hyeshik
Error: Unknown entries in loss dictionary:
Hi,
I tried to run poreplex on a minION run using the follwing command to basecall and demultiplex barcodes from direct RNA sequencing:
poreplex -i 20191122_1000_MN24929_FAL01495_e9928ec8/fast5/ -o poreplex_demultiplex --barcoding --fast5 --basecall --parallel 20
This results in an error:
== Analysis settings ======================================
* Input: fast5/20191122_1000_MN24929_FAL01495_e9928ec8/fast5/
* Output: poreplex_demultiplex
* Processes: 20
* Presets: rna-r941.cfg
* Basecall on-the-fly: Yes (albacore 2.3.4)
* Trim 3' adapter: No
* 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: [signal_analyzer.py:48] Unhandled exception ValueError: Unknown entries in loss dictionary: ['config', 'class_name']. Only expected following keys: ['dense_2']Task exception was never retrieved
future: <Task finished coro=<ProcessingSession.run_process_batch() done, defined at /home/graf/.local/lib/python3.6/site-packages/poreplex/pipeline.py:193> exception=CancelledError()>
concurrent.futures._base.CancelledError
Is there anything I need to do to get around that error?
First I tried the Fast5 files basecalled with Guppy with the same result. So I thought running the internal albacore basecalling will help, but unfortunately no luck! Could you give me a hint what to do to solve that issue?
Thank you in advance for your help Best Alex
same problems! Poreplex is the latest version (v0.5). How to solve this bug??? it seems that many persons have counter this problem!
Poreplex version 0.5 by Hyeshik Chang [email protected]
- Cuts nanopore direct RNA sequencing data into bite-size pieces for RNA Biology
Output directory poreplex_output/ is not empty. Clear it? (y/N) y
== Analysis settings ======================================
- Input: RS20200115_RNA/RS20200115_RNA_muliplex/RS20200115_RNA_multiplex/20200115_0837_MN23702_FAK99138_e3bc320c/fast5_result/workspace/
- Output: poreplex_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: No
- Basecall table in output: No ===========================================================
==> Processing FAST5 files ERROR: [signal_analyzer.py:48] Unhandled exception ValueError: Unknown entries in loss dictionary: ['class_name', 'config']. Only expected following keys: ['dense_2']WARNING: Logging before flag parsing goes to stderr. E0117 14:43:27.784703 140625390106432 base_events.py:1285] Task exception was never retrieved future: <Task finished coro=<ProcessingSession.run_process_batch() done, defined at /usr/local/lib/python3.6/dist-packages/poreplex/pipeline.py:193> exception=CancelledError()> concurrent.futures._base.CancelledError | 100% of 356000 |#######################################################################################################################################################################| Elapsed: 0:00:00 Time: 0:00:00
==> Terminated.
Which tensorflow version are you using? I suspect it is due to a tf version <2. In my case, using 2.0.0 fixed the issue.
