[out of memory issue] NCBI Entrez protein seq download

Question

[Alewa]

extracting protein sequences from ncbi using entrez in terminal but keep getting error

/home/$USER/edirect/ecommon.sh: xrealloc: cannot allocate 18446744071589123328 bytes (42668032 bytes allocated)

command used

$esearch -db gene -query 'Mycobacterium tuberculosis H37Rv[Organism] AND NC_000962.3[ACCN]' | elink -db gene -target protein | efilter -organism Mycobacterium tuberculosis H37Rv -source refseq | efetch -format protein_fasta > test_elink_tb

thanks

Answer 1

[GenoMax]

Why not use following since you already have the accession of the reference sequence.

$ esearch -db nuccore -query NC_000962.3 | elink -target protein | efetch -format fasta

[Alewa]

Thanks @GenoMax, that works! do you know the memory issue was happening?