[2024-01-24 12:22:37,836] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:37,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:37,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg36f9941b-7408-41b8-90aa-dc0072bc27ea/dqc_reference
[2024-01-24 12:22:39,182] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,182] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,183] [INFO] Running command: gunzip -c /var/lib/cwl/stg0257f7ef-2605-4729-b6fa-9f1e7a8f3c7b/GCF_007989105.1_ASM798910v1_genomic.fna.gz | prodigal -d GCF_007989105.1_ASM798910v1_genomic.fna/cds.fna -a GCF_007989105.1_ASM798910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:45,067] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:45,068] [INFO] Task started: HMMsearch
[2024-01-24 12:22:45,068] [INFO] Running command: hmmsearch --tblout GCF_007989105.1_ASM798910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36f9941b-7408-41b8-90aa-dc0072bc27ea/dqc_reference/reference_markers.hmm GCF_007989105.1_ASM798910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:45,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:45,319] [INFO] Found 6/6 markers.
[2024-01-24 12:22:45,349] [INFO] Query marker FASTA was written to GCF_007989105.1_ASM798910v1_genomic.fna/markers.fasta
[2024-01-24 12:22:45,350] [INFO] Task started: Blastn
[2024-01-24 12:22:45,350] [INFO] Running command: blastn -query GCF_007989105.1_ASM798910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36f9941b-7408-41b8-90aa-dc0072bc27ea/dqc_reference/reference_markers.fasta -out GCF_007989105.1_ASM798910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:45,952] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:45,956] [INFO] Selected 11 target genomes.
[2024-01-24 12:22:45,957] [INFO] Target genome list was writen to GCF_007989105.1_ASM798910v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:45,962] [INFO] Task started: fastANI
[2024-01-24 12:22:45,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg0257f7ef-2605-4729-b6fa-9f1e7a8f3c7b/GCF_007989105.1_ASM798910v1_genomic.fna.gz --refList GCF_007989105.1_ASM798910v1_genomic.fna/target_genomes.txt --output GCF_007989105.1_ASM798910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:51,058] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:51,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36f9941b-7408-41b8-90aa-dc0072bc27ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:51,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36f9941b-7408-41b8-90aa-dc0072bc27ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:51,070] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:51,070] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:51,071] [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
Lentilactobacillus kefiri	strain=NBRC 15888	GCA_007989105.1	33962	33962	type	True	100.0	776	779	95	conclusive
Lentilactobacillus kefiri	strain=DSM 20587	GCA_001436175.1	33962	33962	type	True	99.9928	694	779	95	conclusive
Lentilactobacillus sunkii	strain=DSM 19904	GCA_001435575.1	481719	481719	type	True	84.0485	570	779	95	below_threshold
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	83.6759	534	779	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_000415925.1	481720	481720	type	True	83.6036	542	779	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	83.5497	535	779	95	below_threshold
Lentilactobacillus buchneri	strain=ATCC 4005	GCA_018314255.1	1581	1581	type	True	82.3598	490	779	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	78.8354	74	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:51,072] [INFO] DFAST Taxonomy check result was written to GCF_007989105.1_ASM798910v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:51,073] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:51,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:51,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36f9941b-7408-41b8-90aa-dc0072bc27ea/dqc_reference/checkm_data
[2024-01-24 12:22:51,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:51,106] [INFO] Task started: CheckM
[2024-01-24 12:22:51,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989105.1_ASM798910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989105.1_ASM798910v1_genomic.fna/checkm_input GCF_007989105.1_ASM798910v1_genomic.fna/checkm_result
[2024-01-24 12:23:16,255] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:16,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:16,277] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:16,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:16,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989105.1_ASM798910v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:16,278] [INFO] Task started: Blastn
[2024-01-24 12:23:16,278] [INFO] Running command: blastn -query GCF_007989105.1_ASM798910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36f9941b-7408-41b8-90aa-dc0072bc27ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989105.1_ASM798910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:17,055] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:17,059] [INFO] Selected 8 target genomes.
[2024-01-24 12:23:17,059] [INFO] Target genome list was writen to GCF_007989105.1_ASM798910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:17,067] [INFO] Task started: fastANI
[2024-01-24 12:23:17,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg0257f7ef-2605-4729-b6fa-9f1e7a8f3c7b/GCF_007989105.1_ASM798910v1_genomic.fna.gz --refList GCF_007989105.1_ASM798910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989105.1_ASM798910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:21,320] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:21,333] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:21,333] [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_007989105.1	s__Lentilactobacillus kefiri	100.0	776	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.76	99.64	0.95	0.93	9	conclusive
GCF_001435575.1	s__Lentilactobacillus sunkii	84.0481	569	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	96.44	96.44	0.90	0.90	2	-
GCF_001434145.1	s__Lentilactobacillus otakiensis	83.6759	534	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.95	99.91	1.00	1.00	3	-
GCF_018314255.1	s__Lentilactobacillus buchneri	82.3714	489	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.61	97.12	0.94	0.90	27	-
GCF_002157585.1	s__Lentilactobacillus parakefiri	81.8376	442	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.39	0.94	0.92	4	-
GCF_001435315.1	s__Lentilactobacillus parabuchneri	81.4545	454	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.90	97.37	0.94	0.87	27	-
GCF_000583655.1	s__Lentilactobacillus farraginis	78.9519	191	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_900411375.1	s__Lentilactobacillus raoultii	78.1768	182	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:21,335] [INFO] GTDB search result was written to GCF_007989105.1_ASM798910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:21,336] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:21,339] [INFO] DFAST_QC result json was written to GCF_007989105.1_ASM798910v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:21,339] [INFO] DFAST_QC completed!
[2024-01-24 12:23:21,339] [INFO] Total running time: 0h0m44s