[2024-01-24 13:31:44,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,324] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg83e8f5f5-f208-40fe-bd71-8a43b8779c28/dqc_reference
[2024-01-24 13:31:45,669] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,670] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,670] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2d4bcbc-935f-4a6c-a759-93e0fa05af8d/GCF_001436735.1_ASM143673v1_genomic.fna.gz | prodigal -d GCF_001436735.1_ASM143673v1_genomic.fna/cds.fna -a GCF_001436735.1_ASM143673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:49,533] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:49,534] [INFO] Task started: HMMsearch
[2024-01-24 13:31:49,534] [INFO] Running command: hmmsearch --tblout GCF_001436735.1_ASM143673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83e8f5f5-f208-40fe-bd71-8a43b8779c28/dqc_reference/reference_markers.hmm GCF_001436735.1_ASM143673v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:49,773] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:49,775] [INFO] Found 6/6 markers.
[2024-01-24 13:31:49,802] [INFO] Query marker FASTA was written to GCF_001436735.1_ASM143673v1_genomic.fna/markers.fasta
[2024-01-24 13:31:49,802] [INFO] Task started: Blastn
[2024-01-24 13:31:49,803] [INFO] Running command: blastn -query GCF_001436735.1_ASM143673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83e8f5f5-f208-40fe-bd71-8a43b8779c28/dqc_reference/reference_markers.fasta -out GCF_001436735.1_ASM143673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:50,398] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:50,401] [INFO] Selected 25 target genomes.
[2024-01-24 13:31:50,402] [INFO] Target genome list was writen to GCF_001436735.1_ASM143673v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:50,417] [INFO] Task started: fastANI
[2024-01-24 13:31:50,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d4bcbc-935f-4a6c-a759-93e0fa05af8d/GCF_001436735.1_ASM143673v1_genomic.fna.gz --refList GCF_001436735.1_ASM143673v1_genomic.fna/target_genomes.txt --output GCF_001436735.1_ASM143673v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:59,183] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:59,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83e8f5f5-f208-40fe-bd71-8a43b8779c28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:59,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83e8f5f5-f208-40fe-bd71-8a43b8779c28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:59,197] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:59,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:59,198] [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
Liquorilactobacillus cacaonum	strain=DSM 21116	GCA_001436735.1	483012	483012	type	True	100.0	632	633	95	conclusive
Liquorilactobacillus hordei	strain=DSM 19519	GCA_019443985.1	468911	468911	type	True	80.3491	333	633	95	below_threshold
Liquorilactobacillus hordei	strain=DSM 19519	GCA_001434845.1	468911	468911	type	True	80.3013	329	633	95	below_threshold
Liquorilactobacillus mali	strain=DSM 20444	GCA_000276905.1	1618	1618	type	True	79.8888	266	633	95	below_threshold
Liquorilactobacillus mali	strain=KCTC 3596	GCA_000260415.1	1618	1618	type	True	79.8208	313	633	95	below_threshold
Liquorilactobacillus mali	strain=DSM 20444	GCA_001436535.1	1618	1618	type	True	79.7443	302	633	95	below_threshold
Liquorilactobacillus sucicola	strain=JCM 15457	GCA_000612445.1	519050	519050	type	True	78.132	92	633	95	below_threshold
Liquorilactobacillus satsumensis	strain=JCM 12392	GCA_001312045.1	259059	259059	type	True	77.7717	110	633	95	below_threshold
Liquorilactobacillus satsumensis	strain=DSM 16230	GCA_001435195.1	259059	259059	type	True	77.7436	115	633	95	below_threshold
Liquorilactobacillus nagelii	strain=DSM 13675	GCA_019444005.1	82688	82688	type	True	77.6798	107	633	95	below_threshold
Liquorilactobacillus nagelii	strain=DSM 13675	GCA_001434225.1	82688	82688	type	True	77.4495	110	633	95	below_threshold
Ligilactobacillus salivarius	strain=DSM 20554	GCA_002079585.1	1624	1624	type	True	77.2682	74	633	95	below_threshold
Liquorilactobacillus vini	strain=DSM 20605	GCA_000255495.2	238015	238015	type	True	77.2556	73	633	95	below_threshold
Liquorilactobacillus vini	strain=DSM 20605	GCA_001435395.1	238015	238015	type	True	77.08	76	633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:59,199] [INFO] DFAST Taxonomy check result was written to GCF_001436735.1_ASM143673v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:59,200] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:59,200] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:59,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83e8f5f5-f208-40fe-bd71-8a43b8779c28/dqc_reference/checkm_data
[2024-01-24 13:31:59,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:59,223] [INFO] Task started: CheckM
[2024-01-24 13:31:59,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001436735.1_ASM143673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001436735.1_ASM143673v1_genomic.fna/checkm_input GCF_001436735.1_ASM143673v1_genomic.fna/checkm_result
[2024-01-24 13:32:19,884] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:19,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:19,909] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:19,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:19,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001436735.1_ASM143673v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:19,911] [INFO] Task started: Blastn
[2024-01-24 13:32:19,911] [INFO] Running command: blastn -query GCF_001436735.1_ASM143673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83e8f5f5-f208-40fe-bd71-8a43b8779c28/dqc_reference/reference_markers_gtdb.fasta -out GCF_001436735.1_ASM143673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:20,696] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:20,699] [INFO] Selected 22 target genomes.
[2024-01-24 13:32:20,700] [INFO] Target genome list was writen to GCF_001436735.1_ASM143673v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:20,722] [INFO] Task started: fastANI
[2024-01-24 13:32:20,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d4bcbc-935f-4a6c-a759-93e0fa05af8d/GCF_001436735.1_ASM143673v1_genomic.fna.gz --refList GCF_001436735.1_ASM143673v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001436735.1_ASM143673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:29,081] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:29,091] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:29,091] [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_001436735.1	s__Liquorilactobacillus cacaonum	100.0	632	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001434845.1	s__Liquorilactobacillus hordei	80.3013	329	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.13	98.13	0.87	0.87	2	-
GCF_000260415.1	s__Liquorilactobacillus mali	79.8228	311	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.97	99.95	0.96	0.94	4	-
GCF_001437155.1	s__Liquorilactobacillus mali_A	79.7043	299	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612445.1	s__Liquorilactobacillus sucicola	78.1712	91	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001435195.1	s__Liquorilactobacillus satsumensis	77.7436	115	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.78	99.78	0.99	0.99	2	-
GCF_001434225.1	s__Liquorilactobacillus nagelii	77.4495	110	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.67	98.67	0.89	0.89	2	-
GCF_001435235.1	s__Liquorilactobacillus ghanensis	77.2964	92	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000255495.1	s__Liquorilactobacillus vini	77.2556	73	633	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 13:32:29,093] [INFO] GTDB search result was written to GCF_001436735.1_ASM143673v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:29,094] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:29,101] [INFO] DFAST_QC result json was written to GCF_001436735.1_ASM143673v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:29,102] [INFO] DFAST_QC completed!
[2024-01-24 13:32:29,102] [INFO] Total running time: 0h0m45s