nucmer

[pengyan19]

你好，我用软件的环境按照的nucmer，运行报错，看起来是版本低了，没有-t参数，请问该怎么配置高版本的nucmer?

Unknown option: t

USAGE: nucmer [options]

Try '/public/home/pengyan/anaconda3/envs/panpop/bin/nucmer -h' for more information.

[starskyzheng]

是哪步出错的？

[pengyan19]

你好，是这个哈 Error in rule Assemblytics1nucmer: jobid: 354 input: OS-1.fa, /public/home/pengyan/biosoft/panpop/panpop-starskyzheng-patch-1/example/ACB/of-5.fa output: 03_vcf/05_Assemblytics/of-5/1.nucmer.delta, 03_vcf/05_Assemblytics/of-5 log: logs/2.of-5.Assemblytics.1.nucmer.log (check log file(s) for error details) shell:

    mkdir -p 03_vcf/05_Assemblytics/of-5
    /public/home/pengyan/anaconda3/envs/panpop/bin/nucmer --maxmatch -c 500 -b 500 -l 100 -t 10 OS-1.fa /public/home/pengyan/biosoft/panpop/panpop-starskyzheng-patch-1/example/ACB/of-5.fa --prefix 03_vcf/05_Assemblytics/of-5/1.nucmer >logs/2.of-5.Assemblytics.1.nucmer.log 2>&1

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job Assemblytics1nucmer since they might be corrupted: 03_vcf/05_Assemblytics/of-5 Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: ../../.snakemake/log/2024-04-12T152510.828358.snakemake.log

[starskyzheng]

确实是版本不合适。 您方便吧subworkflows/callSV3.py文件的第250行改一下么？吧-t {threads}这个参数删掉，再试试

[starskyzheng]

另外呀，Assemblytics的准确性我评估过，很低，不建议用，建议用svim-asm

[pengyan19]

哦哦，好呢，svim-asm用到nucmer吗

[starskyzheng]

用不到的