This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error during mapping using bwa mem

Hi , any suggestion to fix this error during using bwa mem by this command:

bwa mem hg38.fasta  Z#1.fq > Z#1.sam

Got error

[bwt_restore_bwt] Failed to allocate 3217346964 bytes at bwt.c line 452: Cannot allocate memory

how to fix it, I have already tried to update bwa but still same error

software error alignment
• 2,452 views • link
updated by GenoMax GenoMax • written by Begali • Begali

How much memory do you have available? The error is clear. bwa is not able to allocate enough memory.

• 1 views • link
written by GenoMax GenoMax

Are your files really called Z#1.fq and Z#2.fq? After the first #, the shell will stop interpreting the rest of the command line.

• 1 views • link
written by h.mon h.mon

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • slurm error
    written by rheab1230 • rheab1230
    Hello everyone: I submitted a job via slurm and got this error: Error: cannot allocate vector of size 7.8 Gb Execution halted Warning message: system …
  • scATAC-pro command issue
    written by sidrah.maryam • sidrah.maryam
    Hello everyone, I am trying to run scATAC-pro protocol, however, I am receiving the following error: Aligning ... Starting alignment ... [M::bwa_idx_load_from_disk] read 0 ALT …
  • BWA mem failing to locate index files
    written by aalith • aalith
    I've seen a million forum posts about this topic, however, I still cannot figure out the issue with my command line I indexed my reference …
  • BWA. Allocate memory
    written by windsur • windsur
    Dear all, I have changed the work station and now I am using Centos 7 as operating system. And if I write this I found …
  • velvetg failed during the assembly
    written by slimane.khayi • slimane.khayi
    Dear all, I have problem during my denovo assembly process, I have launched velveth for mypaired.fastq containing 600 millions reads in total (length 150) : …
  • bwa index error : Floating point exception
    written by comma1993 • comma1993
    I have one sequence with size of 2.4G. And I built index with bwa using the following command: bwa index -a bwtsw test.fa But it …
  • bwa mem failed to allocate memory
    written by cmo cmo
    I am aligning a modest number of short reads (10.5 M) to a large genome (~4 Gb) with `bwa mem`. I expect a high error …
  • How To Solve Gapfiller Error
    written by HG HG
    <p>HI everyone, I am using GapFiller (<a href='http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/'>http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/</a>) While running GapFiller getting an error message like this : </p> <pre><code>[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to …
  • Warnings In Bowtie Mapping
    written by bashwin.u • bashwin.u
    <p>Hello,</p> <p>I am trying to use bowtie on small synthetic data for short read mapping. My command is <code>./bowtie -p 8 -t -S hg19 -1 …
  • Duplicate @Sq Lines In Sam File Header
    written by Ram Ram
    Hi, I'm working on RNA-seq data and have aligned my reads to the assembled transcript using bwa-mem. When I tried to run Picard Tools (`SamFormatConverter.jar`), …