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GuipengLi / ChIA-PET2

a versatile and flexible pipeline for analysing different variants of ChIA-PET data
GNU General Public License v3.0
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std::bad_alloc error #15

Closed RubD closed 6 years ago

RubD commented 6 years ago

Hi,

The pipeline always throws an error at the 'buildBedpe' step:

terminate called after throwing an instance of ‘std::bad_alloc’ what(): std::bad_alloc Aborted (core dumped)

I'm not sure why this is. I tried 3 different servers and all of them should have enough available memory.

Thanks, Ruben

GuipengLi commented 6 years ago

What's the command you used?

RubD commented 6 years ago

This is the command I used: ChIA-PET2 --genome $bwa_genome_index --bedtoolsgenome $bedtools_genome --linkerA CGCGATATCTATCTG --linkerB ACGCGATATCTTATC --output $output_dir --name shLUC_subtest --mode 1 --err 1 --keepempty 2 --thread 10 --forward $forward_read --reverse $reverse_read

Initially I got an error at the buildBedpe stage about a problem with the names in the .sam files. So I first ran samtools sort -n file_1_R.sam > file_1_R.nsorted.sam for all .sam files.

Then I ran the buildBedpe command buildBedpe file_1_R.nsorted.sam file_2_R.nsorted.sam 30 10 1 or the ChIA-PET2 command starting from point 3 with both of them ending with the same error.

RubD commented 6 years ago

Nevermind, I figured it out eventually by creating my own pipeline. It turns out there was a naming problem in the fastq files and now your pipeline runs perfect. Thanks.

GuipengLi commented 6 years ago

Great