[2024-01-24 12:31:34,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,933] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb74bec8-ba8e-4fc4-9482-6bbe9ef330c0/dqc_reference
[2024-01-24 12:31:36,281] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:36,282] [INFO] Task started: Prodigal
[2024-01-24 12:31:36,282] [INFO] Running command: gunzip -c /var/lib/cwl/stgec448507-b79e-4828-9c09-32880b570acb/GCF_001436175.1_ASM143617v1_genomic.fna.gz | prodigal -d GCF_001436175.1_ASM143617v1_genomic.fna/cds.fna -a GCF_001436175.1_ASM143617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:41,969] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:41,970] [INFO] Task started: HMMsearch
[2024-01-24 12:31:41,970] [INFO] Running command: hmmsearch --tblout GCF_001436175.1_ASM143617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb74bec8-ba8e-4fc4-9482-6bbe9ef330c0/dqc_reference/reference_markers.hmm GCF_001436175.1_ASM143617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:42,227] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:42,228] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgec448507-b79e-4828-9c09-32880b570acb/GCF_001436175.1_ASM143617v1_genomic.fna.gz]
[2024-01-24 12:31:42,255] [INFO] Query marker FASTA was written to GCF_001436175.1_ASM143617v1_genomic.fna/markers.fasta
[2024-01-24 12:31:42,255] [INFO] Task started: Blastn
[2024-01-24 12:31:42,255] [INFO] Running command: blastn -query GCF_001436175.1_ASM143617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb74bec8-ba8e-4fc4-9482-6bbe9ef330c0/dqc_reference/reference_markers.fasta -out GCF_001436175.1_ASM143617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:42,876] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:42,881] [INFO] Selected 6 target genomes.
[2024-01-24 12:31:42,881] [INFO] Target genome list was writen to GCF_001436175.1_ASM143617v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:42,886] [INFO] Task started: fastANI
[2024-01-24 12:31:42,886] [INFO] Running command: fastANI --query /var/lib/cwl/stgec448507-b79e-4828-9c09-32880b570acb/GCF_001436175.1_ASM143617v1_genomic.fna.gz --refList GCF_001436175.1_ASM143617v1_genomic.fna/target_genomes.txt --output GCF_001436175.1_ASM143617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:45,957] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:45,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb74bec8-ba8e-4fc4-9482-6bbe9ef330c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:45,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb74bec8-ba8e-4fc4-9482-6bbe9ef330c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:45,965] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:45,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:45,965] [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=DSM 20587	GCA_001436175.1	33962	33962	type	True	100.0	702	704	95	conclusive
Lentilactobacillus kefiri	strain=NBRC 15888	GCA_007989105.1	33962	33962	type	True	99.9339	674	704	95	conclusive
Lentilactobacillus sunkii	strain=DSM 19904	GCA_001435575.1	481719	481719	type	True	84.1327	520	704	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_000415925.1	481720	481720	type	True	83.7503	483	704	95	below_threshold
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	83.7242	483	704	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	83.6938	480	704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:45,967] [INFO] DFAST Taxonomy check result was written to GCF_001436175.1_ASM143617v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:45,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:45,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:45,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb74bec8-ba8e-4fc4-9482-6bbe9ef330c0/dqc_reference/checkm_data
[2024-01-24 12:31:45,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:45,995] [INFO] Task started: CheckM
[2024-01-24 12:31:45,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001436175.1_ASM143617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001436175.1_ASM143617v1_genomic.fna/checkm_input GCF_001436175.1_ASM143617v1_genomic.fna/checkm_result
[2024-01-24 12:32:10,661] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:10,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:10,690] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:10,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:10,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001436175.1_ASM143617v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:10,692] [INFO] Task started: Blastn
[2024-01-24 12:32:10,692] [INFO] Running command: blastn -query GCF_001436175.1_ASM143617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb74bec8-ba8e-4fc4-9482-6bbe9ef330c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001436175.1_ASM143617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:11,497] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:11,502] [INFO] Selected 8 target genomes.
[2024-01-24 12:32:11,503] [INFO] Target genome list was writen to GCF_001436175.1_ASM143617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:11,510] [INFO] Task started: fastANI
[2024-01-24 12:32:11,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgec448507-b79e-4828-9c09-32880b570acb/GCF_001436175.1_ASM143617v1_genomic.fna.gz --refList GCF_001436175.1_ASM143617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001436175.1_ASM143617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:15,867] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:15,880] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:15,880] [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	99.9339	674	704	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	84.143	519	704	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	83.7239	483	704	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	82.3184	452	704	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.61	97.12	0.94	0.90	27	-
GCF_001435315.1	s__Lentilactobacillus parabuchneri	81.5633	415	704	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.90	97.37	0.94	0.87	27	-
GCF_002157585.1	s__Lentilactobacillus parakefiri	81.4431	388	704	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.39	0.94	0.92	4	-
GCF_000583655.1	s__Lentilactobacillus farraginis	79.0085	184	704	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	78.2718	161	704	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 12:32:15,881] [INFO] GTDB search result was written to GCF_001436175.1_ASM143617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:15,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:15,886] [INFO] DFAST_QC result json was written to GCF_001436175.1_ASM143617v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:15,886] [INFO] DFAST_QC completed!
[2024-01-24 12:32:15,886] [INFO] Total running time: 0h0m41s