ERROR: Unhandled exception KeyError: 'read_id'Task exception was never retrieved

[EPKok]

Hi Hyeshik,

I was trying to execute the command as below and there was error.

poreplex -i ./fast5 -o ./output --trim-adapter --barcoding --keep-unsplit --fast5

Poreplex version 0.1 by Hyeshik Chang <hyeshik@snu.ac.kr>
- Cuts nanopore direct RNA sequencing data into bite-size pieces for RNA Biology

== Analysis settings ======================================
 * Input:       ./fast5
 * Output:      ./output
 * Processes:   1
 * Presets:     rna-r941.cfg
 * Basecall on-the-fly:         No (use previous analyses)
 * 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 exception KeyError: 'read_id'Task exception was never retrieved                                                            | Elapsed: 0:00:00 ETA:  --:--:--
future: <Task finished coro=<ProcessingSession.run_process_batch() done, defined at /mnt/projects/kokep/kokep/devel/miniconda3/lib/python3.6/site-packages/poreplex/pipeline.py:207> exception=CancelledError()>
concurrent.futures._base.CancelledError
| 100% of 13868 |############################################################################################################################| Elapsed: 0:00:00 Time: 0:00:00

==> Terminated.

I wonder how this error could be fixed. Thank you.

[hyeshik]

Thank you for the report!

Can you check whether the change 980384c fixes the problem?

[EPKok]

Hi Hyeshik. The problem is still the same. I could generate fast5 and fastq but could not demultiplex it.

[hyeshik]

Can you post the new error message here? The updated code will show the exact filename and line number where the exception was raised.

[EPKok]

Hi, Please find the error message for --barcoding option as below. For your information, we have used BC1 and BC3 for two samples.

poreplex -i workspace/ -o test_basecalled_barcoding --fast5 --barcoding

Poreplex version 0.1 by Hyeshik Chang <hyeshik@snu.ac.kr>
- Cuts nanopore direct RNA sequencing data into bite-size pieces for RNA Biology

== Analysis settings ======================================
 * Input:   workspace/  
 * Output:  test_basecalled_barcoding
 * Processes:   1
 * Presets: rna-r941.cfg
 * Basecall on-the-fly:     No (use previous analyses)
 * Trim 3' adapter:     No
 * Filter concatenated read:    Yes
 * 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 exception KeyError: 'read_id'Task exception was never retrieved                                                | Elapsed Time: 0:01:18
future: <Task finished coro=<ProcessingSession.run_process_batch() done, defined at /mnt/projects/kokep/kokep/devel/miniconda3/lib/python3.6/site-packages/poreplex/pipeline.py:207> exception=CancelledError()>
concurrent.futures._base.CancelledError

I have also tried the --trim-adaptor option as below and the run is okay.

 poreplex -i workspace/ -o test_basecalled_trim-adapter --fast5 --trim-adapter

Poreplex version 0.1 by Hyeshik Chang <hyeshik@snu.ac.kr>
- Cuts nanopore direct RNA sequencing data into bite-size pieces for RNA Biology

== Analysis settings ======================================
 * Input:   workspace/  
 * Output:  test_basecalled_trim-adapter
 * Processes:   1
 * Presets: rna-r941.cfg
 * Basecall on-the-fly:     No (use previous analyses)
 * Trim 3' adapter:     Yes
 * Filter concatenated read:    Yes
 * Separate by barcode:     No
 * Real-time alignment:     No
 * FASTQ in output:     Yes
 * FAST5 in output:     Yes 
 * Basecall table in output:    No
===========================================================

==> Processing FAST5 files
| 100% of 13868 |######################################################################################################| Elapsed: 0:35:55 Time: 0:35:55

==> Finished.
== Result Summary ==
 * Successfully processed:  12335
 * Possibly artifact:       908
    - Two or more molecules found in a single read: 908
 * Processing failed:       620
    - Signal is too short:  465
    - No albacore basecall data found:  155
 * Failed to open:      5
    - File could not be opened due to unknown error:    5

Thanks.

[hyeshik]

Hi, it seems that you're still invoking the old version that was not fixed for the problem. The updated version should show the version number 0.2.1a1.

Can you try it again after updating it to the fixed version with this command?

pip install git+https://github.com/hyeshik/poreplex.git

[EPKok]

My bad. I thought the updated version was installed but it was not successful. It works now. Thanks a lot for rectifying the issue.

[hyeshik]

That's good! Thank you for the feedback.