result in error running assemble-complexSVs

[zhangli271828]

I ran assemble-complexSVs. The SVs are deletions and duplications. I got no output. The assembleSVs.log file has the fowllowing content:

root INFO @ 08/17/21 19:23:57:

ARGUMENT LIST:

Output Prefix = DIPG

Break Points = SV.txt

Minimum fragment size = 100000bp

Cooler URI = inter.cool

Extended Genomic Span = 5000000bp

Balance Type = CNV

Experimental protocol = insitu

Number of Processes = 16

Log file name = assembleSVs.log

root INFO @ 08/17/21 19:24:32: Filtering SVs by checking distance decay of the induced contacts .. . joblib.externals.loky.process_executor._RemoteTraceback: """ Traceback (most recent call last): File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/joblib/externals/loky/process_executor.py", lin e 418, in _process_worker r = call_item() File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/joblib/externals/loky/process_executor.py", lin e 272, in call return self.fn(*self.args, self.kwargs) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/joblib/_parallel_backends.py", line 567, in c all return self.func(*args, *kwargs) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/joblib/parallel.py", line 225, in call for func, args, kwargs in self.items] File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/joblib/parallel.py", line 225, in for func, args, kwargs in self.items] File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/neoloop/assembly.py", line 14, in filterSV fu = Fusion(clr, c1, c2, p1, p2, s1, s2, note, span=span, col=col, protocol=protocol, trim=False) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/neoloop/callers.py", line 88, in init self.get_matrix(span, col, trim) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/neoloop/callers.py", line 155, in get_matrix M2 = self.clr.matrix(balance=col).fetch((self.c2, k_p[2], k_p[3])) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/cooler/core.py", line 569, in fetch i0, i1, j0, j1 = self._fetch(args, kwargs) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/cooler/api.py", line 349, in _fetch region1 = parse_region(region, self._chromsizes) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/cooler/util.py", line 181, in parse_region raise ValueError("End cannot be less than start") ValueError: End cannot be less than start """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/usr/local/anaconda3-2020/envs/neoloop/bin/assemble-complexSVs", line 104, in run protocol=args.protocol, minIntra=args.minimum_size) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/neoloop/assembly.py", line 57, in init results = Parallel(n_jobs=n_jobs, verbose=10)(delayed(filterSV)(*i) for i in params) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/joblib/parallel.py", line 934, in call self.retrieve() File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/joblib/parallel.py", line 833, in retrieve self._output.extend(job.get(timeout=self.timeout)) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/site-packages/joblib/_parallel_backends.py", line 521, in wra p_future_result return future.result(timeout=timeout) File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/concurrent/futures/_base.py", line 425, in result return self.get_result() File "/usr/local/anaconda3-2020/envs/neoloop/lib/python3.7/concurrent/futures/_base.py", line 384, in get_result raise self._exception ValueError: End cannot be less than start