python - Python ray get TypeError: no default __reduce__ due to non-trivial __cinit__

Question

我正在尝试制作一个返回唯一读取和 %GC 的 pysam 脚本，其中一部分是列出每个染色体的读取列表（因为我需要稍后读取每个染色体用于其他目的）。为了节省时间，我希望脚本使用 ray 在 4 个线程中并行运行分析：

import pysam
import ray
ray.init()
nst = []
for x in range(1,25):
    if x == 23:
        nst.append('chrX')
    elif x == 24:
        nst.append('chrY')
    else:
        nst.append('chr%d'%x)
filebam = 'sample.bam'
bam = pysam.AlignmentFile(filebam, 'rb')
f = open('readandgc.txt','w')
f.write('chr\tgc\ttotal')       
f.close()
def analyze(r): 
    begin = int(self.r.split('-')[0])
    end = int(self.r.split('-')[1])
    total = 0
    gc = 0
    for x in range(begin, end):
        c = nst[x]
        print('Reading %s'%c)
        read_data = bam.fetch(c)
        for read in read_data:
            seq = read.query_sequence
            total += len(seq)
            gc += len([x for x in seq if x == 'C' or x == 'G'])
        f = open(tempdir + '/' + 'readandgc.txt','a')
        f.write(chr + '\t' + str(gc) + '\t' + str(total))
        f.close()
@ray.remote
def core1():
    analyze('1-7')
@ray.remote
def core2():
    analyze('7-13')
@ray.remote
def core3():
    analyze('13-19')
@ray.remote
def core4():
    analyze('19-24')        
    
values = ray.get([core1.remote(), core2.remote(), core3.remote(), core4.remote()])

但我对这个错误日志感到震惊：

2021-04-19 15:39:49,840 INFO services.py:1174 -- View the Ray dashboard at ←[1m←[32mhttp://127.0.0.1:8265←[39m←[22m
Traceback (most recent call last):
  File "gccount.py", line 45, in <module>
    values = ray.get([core1.remote(), core2.remote(), core3.remote(), core4.remote()])
  File "C:\ProgramData\Anaconda3\lib\site-packages\ray\remote_function.py", line 101, in _remote_proxy
    return self._remote(args=args, kwargs=kwargs)
  File "C:\ProgramData\Anaconda3\lib\site-packages\ray\remote_function.py", line 201, in _remote
    self._pickled_function = pickle.dumps(self._function)
  File "C:\ProgramData\Anaconda3\lib\site-packages\ray\cloudpickle\cloudpickle_fast.py", line 73, in dumps
    cp.dump(obj)
  File "C:\ProgramData\Anaconda3\lib\site-packages\ray\cloudpickle\cloudpickle_fast.py", line 574, in dump
    return Pickler.dump(self, obj)
  File "stringsource", line 2, in pysam.libcalignmentfile.AlignmentFile.__reduce_cython__
TypeError: no default __reduce__ due to non-trivial __cinit__

有人可以告诉我我的代码有什么问题吗？

标签： pythonray