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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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dataprep control error #152

Closed rania-o closed 1 year ago

rania-o commented 1 year ago

Hello,

I used the dataprep command for my in vivo sample with a depth around (~9000 reads) and it worked fine :+1:

xpore dataprep --eventalign /nanopolish/output.eventalign.txt --out_dir results --readcount_min 20 --readcount_max 1000000

But for my control sample with more depth (>500,000 reads) I got this error after a long time running :

xpore dataprep --eventalign /nanopolish/output.eventalign.txt --out_dir ctrl_results --readcount_min 20 --readcount_max 1000000
Traceback (most recent call last):
  File "/usr/lib/python3.6/multiprocessing/queues.py", line 240, in _feed
    send_bytes(obj)
  File "/usr/lib/python3.6/multiprocessing/connection.py", line 200, in send_bytes
    self._send_bytes(m[offset:offset + size])
  File "/usr/lib/python3.6/multiprocessing/connection.py", line 393, in _send_bytes
    header = struct.pack("!i", n)
struct.error: 'i' format requires -2147483648 <= number <= 2147483647

Can Xpore handle samples with high coverage?

Thank you Rania