v1_genomic.fna.gz --refList GCF_007991295.1_ASM799129v1_genomic.fna/target_genomes.txt --output GCF_007991295.1_ASM799129v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:21,410] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:21,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8856cb03-3338-4e96-b26c-ac06506fab41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:21,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8856cb03-3338-4e96-b26c-ac06506fab41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:21,418] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:47:21,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:21,418] [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
Ligilactobacillus pobuzihii	strain=NBRC 103219	GCA_007991295.1	449659	449659	type	True	100.0	744	749	95	conclusive
Ligilactobacillus pobuzihii	strain=NBRC 103219	GCA_001438865.1	449659	449659	type	True	99.9952	743	749	95	conclusive
Ligilactobacillus pobuzihii	strain=E100301	GCA_000349725.1	449659	449659	type	True	99.9878	747	749	95	conclusive
Ligilactobacillus pobuzihii	strain=KCTC 13174	GCA_001433815.1	449659	449659	type	True	99.9801	732	749	95	conclusive
Ligilactobacillus acidipiscis	strain=DSM 15836	GCA_001435755.1	89059	89059	type	True	80.4057	321	749	95	below_threshold
Ligilactobacillus salitolerans	strain=YK43	GCA_003864415.1	1808352	1808352	type	True	78.1703	199	749	95	below_threshold
Liquorilactobacillus vini	strain=DSM 20605	GCA_000255495.2	238015	238015	type	True	76.4093	61	749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:21,420] [INFO] DFAST Taxonomy check result was written to GCF_007991295.1_ASM799129v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:21,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:21,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:21,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8856cb03-3338-4e96-b26c-ac06506fab41/dqc_reference/checkm_data
[2024-01-24 12:47:21,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:21,447] [INFO] Task started: CheckM
[2024-01-24 12:47:21,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991295.1_ASM799129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991295.1_ASM799129v1_genomic.fna/checkm_input GCF_007991295.1_ASM799129v1_genomic.fna/checkm_result
[2024-01-24 12:47:43,192] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:43,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:43,210] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:43,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:43,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991295.1_ASM799129v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:43,211] [INFO] Task started: Blastn
[2024-01-24 12:47:43,211] [INFO] Running command: blastn -query GCF_007991295.1_ASM799129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8856cb03-3338-4e96-b26c-ac06506fab41/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991295.1_ASM799129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:43,943] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:43,946] [INFO] Selected 16 target genomes.
[2024-01-24 12:47:43,946] [INFO] Target genome list was writen to GCF_007991295.1_ASM799129v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:43,956] [INFO] Task started: fastANI
[2024-01-24 12:47:43,956] [INFO] Running command: fastANI --query /var/lib/cwl/stga0f021b4-d062-43bf-87b1-da39d9f5f5d3/GCF_007991295.1_ASM799129v1_genomic.fna.gz --refList GCF_007991295.1_ASM799129v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991295.1_ASM799129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:50,272] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:50,281] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:50,281] [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_000349725.1	s__Ligilactobacillus pobuzihii	99.9878	747	749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.99	99.98	1.00	0.99	4	conclusive
GCA_019116985.1	s__Ligilactobacillus excrementavium	93.9252	517	749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.12	97.12	0.91	0.91	2	-
GCF_001435755.1	s__Ligilactobacillus acidipiscis	80.4242	320	749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.45	97.83	0.82	0.76	9	-
GCA_019114105.1	s__Ligilactobacillus excrementipullorum	78.475	203	749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003864415.1	s__Ligilactobacillus salitolerans	78.1774	198	749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587695.1	s__Ligilactobacillus sp910587695	77.1164	63	749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423245.1	s__Ligilactobacillus ceti	76.7359	55	749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000615845.1	s__Ligilactobacillus hayakitensis	76.73	51	749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000255495.1	s__Liquorilactobacillus vini	76.4093	61	749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.24	98.67	0.86	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:50,282] [INFO] GTDB search result was written to GCF_007991295.1_ASM799129v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:50,283] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:50,285] [INFO] DFAST_QC result json was written to GCF_007991295.1_ASM799129v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:50,286] [INFO] DFAST_QC completed!
[2024-01-24 12:47:50,286] [INFO] Total running time: 0h0m43s