使用PEAKachu进行峰值调用时出错

Question

我正在尝试使用 PEAKachu 调用 RNA eclip pair-end 数据的峰值。我通过从源代码构建在 slurm 上安装了 PEAKachu：

make readme_rst
make package
pip3 install --user dist/PEAKachu-0.2.0.tar.gz

然后，我使用命令运行PEAKachu：

peakachu adaptive -M 200 -m 0.0 -Q 0.05 -c control.bam -t experiment.bam  -o peakachu

但是运行1分钟就报错了：

** Converting reads to bed format for 1 libraries...
expdupsorted generated an exception: A process in the process pool was terminated abruptly while the future was running or pending.
Traceback (most recent call last):
  File "/jet/home/li6/.local/bin/peakachu", line 162, in <module>
    sys.exit(main())
  File "/jet/home/li6/.local/bin/peakachu", line 140, in main
    args.func(controller)
  File "/jet/home/li6/.local/bin/peakachu", line 150, in adaptive_approach
    controller.adaptive_approach()
  File "/jet/home/li6/.local/lib/python3.8/site-packages/peakachulib/controller.py", line 131, in adaptive_approach
    adaptive.generate_combined_bed_file()
  File "/jet/home/li6/.local/lib/python3.8/site-packages/peakachulib/adaptive.py", line 84, in generate_combined_bed_file
    replicon]["reads"].add(lib.replicon_dict[replicon][
KeyError: 'reads'

我很困惑，因为我回溯查看代码在做什么，而code的相关部分是：

80 for replicon in sorted(self._replicon_dict):
81             self._replicon_dict[replicon]["reads"] = pd.Series()
82             for lib_name, lib in exp_lib_dict.items():
83                 self._replicon_dict[replicon]["reads"] = self._replicon_dict[
84                    replicon]["reads"].add(lib.replicon_dict[replicon][
85                        "reads"], fill_value=0)

在第81行，它为_replicon_dict[replicon]创建了键“reads”，我该如何解决这个问题？提前致谢。

Answer 1

刚遇到和你类似的问题。我注意到这个错误与 pandas 库中一些已弃用的函数有关，因此将 pandas 降级到 1.4.0 解决了这个问题，即：

mamba create -c bioconda -n peakachu peakachu pandas==1.4.0

希望有帮助，

阿姆德