[2024-01-24 11:35:34,276] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,278] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg37f45103-5881-4b1a-9152-025c5e1bfbeb/dqc_reference
[2024-01-24 11:35:35,538] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,539] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,539] [INFO] Running command: gunzip -c /var/lib/cwl/stgb666e4dc-b9f0-4b1b-9312-425d13b420d7/GCF_001434705.1_ASM143470v1_genomic.fna.gz | prodigal -d GCF_001434705.1_ASM143470v1_genomic.fna/cds.fna -a GCF_001434705.1_ASM143470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:42,778] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:42,778] [INFO] Task started: HMMsearch
[2024-01-24 11:35:42,779] [INFO] Running command: hmmsearch --tblout GCF_001434705.1_ASM143470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37f45103-5881-4b1a-9152-025c5e1bfbeb/dqc_reference/reference_markers.hmm GCF_001434705.1_ASM143470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:43,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:43,024] [INFO] Found 6/6 markers.
[2024-01-24 11:35:43,049] [INFO] Query marker FASTA was written to GCF_001434705.1_ASM143470v1_genomic.fna/markers.fasta
[2024-01-24 11:35:43,049] [INFO] Task started: Blastn
[2024-01-24 11:35:43,049] [INFO] Running command: blastn -query GCF_001434705.1_ASM143470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37f45103-5881-4b1a-9152-025c5e1bfbeb/dqc_reference/reference_markers.fasta -out GCF_001434705.1_ASM143470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:43,650] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:43,654] [INFO] Selected 19 target genomes.
[2024-01-24 11:35:43,654] [INFO] Target genome list was writen to GCF_001434705.1_ASM143470v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:43,753] [INFO] Task started: fastANI
[2024-01-24 11:35:43,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgb666e4dc-b9f0-4b1b-9312-425d13b420d7/GCF_001434705.1_ASM143470v1_genomic.fna.gz --refList GCF_001434705.1_ASM143470v1_genomic.fna/target_genomes.txt --output GCF_001434705.1_ASM143470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:53,187] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:53,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37f45103-5881-4b1a-9152-025c5e1bfbeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:53,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37f45103-5881-4b1a-9152-025c5e1bfbeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:53,201] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:53,201] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:53,201] [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 nasuensis	strain=JCM 17158	GCA_001434705.1	944671	944671	type	True	100.0	749	750	95	conclusive
Lacticaseibacillus nasuensis	strain=JCM 17158	GCA_001311255.1	944671	944671	type	True	99.7369	644	750	95	conclusive
Lacticaseibacillus hegangensis	strain=73-4	GCA_003946465.1	2486010	2486010	type	True	78.7196	181	750	95	below_threshold
Lacticaseibacillus daqingensis	strain=143-4(a)	GCA_003946115.1	2486014	2486014	type	True	78.3637	190	750	95	below_threshold
Lacticaseibacillus baoqingensis	strain=47-3	GCA_003946165.1	2486013	2486013	type	True	78.2339	129	750	95	below_threshold
Lacticaseibacillus jixianensis	strain=159-4	GCA_003946485.1	2486012	2486012	type	True	77.8343	192	750	95	below_threshold
Lacticaseibacillus suilingensis	strain=ZW152	GCA_016861845.1	2799577	2799577	type	True	77.8326	159	750	95	below_threshold
Lacticaseibacillus mingshuiensis	strain=117-1	GCA_016861785.1	2799574	2799574	type	True	77.8323	161	750	95	below_threshold
Lacticaseibacillus camelliae	strain=JCM 13995	GCA_001311195.1	381742	381742	type	True	77.7965	161	750	95	below_threshold
Lacticaseibacillus camelliae	strain=DSM 22697	GCA_001436615.1	381742	381742	type	True	77.7851	170	750	95	below_threshold
Lacticaseibacillus sharpeae	strain=JCM 1186	GCA_001311055.1	1626	1626	type	True	76.4917	77	750	95	below_threshold
Schleiferilactobacillus shenzhenensis	strain=LY-73	GCA_000469325.1	1231337	1231337	type	True	76.0499	65	750	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:53,203] [INFO] DFAST Taxonomy check result was written to GCF_001434705.1_ASM143470v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:53,203] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:53,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:53,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37f45103-5881-4b1a-9152-025c5e1bfbeb/dqc_reference/checkm_data
[2024-01-24 11:35:53,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:53,228] [INFO] Task started: CheckM
[2024-01-24 11:35:53,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001434705.1_ASM143470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001434705.1_ASM143470v1_genomic.fna/checkm_input GCF_001434705.1_ASM143470v1_genomic.fna/checkm_result
[2024-01-24 11:36:19,783] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:19,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:19,802] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:19,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:19,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001434705.1_ASM143470v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:19,803] [INFO] Task started: Blastn
[2024-01-24 11:36:19,803] [INFO] Running command: blastn -query GCF_001434705.1_ASM143470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37f45103-5881-4b1a-9152-025c5e1bfbeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_001434705.1_ASM143470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:20,617] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:20,622] [INFO] Selected 18 target genomes.
[2024-01-24 11:36:20,622] [INFO] Target genome list was writen to GCF_001434705.1_ASM143470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:20,636] [INFO] Task started: fastANI
[2024-01-24 11:36:20,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgb666e4dc-b9f0-4b1b-9312-425d13b420d7/GCF_001434705.1_ASM143470v1_genomic.fna.gz --refList GCF_001434705.1_ASM143470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001434705.1_ASM143470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:28,951] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:28,969] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:28,970] [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_001434705.1	s__Lacticaseibacillus nasuensis	100.0	749	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.88	99.88	1.00	1.00	2	conclusive
GCF_003946465.1	s__Lacticaseibacillus hegangensis	78.7196	181	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	95.70	95.61	0.83	0.83	3	-
GCF_003946115.1	s__Lacticaseibacillus daqingensis	78.344	191	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946165.1	s__Lacticaseibacillus baoqingensis	78.2064	130	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946485.1	s__Lacticaseibacillus jixianensis	77.8343	192	750	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	77.812	160	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.61	99.51	0.94	0.94	3	-
GCF_001311195.1	s__Lacticaseibacillus camelliae	77.8008	160	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	1.00	1.00	2	-
GCF_003946405.1	s__Lacticaseibacillus yichunensis	77.4879	155	750	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	77.4122	153	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.52	99.51	0.95	0.95	3	-
GCF_003946305.1	s__Lacticaseibacillus porcinae	77.3685	103	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435035.1	s__Lacticaseibacillus manihotivorans	77.3216	131	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.87	99.83	0.97	0.96	3	-
GCF_000469325.1	s__Schleiferilactobacillus shenzhenensis	76.0755	64	750	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Schleiferilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:28,972] [INFO] GTDB search result was written to GCF_001434705.1_ASM143470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:28,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:28,975] [INFO] DFAST_QC result json was written to GCF_001434705.1_ASM143470v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:28,976] [INFO] DFAST_QC completed!
[2024-01-24 11:36:28,976] [INFO] Total running time: 0h0m55s