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error when barcoding and fast5 flags used #19

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teshomeb opened this issue May 10, 2019 · 0 comments
Open

error when barcoding and fast5 flags used #19

teshomeb opened this issue May 10, 2019 · 0 comments

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@teshomeb
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Hi,
Use of --barcoding and --fast5 give error. Here is the command and the error.
Thanks
poreplex -i INPUT -o OUTPUT --barcoding --trim-adapter --basecall --parallel 5 --fast5

Poreplex version 0.4.1 by Hyeshik Chang hyeshik@snu.ac.kr

  • Cuts nanopore direct RNA sequencing data into bite-size pieces for RNA Biology

== Analysis settings ======================================

  • Input: INPUT
  • Output: OUTPUT
  • Processes: 5
  • Presets: rna-r941.cfg
  • Basecall on-the-fly: Yes (albacore 2.3.1)
  • Trim 3' adapter: Yes
  • Filter concatenated read: No
  • Separate by barcode: Yes
  • Real-time alignment: No
  • FASTQ in output: Yes
  • FAST5 in output: Yes
  • Basecall table in output: No
    ===========================================================

==> Processing FAST5 files
ERROR: Unhandled error [Errno 2] No such file or directory: '~/fast5/pass/BC3/FAK84611_6b938d7e6efe081830fee799484ebdfbbf1725f6_3.fast5'Task exception was never retrieved
future: <Task finished coro=<ProcessingSession.run_process_batch() done, defined at ~/lib/python3.5/site-packages/poreplex/pipeline.py:183> exception=CancelledError()>
concurrent.futures._base.CancelledError
| 100% of 665704 |################################| Elapsed: 0:00:19 Time: 0:00:19

==> Terminated.

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