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Error when running pairLiftOver #7

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ljharrison1 opened this issue Dec 2, 2022 · 1 comment
Open

Error when running pairLiftOver #7

ljharrison1 opened this issue Dec 2, 2022 · 1 comment

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@ljharrison1
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Hi, when I run pairLiftOver I keep on getting the error: TypeError: expected str, bytes or os.PathLike object, not NoneType

The code I am running is as follows:
pairLiftOver --input <path to .hic file> --input-format juicer --output-format hic --high-res --out-chromsizes < path to chrom sizes file> --in-assembly hg38 --out-assembly hg19 --chain-file <path to chain file>

Do you have any idea why I might be getting this error? Thank you!

@XiaoTaoWang
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Hi, you also need to specify the prefix of the output file names through the parameter --out-pre. By the way, since you selected to output the contact matrices in the ".hic" format, I suggest increasing the allocated memory to a higher value, perhaps 40G or 50G, through the --memory parameter.

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