The command validate checks for consistency of some data and system configuration.

Validate db

Use this command to quickly check the database parameters and find those that might need an optimization.

PS> validate db
Checking DB settings:
time_zone != +00:00
tx_isolation (REPEATABLE-READ) != read-committed
innodb_log_file_size (100663296) < 536870912
tmp_table_size (16777216) < 33554432
max_heap_table_size (16777216) < 33554432
join_buffer_size (262144) < 2097152
query_cache_size (1048576) != 0
max_allowed_packet (16777216) < 67108864
max_connections (151) < 500
Please review the warnings, they may help with the database performance issues.
The recommended parameters are listed at https://help.persephonesoft.com/SettingupthePersephoneSystem.html

Deviation from recommended configuration values can degrade database performance or even prevent certain commands from completing successfully. For example, when loading large chromosomes, histogram records stored as binary blobs can only be imported if max_allowed_packet is sufficiently large to hold the data blocks. As a rule of thumb, for a chromosome of approximately 2 Gbp, the corresponding histogram block is about 100 times smaller—roughly 20 MB—so max_allowed_packet must be set above that threshold.

Validate variant

When PersephoneShell is updated after a long gap between versions, there is a small chance that some data may become inconsistent. To inspect the variant data blocks—stored both in the database and in the file system—run the command validate variant. This tool can detect issues such as “orphaned” sample metadata entries that no longer have corresponding data blocks on disk.

PS> validate variant
Validate vcf storages

Storage path: /data/FileStorage/_sub_VcfStorage/000000000013
VCFStorage '' open from /data/FileStorage/_sub_VcfStorage/000000000013
Info:
  Created on: 2024-01-27 16:32:14Z
  Origin VCF file: '/HDD4Gb/bio/data/rice/ordered_rice3K.vcf.gz', size: unknown
  Map count: 12
  Sample count: 3,024
  Ploidy level: 2
  Structural Variants: not present
  Horizontal data: present
VCF storage is valid (/data/FileStorage/_sub_VcfStorage/000000000013)


Storage path: /data/FileStorage/_sub_VcfStorage/000000000014
VCFStorage '' open from /data/FileStorage/_sub_VcfStorage/000000000014
Info:
  Created on: 2024-01-27 16:41:24Z
  Origin VCF file: '/HDD4Gb/bio/data/sorghum/Sbicolor_Patterson_454.vcf.gz', size: unknown
  Map count: 275
  Sample count: 23
  Ploidy level: 2
  Structural Variants: not present
  Horizontal data: present
VCF storage is valid (/data/FileStorage/_sub_VcfStorage/000000000014)