[2024-01-24 14:46:35,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,703] [INFO] DQC Reference Directory: /var/lib/cwl/stga67fef0e-3a80-4000-b490-2f64db883a29/dqc_reference
[2024-01-24 14:46:37,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,181] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg048c174b-91c3-4d96-936e-c75f8dfdea31/GCF_003641165.1_ASM364116v1_genomic.fna.gz | prodigal -d GCF_003641165.1_ASM364116v1_genomic.fna/cds.fna -a GCF_003641165.1_ASM364116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:44,869] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:44,870] [INFO] Task started: HMMsearch
[2024-01-24 14:46:44,870] [INFO] Running command: hmmsearch --tblout GCF_003641165.1_ASM364116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga67fef0e-3a80-4000-b490-2f64db883a29/dqc_reference/reference_markers.hmm GCF_003641165.1_ASM364116v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:45,064] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:45,065] [INFO] Found 6/6 markers.
[2024-01-24 14:46:45,090] [INFO] Query marker FASTA was written to GCF_003641165.1_ASM364116v1_genomic.fna/markers.fasta
[2024-01-24 14:46:45,091] [INFO] Task started: Blastn
[2024-01-24 14:46:45,091] [INFO] Running command: blastn -query GCF_003641165.1_ASM364116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga67fef0e-3a80-4000-b490-2f64db883a29/dqc_reference/reference_markers.fasta -out GCF_003641165.1_ASM364116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:45,651] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:45,654] [INFO] Selected 9 target genomes.
[2024-01-24 14:46:45,654] [INFO] Target genome list was writen to GCF_003641165.1_ASM364116v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:45,687] [INFO] Task started: fastANI
[2024-01-24 14:46:45,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg048c174b-91c3-4d96-936e-c75f8dfdea31/GCF_003641165.1_ASM364116v1_genomic.fna.gz --refList GCF_003641165.1_ASM364116v1_genomic.fna/target_genomes.txt --output GCF_003641165.1_ASM364116v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:46:52,014] [INFO] Task succeeded: fastANI
[2024-01-24 14:46:52,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga67fef0e-3a80-4000-b490-2f64db883a29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:46:52,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga67fef0e-3a80-4000-b490-2f64db883a29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:46:52,021] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:46:52,021] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:46:52,021] [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 argentoratensis	strain=DSM 16365	GCA_003641165.1	271881	271881	type	True	100.0	1100	1112	95	inconclusive
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_001435215.1	271881	271881	type	True	99.9275	982	1112	95	inconclusive
Lactiplantibacillus plantarum	strain=DSM 20174	GCA_014131735.1	1590	1590	type	True	95.7184	935	1112	95	inconclusive
Lactiplantibacillus plantarum subsp. plantarum	strain=CGMCC 1.2437	GCA_001434175.1	337330	1590	type	True	95.7025	902	1112	95	inconclusive
Lactiplantibacillus plantarum subsp. plantarum	strain=NBRC 15891	GCA_007989145.1	337330	1590	type	True	95.6509	888	1112	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 14:46:52,022] [INFO] DFAST Taxonomy check result was written to GCF_003641165.1_ASM364116v1_genomic.fna/tc_result.tsv
[2024-01-24 14:46:52,023] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:46:52,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:46:52,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga67fef0e-3a80-4000-b490-2f64db883a29/dqc_reference/checkm_data
[2024-01-24 14:46:52,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:46:52,055] [INFO] Task started: CheckM
[2024-01-24 14:46:52,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003641165.1_ASM364116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003641165.1_ASM364116v1_genomic.fna/checkm_input GCF_003641165.1_ASM364116v1_genomic.fna/checkm_result
[2024-01-24 14:47:19,679] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:19,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:19,698] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:19,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:19,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003641165.1_ASM364116v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:19,699] [INFO] Task started: Blastn
[2024-01-24 14:47:19,699] [INFO] Running command: blastn -query GCF_003641165.1_ASM364116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga67fef0e-3a80-4000-b490-2f64db883a29/dqc_reference/reference_markers_gtdb.fasta -out GCF_003641165.1_ASM364116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:20,449] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:20,452] [INFO] Selected 9 target genomes.
[2024-01-24 14:47:20,452] [INFO] Target genome list was writen to GCF_003641165.1_ASM364116v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:20,459] [INFO] Task started: fastANI
[2024-01-24 14:47:20,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg048c174b-91c3-4d96-936e-c75f8dfdea31/GCF_003641165.1_ASM364116v1_genomic.fna.gz --refList GCF_003641165.1_ASM364116v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003641165.1_ASM364116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:26,814] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:26,822] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:26,822] [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_014131735.1	s__Lactiplantibacillus plantarum	95.7294	934	1112	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.89	95.74	0.92	0.82	629	conclusive
GCF_003641145.1	s__Lactiplantibacillus paraplantarum	87.5837	821	1112	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.82	97.28	0.92	0.86	13	-
GCF_003641185.1	s__Lactiplantibacillus pentosus	82.992	686	1112	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.89	96.07	0.90	0.86	56	-
GCF_000463075.2	s__Lactiplantibacillus plantarum_A	82.7014	635	1112	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_003885105.1	s__Lactiplantibacillus garii	80.956	402	1112	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	80.7762	381	1112	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405425.1	s__Lactiplantibacillus modestisalitolerans	80.1792	304	1112	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405065.1	s__Lactiplantibacillus nangangensis	80.0622	327	1112	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002970915.1	s__Lactiplantibacillus sp002970915	79.96	293	1112	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 14:47:26,824] [INFO] GTDB search result was written to GCF_003641165.1_ASM364116v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:26,825] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:26,827] [INFO] DFAST_QC result json was written to GCF_003641165.1_ASM364116v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:26,828] [INFO] DFAST_QC completed!
[2024-01-24 14:47:26,828] [INFO] Total running time: 0h0m51s