[2024-01-25 20:16:50,843] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:50,845] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:50,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg92e7327c-7fb1-4288-99ce-0baf296881bb/dqc_reference
[2024-01-25 20:16:52,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:52,056] [INFO] Task started: Prodigal
[2024-01-25 20:16:52,056] [INFO] Running command: gunzip -c /var/lib/cwl/stg2648e176-54fa-4860-ae2e-6ab745b3edc1/GCF_000166795.1_ASM16679v1_genomic.fna.gz | prodigal -d GCF_000166795.1_ASM16679v1_genomic.fna/cds.fna -a GCF_000166795.1_ASM16679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:57,358] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:57,359] [INFO] Task started: HMMsearch
[2024-01-25 20:16:57,359] [INFO] Running command: hmmsearch --tblout GCF_000166795.1_ASM16679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92e7327c-7fb1-4288-99ce-0baf296881bb/dqc_reference/reference_markers.hmm GCF_000166795.1_ASM16679v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:57,565] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:57,566] [INFO] Found 6/6 markers.
[2024-01-25 20:16:57,595] [INFO] Query marker FASTA was written to GCF_000166795.1_ASM16679v1_genomic.fna/markers.fasta
[2024-01-25 20:16:57,595] [INFO] Task started: Blastn
[2024-01-25 20:16:57,595] [INFO] Running command: blastn -query GCF_000166795.1_ASM16679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92e7327c-7fb1-4288-99ce-0baf296881bb/dqc_reference/reference_markers.fasta -out GCF_000166795.1_ASM16679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:58,138] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:58,142] [INFO] Selected 11 target genomes.
[2024-01-25 20:16:58,142] [INFO] Target genome list was writen to GCF_000166795.1_ASM16679v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:58,146] [INFO] Task started: fastANI
[2024-01-25 20:16:58,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg2648e176-54fa-4860-ae2e-6ab745b3edc1/GCF_000166795.1_ASM16679v1_genomic.fna.gz --refList GCF_000166795.1_ASM16679v1_genomic.fna/target_genomes.txt --output GCF_000166795.1_ASM16679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:04,829] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:04,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92e7327c-7fb1-4288-99ce-0baf296881bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:04,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92e7327c-7fb1-4288-99ce-0baf296881bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:04,837] [INFO] Found 9 fastANI hits (6 hits with ANI > threshold)
[2024-01-25 20:17:04,837] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:04,837] [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
Loigolactobacillus coryniformis subsp. coryniformis	strain=KCTC 3167	GCA_000166795.1	115541	1610	type	True	99.9995	926	961	95	conclusive
Loigolactobacillus coryniformis subsp. coryniformis	strain=DSM 20001	GCA_001433765.1	115541	1610	type	True	99.8035	786	961	95	conclusive
Loigolactobacillus coryniformis subsp. coryniformis	strain=DSM 20001	GCA_002706425.1	115541	1610	type	True	99.6576	889	961	95	conclusive
Loigolactobacillus coryniformis subsp. torquens	strain=DSM 20004	GCA_001435425.1	115542	1610	type	True	97.4707	675	961	95	conclusive
Loigolactobacillus coryniformis subsp. torquens	strain=KCTC 3535	GCA_000184285.2	115542	1610	type	True	97.425	672	961	95	conclusive
Loigolactobacillus coryniformis subsp. torquens	strain=DSM 20004	GCA_002706705.1	115542	1610	type	True	97.33	801	961	95	conclusive
Loigolactobacillus jiayinensis	strain=257-1	GCA_003946445.1	2486016	2486016	type	True	81.153	526	961	95	below_threshold
Loigolactobacillus zhaoyuanensis	strain=187-3	GCA_003946385.1	2486017	2486017	type	True	81.1426	469	961	95	below_threshold
Agrilactobacillus fermenti	strain=CC-MHH1034	GCA_021030645.1	2586909	2586909	type	True	76.4524	71	961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:04,839] [INFO] DFAST Taxonomy check result was written to GCF_000166795.1_ASM16679v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:04,839] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:04,839] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:04,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92e7327c-7fb1-4288-99ce-0baf296881bb/dqc_reference/checkm_data
[2024-01-25 20:17:04,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:04,870] [INFO] Task started: CheckM
[2024-01-25 20:17:04,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000166795.1_ASM16679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000166795.1_ASM16679v1_genomic.fna/checkm_input GCF_000166795.1_ASM16679v1_genomic.fna/checkm_result
[2024-01-25 20:17:25,751] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:25,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:25,768] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:25,768] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:25,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000166795.1_ASM16679v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:25,769] [INFO] Task started: Blastn
[2024-01-25 20:17:25,769] [INFO] Running command: blastn -query GCF_000166795.1_ASM16679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92e7327c-7fb1-4288-99ce-0baf296881bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000166795.1_ASM16679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:26,492] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:26,497] [INFO] Selected 14 target genomes.
[2024-01-25 20:17:26,497] [INFO] Target genome list was writen to GCF_000166795.1_ASM16679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:26,511] [INFO] Task started: fastANI
[2024-01-25 20:17:26,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg2648e176-54fa-4860-ae2e-6ab745b3edc1/GCF_000166795.1_ASM16679v1_genomic.fna.gz --refList GCF_000166795.1_ASM16679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000166795.1_ASM16679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:33,671] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:33,678] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:33,679] [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_002706425.1	s__Loigolactobacillus coryniformis	99.6576	889	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	98.39	97.42	0.89	0.81	10	conclusive
GCF_005405165.1	s__Loigolactobacillus binensis	81.58	482	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946445.1	s__Loigolactobacillus jiayinensis	81.1512	523	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946385.1	s__Loigolactobacillus zhaoyuanensis	81.1278	470	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946275.1	s__Loigolactobacillus backii	78.9826	142	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	99.33	98.15	0.95	0.91	9	-
GCF_003950295.1	s__Loigolactobacillus iwatensis	78.4582	144	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434575.1	s__Loigolactobacillus bifermentans	77.5322	137	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001436505.1	s__Loigolactobacillus rennini	77.3952	178	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014131735.1	s__Lactiplantibacillus plantarum	76.7901	62	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.89	95.74	0.92	0.82	629	-
GCF_002953655.1	s__Latilactobacillus sakei_A	76.7255	64	961	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Latilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:33,681] [INFO] GTDB search result was written to GCF_000166795.1_ASM16679v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:33,681] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:33,684] [INFO] DFAST_QC result json was written to GCF_000166795.1_ASM16679v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:33,684] [INFO] DFAST_QC completed!
[2024-01-25 20:17:33,684] [INFO] Total running time: 0h0m43s