[2024-01-24 14:31:01,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:01,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:01,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg87b9a9ac-9694-435c-91c3-2d87f92c532a/dqc_reference
[2024-01-24 14:31:04,074] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:04,075] [INFO] Task started: Prodigal
[2024-01-24 14:31:04,075] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b2a2446-93cd-45db-8cd2-8388bde0ad4c/GCF_005405385.1_ASM540538v1_genomic.fna.gz | prodigal -d GCF_005405385.1_ASM540538v1_genomic.fna/cds.fna -a GCF_005405385.1_ASM540538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:12,054] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:12,054] [INFO] Task started: HMMsearch
[2024-01-24 14:31:12,054] [INFO] Running command: hmmsearch --tblout GCF_005405385.1_ASM540538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87b9a9ac-9694-435c-91c3-2d87f92c532a/dqc_reference/reference_markers.hmm GCF_005405385.1_ASM540538v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:12,329] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:12,331] [INFO] Found 6/6 markers.
[2024-01-24 14:31:12,378] [INFO] Query marker FASTA was written to GCF_005405385.1_ASM540538v1_genomic.fna/markers.fasta
[2024-01-24 14:31:12,378] [INFO] Task started: Blastn
[2024-01-24 14:31:12,378] [INFO] Running command: blastn -query GCF_005405385.1_ASM540538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87b9a9ac-9694-435c-91c3-2d87f92c532a/dqc_reference/reference_markers.fasta -out GCF_005405385.1_ASM540538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:13,067] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:13,071] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:13,071] [INFO] Target genome list was writen to GCF_005405385.1_ASM540538v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:13,085] [INFO] Task started: fastANI
[2024-01-24 14:31:13,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b2a2446-93cd-45db-8cd2-8388bde0ad4c/GCF_005405385.1_ASM540538v1_genomic.fna.gz --refList GCF_005405385.1_ASM540538v1_genomic.fna/target_genomes.txt --output GCF_005405385.1_ASM540538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:24,032] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:24,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87b9a9ac-9694-435c-91c3-2d87f92c532a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:24,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87b9a9ac-9694-435c-91c3-2d87f92c532a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:24,043] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:24,044] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:24,044] [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 mudanjiangensis	strain=11050	GCA_005405385.1	1296538	1296538	type	True	100.0	1090	1091	95	conclusive
Lactiplantibacillus daowaiensis	strain=203-3	GCA_005405085.1	2559918	2559918	type	True	81.9833	568	1091	95	below_threshold
Lactiplantibacillus songbeiensis	strain=398-2	GCA_005405125.1	2559920	2559920	type	True	80.7681	465	1091	95	below_threshold
Lactiplantibacillus dongliensis	strain=218-3	GCA_005405105.1	2559919	2559919	type	True	80.5884	470	1091	95	below_threshold
Lactiplantibacillus daoliensis	strain=116-1A	GCA_005405005.1	2559916	2559916	type	True	80.3651	354	1091	95	below_threshold
Lactiplantibacillus fabifermentans	strain=DSM 21115	GCA_000498955.2	483011	483011	type	True	80.2305	398	1091	95	below_threshold
Lactiplantibacillus nangangensis	strain=381-7	GCA_005405065.1	2559917	2559917	type	True	79.9956	391	1091	95	below_threshold
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_001435215.1	271881	271881	type	True	79.4296	332	1091	95	below_threshold
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_003641165.1	271881	271881	type	True	79.3778	333	1091	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	77.5607	61	1091	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:24,045] [INFO] DFAST Taxonomy check result was written to GCF_005405385.1_ASM540538v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:24,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:24,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:24,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87b9a9ac-9694-435c-91c3-2d87f92c532a/dqc_reference/checkm_data
[2024-01-24 14:31:24,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:24,082] [INFO] Task started: CheckM
[2024-01-24 14:31:24,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405385.1_ASM540538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405385.1_ASM540538v1_genomic.fna/checkm_input GCF_005405385.1_ASM540538v1_genomic.fna/checkm_result
[2024-01-24 14:31:54,044] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:54,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:54,066] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:54,066] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:54,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405385.1_ASM540538v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:54,067] [INFO] Task started: Blastn
[2024-01-24 14:31:54,068] [INFO] Running command: blastn -query GCF_005405385.1_ASM540538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87b9a9ac-9694-435c-91c3-2d87f92c532a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405385.1_ASM540538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:54,857] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:54,861] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:54,862] [INFO] Target genome list was writen to GCF_005405385.1_ASM540538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:54,868] [INFO] Task started: fastANI
[2024-01-24 14:31:54,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b2a2446-93cd-45db-8cd2-8388bde0ad4c/GCF_005405385.1_ASM540538v1_genomic.fna.gz --refList GCF_005405385.1_ASM540538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405385.1_ASM540538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:04,657] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:04,666] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:04,667] [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_005405385.1	s__Lactiplantibacillus mudanjiangensis	100.0	1090	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.38	99.14	0.94	0.91	5	conclusive
GCF_005405085.1	s__Lactiplantibacillus daowaiensis	81.9833	568	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405125.1	s__Lactiplantibacillus songbeiensis	80.7596	466	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405105.1	s__Lactiplantibacillus dongliensis	80.5884	470	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405005.1	s__Lactiplantibacillus daoliensis	80.3651	354	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498955.2	s__Lactiplantibacillus fabifermentans	80.2452	397	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_005405065.1	s__Lactiplantibacillus nangangensis	79.9815	392	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002970935.1	s__Lactiplantibacillus sp002970935	79.7672	367	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000463075.2	s__Lactiplantibacillus plantarum_A	79.7388	324	1091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_002970915.1	s__Lactiplantibacillus sp002970915	79.7301	362	1091	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 14:32:04,668] [INFO] GTDB search result was written to GCF_005405385.1_ASM540538v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:04,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:04,672] [INFO] DFAST_QC result json was written to GCF_005405385.1_ASM540538v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:04,673] [INFO] DFAST_QC completed!
[2024-01-24 14:32:04,673] [INFO] Total running time: 0h1m3s