Error in Blast+

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3.3 years ago

a.mostafa5050 ▴ 10

Hi everyone,

I downloaded the nr database from NCBI in order to run Blast on Linux.

I got the error message

"Error: mdb_env_open: No such file or directory"

My slurm script is

blastp -query /cluster/work/users/ahmedbar/prokka_result_AC/$SAMPLE_ID_1 -db /cluster/work/users/ahmedbar/DB/nr -max_target_seqs 5 -out /$OUTPUTFILE.txt

Could you please help me in this? Thanks

alignment sequence • 719 views

ADD COMMENT • link 3.3 years ago by a.mostafa5050 ▴ 10

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Could you please help me in this?

unfortunately no, the error is clearly showing your job cannot find the db, which means your worker node is not syncing the directory where is your db located. You need help from your cluster sysadmin.

ADD REPLY • link 3.3 years ago by JC 13k

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check the memory usage. This error might be linked to the memory usage? what are the specs of your machines (or resources assigned to this job)?

ADD REPLY • link 3.3 years ago by lieven.sterck 15k

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