[2024-01-25 19:51:20,501] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:20,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:20,502] [INFO] DQC Reference Directory: /var/lib/cwl/stg95be7a8d-841f-49f5-9604-ef4a12199fd9/dqc_reference
[2024-01-25 19:51:21,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:21,668] [INFO] Task started: Prodigal
[2024-01-25 19:51:21,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg1403c508-b307-449e-b453-cba74cf37441/GCF_001435095.1_ASM143509v1_genomic.fna.gz | prodigal -d GCF_001435095.1_ASM143509v1_genomic.fna/cds.fna -a GCF_001435095.1_ASM143509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:28,807] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:28,807] [INFO] Task started: HMMsearch
[2024-01-25 19:51:28,807] [INFO] Running command: hmmsearch --tblout GCF_001435095.1_ASM143509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95be7a8d-841f-49f5-9604-ef4a12199fd9/dqc_reference/reference_markers.hmm GCF_001435095.1_ASM143509v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:29,022] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:29,023] [INFO] Found 6/6 markers.
[2024-01-25 19:51:29,046] [INFO] Query marker FASTA was written to GCF_001435095.1_ASM143509v1_genomic.fna/markers.fasta
[2024-01-25 19:51:29,047] [INFO] Task started: Blastn
[2024-01-25 19:51:29,047] [INFO] Running command: blastn -query GCF_001435095.1_ASM143509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95be7a8d-841f-49f5-9604-ef4a12199fd9/dqc_reference/reference_markers.fasta -out GCF_001435095.1_ASM143509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:29,620] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:29,624] [INFO] Selected 14 target genomes.
[2024-01-25 19:51:29,624] [INFO] Target genome list was writen to GCF_001435095.1_ASM143509v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:29,643] [INFO] Task started: fastANI
[2024-01-25 19:51:29,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg1403c508-b307-449e-b453-cba74cf37441/GCF_001435095.1_ASM143509v1_genomic.fna.gz --refList GCF_001435095.1_ASM143509v1_genomic.fna/target_genomes.txt --output GCF_001435095.1_ASM143509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:38,276] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:38,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95be7a8d-841f-49f5-9604-ef4a12199fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:38,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95be7a8d-841f-49f5-9604-ef4a12199fd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:38,284] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:38,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:38,285] [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 spicheri	strain=DSM 15429	GCA_001435095.1	216463	216463	type	True	100.0	902	903	95	conclusive
Levilactobacillus zymae	strain=DSM 19395	GCA_001434115.1	267363	267363	type	True	81.8638	500	903	95	below_threshold
Levilactobacillus namurensis	strain=DSM 19117	GCA_001434785.1	380393	380393	type	True	81.7492	517	903	95	below_threshold
Levilactobacillus acidifarinae	strain=DSM 19394	GCA_001434835.1	267364	267364	type	True	80.8029	478	903	95	below_threshold
Levilactobacillus suantsaii	strain=BCRC 12945	GCA_004115745.1	2292255	2292255	type	True	79.9169	379	903	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	79.761	382	903	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	79.601	355	903	95	below_threshold
Levilactobacillus fuyuanensis	strain=244-4	GCA_003946395.1	2486022	2486022	type	True	79.2508	314	903	95	below_threshold
Levilactobacillus enshiensis	strain=HBUAS57009	GCA_007115095.1	2590213	2590213	type	True	78.9421	301	903	95	below_threshold
Levilactobacillus tujiorum	strain=HBUAS51241	GCA_012641185.1	2912243	2912243	type	True	78.9325	251	903	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	77.7029	74	903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:38,289] [INFO] DFAST Taxonomy check result was written to GCF_001435095.1_ASM143509v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:38,289] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:38,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:38,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95be7a8d-841f-49f5-9604-ef4a12199fd9/dqc_reference/checkm_data
[2024-01-25 19:51:38,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:38,326] [INFO] Task started: CheckM
[2024-01-25 19:51:38,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001435095.1_ASM143509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001435095.1_ASM143509v1_genomic.fna/checkm_input GCF_001435095.1_ASM143509v1_genomic.fna/checkm_result
[2024-01-25 19:52:03,198] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:03,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:03,231] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:03,231] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:03,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001435095.1_ASM143509v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:03,232] [INFO] Task started: Blastn
[2024-01-25 19:52:03,232] [INFO] Running command: blastn -query GCF_001435095.1_ASM143509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95be7a8d-841f-49f5-9604-ef4a12199fd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001435095.1_ASM143509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:04,057] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:04,060] [INFO] Selected 12 target genomes.
[2024-01-25 19:52:04,060] [INFO] Target genome list was writen to GCF_001435095.1_ASM143509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:04,069] [INFO] Task started: fastANI
[2024-01-25 19:52:04,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg1403c508-b307-449e-b453-cba74cf37441/GCF_001435095.1_ASM143509v1_genomic.fna.gz --refList GCF_001435095.1_ASM143509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001435095.1_ASM143509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:11,726] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:11,736] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:11,736] [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_001435095.1	s__Levilactobacillus spicheri	100.0	902	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	98.77	97.54	0.95	0.91	3	conclusive
GCA_019113985.1	s__Levilactobacillus faecigallinarum	82.0176	367	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434115.1	s__Levilactobacillus zymae	81.8887	497	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.08	97.26	0.95	0.86	4	-
GCF_001434785.1	s__Levilactobacillus namurensis	81.7443	518	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	96.48	95.39	0.91	0.87	6	-
GCF_001434835.1	s__Levilactobacillus acidifarinae	80.8029	478	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004115745.1	s__Levilactobacillus suantsaii	79.9241	378	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	1.00	1.00	2	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	79.7474	383	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946045.1	s__Levilactobacillus mulengensis	79.7176	363	903	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	79.6926	376	903	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	79.601	355	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946395.1	s__Levilactobacillus fuyuanensis	79.2508	314	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007115095.1	s__Levilactobacillus enshiensis	78.9351	302	903	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:11,739] [INFO] GTDB search result was written to GCF_001435095.1_ASM143509v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:11,740] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:11,745] [INFO] DFAST_QC result json was written to GCF_001435095.1_ASM143509v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:11,745] [INFO] DFAST_QC completed!
[2024-01-25 19:52:11,745] [INFO] Total running time: 0h0m51s