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region "-o" specifies an unknown reference name #51

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ariannadib opened this issue May 3, 2024 · 1 comment
Open

region "-o" specifies an unknown reference name #51

ariannadib opened this issue May 3, 2024 · 1 comment

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@ariannadib
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HI! I'm having a problem with the cellScann module, in particular I can't understand the reason for this error:
INFO Monopogen.py Get single cell level information from sequencing data...
INFO:main:Get single cell level information from sequencing data...
[main_samview] region "-o" specifies an unknown reference name. Continue anyway.
[main_samview] region "/Users/Arianna/Monopogen/out_D545/Bam/chr1.filter.targeted.bam" specifies an unknown reference name. Continue anyway.

the samtools version should be the correct one (samtools 1.2, htslib1.2.1)
@jinzhuangdou
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Do you still have such issue?

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@jinzhuangdou @ariannadib