[2024-01-25 17:46:50,808] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:50,810] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:50,810] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a04cd8d-f574-4cbb-9c5d-f813998eb6bd/dqc_reference
[2024-01-25 17:46:52,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:52,039] [INFO] Task started: Prodigal
[2024-01-25 17:46:52,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg58cb4228-037d-4362-b9e5-ee92c6469393/GCF_003946485.1_ASM394648v1_genomic.fna.gz | prodigal -d GCF_003946485.1_ASM394648v1_genomic.fna/cds.fna -a GCF_003946485.1_ASM394648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:58,095] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:58,096] [INFO] Task started: HMMsearch
[2024-01-25 17:46:58,096] [INFO] Running command: hmmsearch --tblout GCF_003946485.1_ASM394648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a04cd8d-f574-4cbb-9c5d-f813998eb6bd/dqc_reference/reference_markers.hmm GCF_003946485.1_ASM394648v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:58,307] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:58,308] [INFO] Found 6/6 markers.
[2024-01-25 17:46:58,328] [INFO] Query marker FASTA was written to GCF_003946485.1_ASM394648v1_genomic.fna/markers.fasta
[2024-01-25 17:46:58,329] [INFO] Task started: Blastn
[2024-01-25 17:46:58,329] [INFO] Running command: blastn -query GCF_003946485.1_ASM394648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a04cd8d-f574-4cbb-9c5d-f813998eb6bd/dqc_reference/reference_markers.fasta -out GCF_003946485.1_ASM394648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:58,922] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:58,925] [INFO] Selected 15 target genomes.
[2024-01-25 17:46:58,925] [INFO] Target genome list was writen to GCF_003946485.1_ASM394648v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:58,959] [INFO] Task started: fastANI
[2024-01-25 17:46:58,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg58cb4228-037d-4362-b9e5-ee92c6469393/GCF_003946485.1_ASM394648v1_genomic.fna.gz --refList GCF_003946485.1_ASM394648v1_genomic.fna/target_genomes.txt --output GCF_003946485.1_ASM394648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:07,850] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:07,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a04cd8d-f574-4cbb-9c5d-f813998eb6bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:07,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a04cd8d-f574-4cbb-9c5d-f813998eb6bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:07,857] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:47:07,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:07,858] [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
Lacticaseibacillus jixianensis	strain=159-4	GCA_003946485.1	2486012	2486012	type	True	100.0	796	798	95	conclusive
Lacticaseibacillus hegangensis	strain=73-4	GCA_003946465.1	2486010	2486010	type	True	82.7521	512	798	95	below_threshold
Lacticaseibacillus camelliae	strain=DSM 22697	GCA_001436615.1	381742	381742	type	True	82.5431	495	798	95	below_threshold
Lacticaseibacillus camelliae	strain=JCM 13995	GCA_001311195.1	381742	381742	type	True	82.5	462	798	95	below_threshold
Lacticaseibacillus daqingensis	strain=143-4(a)	GCA_003946115.1	2486014	2486014	type	True	79.0417	256	798	95	below_threshold
Lacticaseibacillus suilingensis	strain=ZW152	GCA_016861845.1	2799577	2799577	type	True	78.9375	247	798	95	below_threshold
Lacticaseibacillus suibinensis	strain=247-3	GCA_003946175.1	2486011	2486011	type	True	78.681	234	798	95	below_threshold
Lacticaseibacillus absianus	strain=YH-lac23	GCA_013407595.1	2729623	2729623	type	True	78.2237	241	798	95	below_threshold
Lacticaseibacillus mingshuiensis	strain=117-1	GCA_016861785.1	2799574	2799574	type	True	77.6822	177	798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:07,859] [INFO] DFAST Taxonomy check result was written to GCF_003946485.1_ASM394648v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:07,859] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:07,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:07,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a04cd8d-f574-4cbb-9c5d-f813998eb6bd/dqc_reference/checkm_data
[2024-01-25 17:47:07,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:07,887] [INFO] Task started: CheckM
[2024-01-25 17:47:07,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003946485.1_ASM394648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003946485.1_ASM394648v1_genomic.fna/checkm_input GCF_003946485.1_ASM394648v1_genomic.fna/checkm_result
[2024-01-25 17:47:30,116] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:30,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:30,133] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:30,134] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:30,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003946485.1_ASM394648v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:30,134] [INFO] Task started: Blastn
[2024-01-25 17:47:30,134] [INFO] Running command: blastn -query GCF_003946485.1_ASM394648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a04cd8d-f574-4cbb-9c5d-f813998eb6bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003946485.1_ASM394648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:30,988] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:30,991] [INFO] Selected 11 target genomes.
[2024-01-25 17:47:30,992] [INFO] Target genome list was writen to GCF_003946485.1_ASM394648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:30,998] [INFO] Task started: fastANI
[2024-01-25 17:47:30,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg58cb4228-037d-4362-b9e5-ee92c6469393/GCF_003946485.1_ASM394648v1_genomic.fna.gz --refList GCF_003946485.1_ASM394648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003946485.1_ASM394648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:37,734] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:37,740] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:37,740] [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_003946485.1	s__Lacticaseibacillus jixianensis	100.0	796	798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003946465.1	s__Lacticaseibacillus hegangensis	82.7521	512	798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	95.70	95.61	0.83	0.83	3	-
GCF_001311195.1	s__Lacticaseibacillus camelliae	82.5193	462	798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	1.00	1.00	2	-
GCF_003946115.1	s__Lacticaseibacillus daqingensis	79.0417	256	798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861845.1	s__Lacticaseibacillus sp900540605	78.919	249	798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.61	99.51	0.94	0.94	3	-
GCF_003946175.1	s__Lacticaseibacillus suibinensis	78.698	233	798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.05	98.05	0.90	0.90	2	-
GCF_013407595.1	s__Lacticaseibacillus absianus	78.2347	241	798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861765.1	s__Lacticaseibacillus sp016861765	77.9789	180	798	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.52	99.51	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:37,741] [INFO] GTDB search result was written to GCF_003946485.1_ASM394648v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:37,742] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:37,744] [INFO] DFAST_QC result json was written to GCF_003946485.1_ASM394648v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:37,744] [INFO] DFAST_QC completed!
[2024-01-25 17:47:37,744] [INFO] Total running time: 0h0m47s