Cannot solve the '--no-pg' issue

CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

MIT License

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Closed lkw159159 closed 2 years ago

lkw159159 commented 2 years ago

Dear team,

Hello, When I tried to dedup step with example.bam file, I stlll got --no-pg error.

I already read your issue reply and updated pysam, samtools, umi-tools.

BTW, when I checked conda packages list, I saw that there are 2 umi-tools packages in my conda list.

why I have two different versions of UMI=tools?

If it is the cause, how can I solve it?

Thanks.

lkw159159 commented 2 years ago

Here's my error message

TomSmithCGAT commented 2 years ago

Hmmm... looks like you've used both pip and conda for the installation. From the above, it looks like the pypi version is first on you $PATH.

The error is actually due to the version of samtools being used though. What do you get with the following which samtools and samtools --version.

lkw159159 commented 2 years ago

Dear Tom,

I also use samtools with conda environment & it's version is 1.3.1

TomSmithCGAT commented 2 years ago

Ah, 1.3.1 is ~ 6 years old. Looks like the --no-PG option was introduced in 1.10 https://github.com/samtools/samtools/releases/tag/1.10

lkw159159 commented 2 years ago

Oh I see! maybe it is I will try it. I appreciate.