python JWR_checker.py aligned_nobarcode.bam NanoSplicer.hdf5
Warning: Mismatches are not explicitly labeled in the CIGAR from the input BAM file.
The JAQs can still be calculated but mismatched bases will be treated as matched bases.
It is recommended to update the mapping setting (e.g., use '--eqx' option in minimap2)
to label the mismatches in CIGAR.
Searching for JWRs ...
Calculating JAQ for 80764086 JWRs found
80764500it [10:47:04, 180.72it/s]Traceback (most recent call last):
File "/net/beegfs/scratch/mhaagmans/data/RNA_diagnostiek/dRNA_clair/NanoSplicer/bin/JWR_checker.py", line 304, in <module>
main()
File "/net/beegfs/scratch/mhaagmans/data/RNA_diagnostiek/dRNA_clair/NanoSplicer/bin/JWR_checker.py", line 296, in main
[d.to](http://d.to/)_hdf(param.outfile, 'data')
File "/trinity/home/mhaagmans/miniconda3/envs/NanoSplicer/lib/python3.7/site-packages/pandas/core/generic.py", line 2718, in to_hdf
encoding=encoding,
File "/trinity/home/mhaagmans/miniconda3/envs/NanoSplicer/lib/python3.7/site-packages/pandas/io/pytables.py", line 314, in to_hdf
f(store)
File "/trinity/home/mhaagmans/miniconda3/envs/NanoSplicer/lib/python3.7/site-packages/pandas/io/pytables.py", line 306, in <lambda>
dropna=dropna,
File "/trinity/home/mhaagmans/miniconda3/envs/NanoSplicer/lib/python3.7/site-packages/pandas/io/pytables.py", line 1136, in put
dropna=dropna,
File "/trinity/home/mhaagmans/miniconda3/envs/NanoSplicer/lib/python3.7/site-packages/pandas/io/pytables.py", line 1785, in _write_to_group
track_times=track_times,
File "/trinity/home/mhaagmans/miniconda3/envs/NanoSplicer/lib/python3.7/site-packages/pandas/io/pytables.py", line 3232, in write
self.write_array(f"block{i}_values", blk.values, items=blk_items)
File "/trinity/home/mhaagmans/miniconda3/envs/NanoSplicer/lib/python3.7/site-packages/pandas/io/pytables.py", line 3078, in write_array
vlarr.append(value)
File "/trinity/home/mhaagmans/miniconda3/envs/NanoSplicer/lib/python3.7/site-packages/tables/vlarray.py", line 528, in append
self._append(nparr, nobjects)
File "tables/hdf5extension.pyx", line 2033, in tables.hdf5extension.VLArray._append
OverflowError: value too large to convert to int
80764500it [10:51:43, 2065.39it/s]
Is there anything I can do? It was an RNA004 ONT run