mpileup errors

[jwinter2]

I'm getting several errors in the mpileup section of the assignment, and I'm not sure if they're related or not. The first is: [flush_bcf_records] Error: failed to write the record to standard output which happens while using mpileup, and the second set is: [E::bgzf_flush] File write failed (wrong size) [main_vcfcall] Error: failed to write to - cat: write error: Broken pipe when trying to create the vcf file. I'm not quite sure why I'm getting these errors.

[sr320]

Line of code in question and page url?

On Thu, May 4, 2023 at 2:23 PM jwinter2 @.***> wrote:

I'm getting several errors in the mpileup section of the assignment, and I'm not sure if they're related or not. The first is: [flush_bcf_records] Error: failed to write the record to standard output which happens while using mpileup, and the second set is: [E::bgzf_flush] File write failed (wrong size) [main_vcfcall] Error: failed to write to - cat: write error: Broken pipe when trying to create the vcf file. I'm not quite sure why I'm getting these errors.

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[jwinter2]

Ok so I think that error was because the file was too big-- to fix this, I did a pipe straight to the vcf.gz file creation, but now am getting an error at lines 150-154 that makes me think I shouldn't have ran the vcf file creation through the pipe ([W::bcf_sr_add_reader] No BGZF EOF marker; file '../output/F143_mpile.vcf.gz' may be truncated Error: could not parse the input VCF)

https://rpubs.com/jwinter2/align06

[sr320]

Not sure what issue is - (note I get same thing, even when I ran code last weekend) You can stop where you are

for others the code that fails:

/home/shared/bcftools-1.14/bcftools call \
-v -c --ploidy 2 ../output/F143_mpile.vcf.gz \
> ../output/F143_mpile_calls.vcf

Everyone should have the VCF ../output/F143_mpile.vcf.gz which can be visualized in IGV

[valeste]

I was getting that same error too but I was able to get that code chunk to work (although I think the file is truncated) after I freed up a lot of space in my output directory by deleting the sam file and other files from old assignments. I think there isn't enough disk space in our output directories to get the vcf file load.