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14 months ago
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Hi, I am using HISAT2 on virtualbox with 4 cores of process for the test of only one sample. My data are from illumina platform. I typed as below :
hisat2 -p 4 --rna-strandness RF -x ./2.Input/GRCm39 -1 ./2.Input/LA50-3-CO_1_paired.fastq -2 ./2.Input/LA50-3-CO_2_paired.fastq 2> ./3.Output/LA50-3-CO_log| samtools view -@ 8 -Sbo ./3.Output/LA50-3-CO.bam
After running within a few seconds, I took a look at log as below :
Warning: the current version of HISAT2 (2.2.1) is older than the version (2.127.0) used to build the index.
Users are strongly recommended to update HISAT2 to the latest version.
Out of memory allocating plen[] in Ebwt::read() at gfm.h:6069
Error: Encountered exception: 'std::bad_alloc'
Command: /home/shkim/apps/hisat2-2.2.1/hisat2-align-s --wrapper basic-0 -p 4 --rna-strandness RF -x ./2.Input/GRCm39 --read-lengths 101,97,99,98,95,93,92,90,96,94,81,91,89,88,84,83,79,75,87,82,78,76,72,70 -1 ./2.Input/LA50-3-CO_1_paired.fastq -2 ./2.Input/LA50-3-CO_2_paired.fastq
(ERR): hisat2-align exited with value 1
kindly help, please :) lack of memory issue only?
Inwould address that warning about versions first. How much memorynsid you wllocate to the VM? Why a VM anyway, on Linux and Mac it runs natively and on Windows the use of WSL2 would be better.