$python2 -m jcvi.compara.catalog ortholog ath rapa --cscore=0.7这一步报错

$python2 -m jcvi.compara.catalog ortholog ath rapa --cscore=0.7

12:25:58 [cbook] File `rapa.prj` exists. Computation skipped.

12:25:58 [base] lastal -u 0 -P 48 -i3G -f BlastTab rapa ath.cds >./ath.rapa.last

12:26:05 [synteny] Assuming --qbed=ath.bed --sbed=rapa.bed

12:26:05 [base] Load file `ath.bed`

12:26:05 [base] Load file `rapa.bed`

Traceback (most recent call last):

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/runpy.py", line 174, in _run_module_as_main

    "__main__", fname, loader, pkg_name)

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/runpy.py", line 72, in _run_code

    exec code in run_globals

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/compara/catalog.py", line 928, in <module>

    main()

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/compara/catalog.py", line 80, in main

    p.dispatch(globals())

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/apps/base.py", line 111, in dispatch

    globals[action](sys.argv[2:])

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/compara/catalog.py", line 678, in ortholog

    blastfilter_main([last, "--cscore={0}".format(ccscore)])

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/compara/blastfilter.py", line 274, in main

    blastfilter_main(blastfile, p, opts)

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/compara/blastfilter.py", line 40, in blastfilter_main

    qbed, sbed, qorder, sorder, is_self = check_beds(blast_file, p, opts)

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/compara/synteny.py", line 490, in check_beds

    sbed = Bed(opts.sbed, sorted=sorted)

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/formats/bed.py", line 148, in __init__

    b = BedLine(line)

  File "/home/spider/soft/miniconda3/envs/py27/lib/python2.7/site-packages/jcvi/formats/bed.py", line 51, in __init__

    self.start = int(args[1]) + 1

IndexError: list index out of range

请先 登录 后评论

2 个回答

间歇性神经病

这是我的四个文件attachments-2020-03-U5R29PIS5e5c957917db9.png

attachments-2020-03-fEBxZvsv5e5c95768fb4d.png

请先 登录 后评论
omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

看你的文件应该没有问题,再检查一下文件结尾是否有多余的空行,有的话删除试一下;

如果还不行,建议使用我们提供的biolinux 里面安装了python 的mcscan,怀疑你的软件安装问题;

https://www.omicsclass.com/article/526  

基因家族分析课程:学习链接:基因家族分析实操课程基因家族文献思路解读

请先 登录 后评论