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Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.
GNU General Public License v3.0
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During the execution of samtools index, I encountered an error: "invalid option -- '@'" #131

Closed jiuyaojiaonini closed 2 months ago

jiuyaojiaonini commented 2 months ago

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 2 months ago

You can update samtools to lastest version.

jiuyaojiaonini commented 2 months ago

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?

moold commented 2 months ago

Yes

jiuyaojiaonini commented 2 months ago

Oki! Thank you very much~