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bcgsc / straglr

Tandem repeat expansion detection or genotyping from long-read alignments
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Error about "ValueError: start out of range (-265)" #18

Closed fjmuzengyiheng closed 1 year ago

fjmuzengyiheng commented 1 year ago

hi, @readmanchiu Thank you for this useful tool. An error occurred when I called STR using nanopore sequencing data. Could you please help me with this? Thank you so much!

multiprocess.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/local/lib/python3.10/site-packages/multiprocess/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/usr/local/lib/python3.10/site-packages/multiprocess/pool.py", line 48, in mapstar return list(map(args)) File "/usr/local/lib/python3.10/site-packages/pathos/helpers/mp_helper.py", line -1, in File "/usr/local/lib/python3.10/site-packages/src/tre.py", line 869, in get_alleles for aln in bam.fetch(locus[0], locus[1] - split_neighbour_size, locus[2] + split_neighbour_size): File "pysam/libcalignmentfile.pyx", line 1091, in pysam.libcalignmentfile.AlignmentFile.fetch File "pysam/libchtslib.pyx", line 690, in pysam.libchtslib.HTSFile.parse_region ValueError: start out of range (-265) """

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

Traceback (most recent call last): File "/usr/local/bin/straglr.py", line 86, in main() File "/usr/local/bin/straglr.py", line 79, in main variants = tre_finder.genotype(args.loci) File "/usr/local/lib/python3.10/site-packages/src/tre.py", line 1130, in genotype return self.collect_alleles(loci) File "/usr/local/lib/python3.10/site-packages/src/tre.py", line 1104, in collect_alleles batched_results = parallel_process(self.get_alleles, batches, self.nprocs) File "/usr/local/lib/python3.10/site-packages/src/utils.py", line 21, in parallel_process results = p.map(func, args) File "/usr/local/lib/python3.10/site-packages/pathos/multiprocessing.py", line 139, in map return _pool.map(star(f), zip(*args)) # chunksize File "/usr/local/lib/python3.10/site-packages/multiprocess/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/usr/local/lib/python3.10/site-packages/multiprocess/pool.py", line 771, in get raise self._value ValueError: start out of range (-265)

readmanchiu commented 1 year ago

Hi @fjmuzengyiheng, the new version (v1.4.0) should hopefully fix this. Please try and let me know if it doesn't. Thanks!

fjmuzengyiheng commented 1 year ago

Hi @fjmuzengyiheng, the new version (v1.4.0) should hopefully fix this. Please try and let me know if it doesn't. Thanks!

Thank you for fixing this. It works well now. : )

readmanchiu commented 1 year ago

Thanks @fjmuzengyiheng I'll close the issue now