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zanglab / SICER2

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SICER2 program run error #26

Closed dkur0006 closed 4 months ago

dkur0006 commented 9 months ago

Start Running SICER with given arguments

Preprocess the Panx2.bed file to remove redundancy with threshold of 1

Removing temporary directory and all files in it. multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/local/python/3.9.10-gcc11.2.0-rv2ln4esaesugyvk2qty4ur6nlwkbtea/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/usr/local/python/3.9.10-gcc11.2.0-rv2ln4esaesugyvk2qty4ur6nlwkbtea/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/usr/local/sicer2/1.0.3/sicer2-1.0.3/lib/python3.9/site-packages/sicer/src/remove_redundant_reads.py", line 133, in find_and_filter_reads chrom_reads = match_by_chrom(path_to_file, chrom) # Separates all reads by chromosome File "/usr/local/sicer2/1.0.3/sicer2-1.0.3/lib/python3.9/site-packages/sicer/src/remove_redundant_reads.py", line 120, in match_by_chrom processed_reads[i] = tuple(reads) ValueError: invalid literal for int() with base 10: '.' """

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

Traceback (most recent call last): Traceback (most recent call last): File "/usr/local/sicer2/1.0.3/sicer2-1.0.3/bin/sicer", line 235, in main() File "/usr/local/sicer2/1.0.3/sicer2-1.0.3/bin/sicer", line 229, in main run_SICER.main(args) File "/usr/local/sicer2/1.0.3/sicer2-1.0.3/lib/python3.9/site-packages/sicer/main/run_SICER.py", line 52, in main total_treatment_read_count = remove_redundant_reads.main(args, args.treatment_file, pool) File "/usr/local/sicer2/1.0.3/sicer2-1.0.3/lib/python3.9/site-packages/sicer/src/remove_redundant_reads.py", line 147, in main filtered_result = pool.map(find_and_filter_reads_partial, chroms) File "/usr/local/python/3.9.10-gcc11.2.0-rv2ln4esaesugyvk2qty4ur6nlwkbtea/lib/python3.9/multiprocessing/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/usr/local/python/3.9.10-gcc11.2.0-rv2ln4esaesugyvk2qty4ur6nlwkbtea/lib/python3.9/multiprocessing/pool.py", line 771, in get raise self._value ValueError: invalid literal for int() with base 10: '.' Finish

JasonJiangs commented 4 months ago

Hi, this should be fixed by now, I am gonna to close this issue.