[2024-01-24 14:19:59,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d8d831e-b06e-465f-8172-a3268dae0200/dqc_reference
[2024-01-24 14:20:01,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:01,224] [INFO] Task started: Prodigal
[2024-01-24 14:20:01,225] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb3ce373-ec4e-4bec-8de4-c1fb76ffe8dc/GCF_007991835.1_ASM799183v1_genomic.fna.gz | prodigal -d GCF_007991835.1_ASM799183v1_genomic.fna/cds.fna -a GCF_007991835.1_ASM799183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:09,584] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:09,585] [INFO] Task started: HMMsearch
[2024-01-24 14:20:09,585] [INFO] Running command: hmmsearch --tblout GCF_007991835.1_ASM799183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d8d831e-b06e-465f-8172-a3268dae0200/dqc_reference/reference_markers.hmm GCF_007991835.1_ASM799183v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:09,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:09,892] [INFO] Found 6/6 markers.
[2024-01-24 14:20:09,928] [INFO] Query marker FASTA was written to GCF_007991835.1_ASM799183v1_genomic.fna/markers.fasta
[2024-01-24 14:20:09,928] [INFO] Task started: Blastn
[2024-01-24 14:20:09,928] [INFO] Running command: blastn -query GCF_007991835.1_ASM799183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d8d831e-b06e-465f-8172-a3268dae0200/dqc_reference/reference_markers.fasta -out GCF_007991835.1_ASM799183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:10,583] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:10,587] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:10,588] [INFO] Target genome list was writen to GCF_007991835.1_ASM799183v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:10,605] [INFO] Task started: fastANI
[2024-01-24 14:20:10,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb3ce373-ec4e-4bec-8de4-c1fb76ffe8dc/GCF_007991835.1_ASM799183v1_genomic.fna.gz --refList GCF_007991835.1_ASM799183v1_genomic.fna/target_genomes.txt --output GCF_007991835.1_ASM799183v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:17,877] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:17,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d8d831e-b06e-465f-8172-a3268dae0200/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:17,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d8d831e-b06e-465f-8172-a3268dae0200/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:17,893] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:20:17,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:17,893] [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
Lactiplantibacillus pentosus	strain=ATCC 8041	GCA_004354685.1	1589	1589	type	True	99.9949	1074	1076	95	conclusive
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_003641185.1	1589	1589	type	True	99.994	1076	1076	95	conclusive
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_001433755.1	1589	1589	type	True	99.9715	1068	1076	95	conclusive
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_003641165.1	271881	271881	type	True	82.5712	630	1076	95	below_threshold
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_001435215.1	271881	271881	type	True	82.5312	606	1076	95	below_threshold
Lactiplantibacillus plantarum subsp. plantarum	strain=CGMCC 1.2437	GCA_001434175.1	337330	1590	type	True	82.4387	614	1076	95	below_threshold
Lactiplantibacillus plantarum	strain=DSM 20174	GCA_014131735.1	1590	1590	type	True	82.4247	621	1076	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	78.627	65	1076	95	below_threshold
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	78.3217	63	1076	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	77.6977	63	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:17,895] [INFO] DFAST Taxonomy check result was written to GCF_007991835.1_ASM799183v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:17,895] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:17,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:17,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d8d831e-b06e-465f-8172-a3268dae0200/dqc_reference/checkm_data
[2024-01-24 14:20:17,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:17,939] [INFO] Task started: CheckM
[2024-01-24 14:20:17,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991835.1_ASM799183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991835.1_ASM799183v1_genomic.fna/checkm_input GCF_007991835.1_ASM799183v1_genomic.fna/checkm_result
[2024-01-24 14:20:49,788] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:49,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:49,812] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:49,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:49,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991835.1_ASM799183v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:49,813] [INFO] Task started: Blastn
[2024-01-24 14:20:49,813] [INFO] Running command: blastn -query GCF_007991835.1_ASM799183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d8d831e-b06e-465f-8172-a3268dae0200/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991835.1_ASM799183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:50,597] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:50,601] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:50,601] [INFO] Target genome list was writen to GCF_007991835.1_ASM799183v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:50,624] [INFO] Task started: fastANI
[2024-01-24 14:20:50,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb3ce373-ec4e-4bec-8de4-c1fb76ffe8dc/GCF_007991835.1_ASM799183v1_genomic.fna.gz --refList GCF_007991835.1_ASM799183v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991835.1_ASM799183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:58,149] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:58,163] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:58,163] [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_003641185.1	s__Lactiplantibacillus pentosus	99.994	1076	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.89	96.07	0.90	0.86	56	conclusive
GCF_000463075.2	s__Lactiplantibacillus plantarum_A	93.3193	923	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_014131735.1	s__Lactiplantibacillus plantarum	82.4247	621	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.89	95.74	0.92	0.82	629	-
GCF_003641145.1	s__Lactiplantibacillus paraplantarum	82.0951	608	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.82	97.28	0.92	0.86	13	-
GCF_001039045.1	s__Lactiplantibacillus herbarum	80.5121	422	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001438845.1	s__Lactiplantibacillus xiangfangensis	80.4678	368	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498955.2	s__Lactiplantibacillus fabifermentans	80.3853	335	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_003885105.1	s__Lactiplantibacillus garii	80.381	361	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405085.1	s__Lactiplantibacillus daowaiensis	79.9888	288	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405125.1	s__Lactiplantibacillus songbeiensis	79.877	288	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:58,165] [INFO] GTDB search result was written to GCF_007991835.1_ASM799183v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:58,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:58,169] [INFO] DFAST_QC result json was written to GCF_007991835.1_ASM799183v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:58,169] [INFO] DFAST_QC completed!
[2024-01-24 14:20:58,170] [INFO] Total running time: 0h0m58s