[2024-01-24 14:47:18,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:18,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:18,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg21370702-3c16-41eb-b00a-6e4fe52ecbb4/dqc_reference
[2024-01-24 14:47:20,051] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:20,052] [INFO] Task started: Prodigal
[2024-01-24 14:47:20,052] [INFO] Running command: gunzip -c /var/lib/cwl/stgc322007d-2d3a-4a9c-a420-0010c80d6b96/GCF_004010095.1_ASM401009v1_genomic.fna.gz | prodigal -d GCF_004010095.1_ASM401009v1_genomic.fna/cds.fna -a GCF_004010095.1_ASM401009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:26,745] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:26,746] [INFO] Task started: HMMsearch
[2024-01-24 14:47:26,746] [INFO] Running command: hmmsearch --tblout GCF_004010095.1_ASM401009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21370702-3c16-41eb-b00a-6e4fe52ecbb4/dqc_reference/reference_markers.hmm GCF_004010095.1_ASM401009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:26,977] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:26,978] [INFO] Found 6/6 markers.
[2024-01-24 14:47:27,006] [INFO] Query marker FASTA was written to GCF_004010095.1_ASM401009v1_genomic.fna/markers.fasta
[2024-01-24 14:47:27,007] [INFO] Task started: Blastn
[2024-01-24 14:47:27,007] [INFO] Running command: blastn -query GCF_004010095.1_ASM401009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21370702-3c16-41eb-b00a-6e4fe52ecbb4/dqc_reference/reference_markers.fasta -out GCF_004010095.1_ASM401009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:27,602] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:27,607] [INFO] Selected 23 target genomes.
[2024-01-24 14:47:27,608] [INFO] Target genome list was writen to GCF_004010095.1_ASM401009v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:27,846] [INFO] Task started: fastANI
[2024-01-24 14:47:27,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgc322007d-2d3a-4a9c-a420-0010c80d6b96/GCF_004010095.1_ASM401009v1_genomic.fna.gz --refList GCF_004010095.1_ASM401009v1_genomic.fna/target_genomes.txt --output GCF_004010095.1_ASM401009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:38,210] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:38,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21370702-3c16-41eb-b00a-6e4fe52ecbb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:38,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21370702-3c16-41eb-b00a-6e4fe52ecbb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:38,220] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:38,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:38,221] [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 hulanensis	strain=ZW163	GCA_004010095.1	2493111	2493111	type	True	100.0	752	753	95	conclusive
Lacticaseibacillus sharpeae	strain=DSM 20505	GCA_001436225.1	1626	1626	type	True	80.9388	385	753	95	below_threshold
Lacticaseibacillus sharpeae	strain=JCM 1186	GCA_001311055.1	1626	1626	type	True	80.897	386	753	95	below_threshold
Lacticaseibacillus yichunensis	strain=33-1	GCA_003946405.1	2486015	2486015	type	True	79.2831	51	753	95	below_threshold
Lacticaseibacillus songhuajiangensis	strain=7-19	GCA_003946025.1	1296539	1296539	type	True	79.1885	199	753	95	below_threshold
Lacticaseibacillus zhaodongensis	strain=1206-1	GCA_009687905.1	2668065	2668065	type	True	78.7237	190	753	95	below_threshold
Lacticaseibacillus pantheris	strain=NBRC 106106	GCA_001591865.1	171523	171523	type	True	78.578	104	753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:38,223] [INFO] DFAST Taxonomy check result was written to GCF_004010095.1_ASM401009v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:38,224] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:38,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:38,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21370702-3c16-41eb-b00a-6e4fe52ecbb4/dqc_reference/checkm_data
[2024-01-24 14:47:38,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:38,261] [INFO] Task started: CheckM
[2024-01-24 14:47:38,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004010095.1_ASM401009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004010095.1_ASM401009v1_genomic.fna/checkm_input GCF_004010095.1_ASM401009v1_genomic.fna/checkm_result
[2024-01-24 14:48:06,860] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:06,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:06,884] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:06,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:06,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004010095.1_ASM401009v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:06,885] [INFO] Task started: Blastn
[2024-01-24 14:48:06,886] [INFO] Running command: blastn -query GCF_004010095.1_ASM401009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21370702-3c16-41eb-b00a-6e4fe52ecbb4/dqc_reference/reference_markers_gtdb.fasta -out GCF_004010095.1_ASM401009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:07,743] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:07,746] [INFO] Selected 21 target genomes.
[2024-01-24 14:48:07,746] [INFO] Target genome list was writen to GCF_004010095.1_ASM401009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:07,784] [INFO] Task started: fastANI
[2024-01-24 14:48:07,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgc322007d-2d3a-4a9c-a420-0010c80d6b96/GCF_004010095.1_ASM401009v1_genomic.fna.gz --refList GCF_004010095.1_ASM401009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004010095.1_ASM401009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:16,691] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:16,704] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:16,704] [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_004010095.1	s__Lacticaseibacillus hulanensis	100.0	752	753	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_001436225.1	s__Lacticaseibacillus sharpeae	80.9387	385	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.95	99.95	0.98	0.98	2	-
GCF_003946405.1	s__Lacticaseibacillus yichunensis	79.2831	51	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946025.1	s__Lacticaseibacillus songhuajiangensis	79.1648	200	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009687905.1	s__Lacticaseibacillus zhaodongensis	78.7237	190	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003946115.1	s__Lacticaseibacillus daqingensis	77.8807	77	753	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	77.3972	73	753	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	77.0552	59	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.61	99.51	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:16,706] [INFO] GTDB search result was written to GCF_004010095.1_ASM401009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:16,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:16,709] [INFO] DFAST_QC result json was written to GCF_004010095.1_ASM401009v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:16,709] [INFO] DFAST_QC completed!
[2024-01-24 14:48:16,709] [INFO] Total running time: 0h0m58s