[2024-01-24 15:18:38,788] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg18ff9a73-f628-4c18-9164-6c47a0195448/dqc_reference
[2024-01-24 15:18:40,148] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,150] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,150] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd9ccb2e-6ddb-4c14-8016-1e64dd1180e1/GCF_004115745.1_ASM411574v1_genomic.fna.gz | prodigal -d GCF_004115745.1_ASM411574v1_genomic.fna/cds.fna -a GCF_004115745.1_ASM411574v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:46,500] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:46,501] [INFO] Task started: HMMsearch
[2024-01-24 15:18:46,501] [INFO] Running command: hmmsearch --tblout GCF_004115745.1_ASM411574v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18ff9a73-f628-4c18-9164-6c47a0195448/dqc_reference/reference_markers.hmm GCF_004115745.1_ASM411574v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:46,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:46,814] [INFO] Found 6/6 markers.
[2024-01-24 15:18:46,843] [INFO] Query marker FASTA was written to GCF_004115745.1_ASM411574v1_genomic.fna/markers.fasta
[2024-01-24 15:18:46,843] [INFO] Task started: Blastn
[2024-01-24 15:18:46,843] [INFO] Running command: blastn -query GCF_004115745.1_ASM411574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18ff9a73-f628-4c18-9164-6c47a0195448/dqc_reference/reference_markers.fasta -out GCF_004115745.1_ASM411574v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:49,182] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:49,185] [INFO] Selected 15 target genomes.
[2024-01-24 15:18:49,185] [INFO] Target genome list was writen to GCF_004115745.1_ASM411574v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:49,236] [INFO] Task started: fastANI
[2024-01-24 15:18:49,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd9ccb2e-6ddb-4c14-8016-1e64dd1180e1/GCF_004115745.1_ASM411574v1_genomic.fna.gz --refList GCF_004115745.1_ASM411574v1_genomic.fna/target_genomes.txt --output GCF_004115745.1_ASM411574v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:57,628] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:57,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18ff9a73-f628-4c18-9164-6c47a0195448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:57,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18ff9a73-f628-4c18-9164-6c47a0195448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:57,637] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:57,638] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:57,638] [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
Levilactobacillus suantsaii	strain=BCRC 12945	GCA_004115745.1	2292255	2292255	type	True	100.0	778	779	95	conclusive
Levilactobacillus zymae	strain=DSM 19395	GCA_001434115.1	267363	267363	type	True	81.1962	475	779	95	below_threshold
Levilactobacillus acidifarinae	strain=DSM 19394	GCA_001434835.1	267364	267364	type	True	80.9844	460	779	95	below_threshold
Levilactobacillus spicheri	strain=DSM 15429	GCA_001435095.1	216463	216463	type	True	79.788	369	779	95	below_threshold
Levilactobacillus namurensis	strain=DSM 19117	GCA_001434785.1	380393	380393	type	True	79.7405	317	779	95	below_threshold
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	79.346	258	779	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	79.3122	290	779	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	79.0487	309	779	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	76.922	75	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:57,639] [INFO] DFAST Taxonomy check result was written to GCF_004115745.1_ASM411574v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:57,640] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:57,640] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:57,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18ff9a73-f628-4c18-9164-6c47a0195448/dqc_reference/checkm_data
[2024-01-24 15:18:57,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:57,671] [INFO] Task started: CheckM
[2024-01-24 15:18:57,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004115745.1_ASM411574v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004115745.1_ASM411574v1_genomic.fna/checkm_input GCF_004115745.1_ASM411574v1_genomic.fna/checkm_result
[2024-01-24 15:19:24,958] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:24,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:24,977] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:24,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:24,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004115745.1_ASM411574v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:24,978] [INFO] Task started: Blastn
[2024-01-24 15:19:24,978] [INFO] Running command: blastn -query GCF_004115745.1_ASM411574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18ff9a73-f628-4c18-9164-6c47a0195448/dqc_reference/reference_markers_gtdb.fasta -out GCF_004115745.1_ASM411574v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:25,913] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:25,917] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:25,917] [INFO] Target genome list was writen to GCF_004115745.1_ASM411574v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:25,927] [INFO] Task started: fastANI
[2024-01-24 15:19:25,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd9ccb2e-6ddb-4c14-8016-1e64dd1180e1/GCF_004115745.1_ASM411574v1_genomic.fna.gz --refList GCF_004115745.1_ASM411574v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004115745.1_ASM411574v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:31,622] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:31,635] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:31,635] [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_004115745.1	s__Levilactobacillus suantsaii	100.0	778	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	1.00	1.00	2	conclusive
GCF_001434115.1	s__Levilactobacillus zymae	81.1962	475	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.08	97.26	0.95	0.86	4	-
GCF_001434835.1	s__Levilactobacillus acidifarinae	80.9797	460	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001435095.1	s__Levilactobacillus spicheri	79.788	369	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	98.77	97.54	0.95	0.91	3	-
GCF_001434785.1	s__Levilactobacillus namurensis	79.7405	317	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	96.48	95.39	0.91	0.87	6	-
GCA_019113985.1	s__Levilactobacillus faecigallinarum	79.6532	237	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861695.1	s__Levilactobacillus sp016861695	79.3496	257	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946085.1	s__Levilactobacillus angrenensis	79.3118	288	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666485.1	s__Levilactobacillus brevis_A	79.1002	285	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	79.0473	310	779	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:31,637] [INFO] GTDB search result was written to GCF_004115745.1_ASM411574v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:31,637] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:31,641] [INFO] DFAST_QC result json was written to GCF_004115745.1_ASM411574v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:31,641] [INFO] DFAST_QC completed!
[2024-01-24 15:19:31,641] [INFO] Total running time: 0h0m53s