During the execution of samtools index, I encountered an error: "invalid option -- '@'"

Question

During the execution of samtools index, I encountered an error: "invalid option -- '@'"

Closed this issue 8 months ago · 4 comments

When I checked the error message here: 00.lgs_polish/03.merge.bam.sh.work/merge_bam1/, I found that there was an invalid parameter prompt when building the bam index: invalid option – ‘@’, and I’m not sure how to resolve this.

moold commented 8 months ago

Yes

Answer 1 · 2024-04-22T02:12:16.000Z

You can update samtools to lastest version.

Answer 2 · 2024-04-22T02:35:22.000Z

I’m delighted to receive your reply, thank you! In fact, I checked and found that the version of samtools in the conda environment where NextPolish is installed is 1.3.1, which does not have the -@ parameter. However, version 1.11 of samtools does have the -@ parameter. Are you suggesting that I need to upgrade the samtools in the conda environment to version 1.11?

Answer 3 · 2024-04-22T02:56:31.000Z

Oki! Thank you very much~