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hellbelly / BS-Snper

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Error: `Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error!`. #22

Closed daniellembecker closed 9 months ago

daniellembecker commented 9 months ago

Hello,

We are trying to use BS-SNPer to filter SNPs from WGBS data extracted from coral tissue. We have conistently been getting this error:

"Too many characters in one row! Try to split the long row into several short rows (fewer than 1000000 characters per row). Error! at /opt/software/BS-Snper/1.0-foss-2021b/bin/BS-Snper.pl line 110."

We have gotten our deduplicated.bam files from the nf-core methylseq pipeline and have detailed how we have ran our scripts here if you could please advise!

daniellembecker commented 9 months ago

We increased the size of characters allowed but are now getting this error:

Screen Shot 2024-02-19 at 12 15 24 PM
daniellembecker commented 9 months ago

The errors we ran into was the original BS-SNPer script had an allocation for number of characters allowed per line in our .bam files and also a restriction on the limit for number of chromosomes it could process in default settings. Our research computing department was able to patch something into the script to allow for more and now it is running! Outline of our solution and the errors are in my GitHub notebook post: https://daniellembecker.github.io/DanielleBecker_Lab_Notebook/Testing-BS-SNPer-Molec-Underpinnings-WGBS/