Closed zhoudreames closed 1 year ago
i had built GLnexus.DB, but i forget to put my chr1_part2.bed file to current directory this code:
$glnexus_cli --config gatk --list ${chr[$line0]}.list --dir ${chr[$line0]}.GLnexus.DB --mem-gbytes 40 --bed chr1_part2.bed
this error :
2767723] [2022-08-02 17:43:23.845] [GLnexus] [info] 100/444 (20D004909.chr1)... [2767753] [2022-08-02 18:11:53.733] [GLnexus] [info] 200/444 (20D008382.chr1)... [2767764] [2022-08-02 18:42:08.396] [GLnexus] [info] 300/444 (20D008553.chr1)... [2767685] [2022-08-02 19:09:53.664] [GLnexus] [info] 400/444 (20D008656.chr1)... [2767241] [2022-08-02 19:17:27.776] [GLnexus] [info] Loaded 444 datasets with 444 samples; 2711335351984 bytes in 27359645837 BCF records (33653> [2767241] [2022-08-02 19:17:27.778] [GLnexus] [info] Created sample set *@444 [2767241] [2022-08-02 19:17:27.778] [GLnexus] [info] Flushing database... [2767241] [2022-08-02 19:18:09.501] [GLnexus] [info] Bulk load complete! [2767241] [2022-08-02 19:18:14.327] [GLnexus] [error] Failed to parse the bed file: IOError: bed file does not exist (chr1_part2.bed)
Is there a way to bypass this check and use the existing database?
i had built GLnexus.DB, but i forget to put my chr1_part2.bed file to current directory this code:
this error :
Is there a way to bypass this check and use the existing database?