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biocore-ntnu / epic2

Ultraperformant reimplementation of SICER
https://doi.org/10.1093/bioinformatics/btz232
MIT License
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epic2 does not work for custom genome #69

Open Turckie opened 1 year ago

Turckie commented 1 year ago

Although in absence of genome data in the epic2 repository the program should work with only chromosizes and effective genome fraction, in our case is does not. We have tried to add our genome data within epic, but did not manage to make it run. This is the error message: Traceback (most recent call last): File "/scratch/ngscourse/lib/miniconda/bin/epic2", line 257, in _main(args) File "/scratch/ngscourse/lib/miniconda/lib/python3.10/site-packages/epic2/main.py", line 35, in _main effective_genome_length, chromsizes = egl_and_chromsizes(args) File "epic2/src/genome_info.pyx", line 352, in epic2.src.genome_info.egl_and_chromsizes File "epic2/src/genome_info.pyx", line 240, in epic2.src.genome_info.create_genome_size_dict

endrebak commented 1 year ago

Are you able to share the data with me?

On Wed, 26 Apr 2023 at 13:39, Franziska @.***> wrote:

Although in absence of genome data in the epic2 repository the program should work with only chromosizes and effective genome fraction, in our case is does not. We have tried to add our genome data within epic, but did not manage to make it run. This is the error message: Traceback (most recent call last): File "/scratch/ngscourse/lib/miniconda/bin/epic2", line 257, in _main(args) File "/scratch/ngscourse/lib/miniconda/lib/python3.10/site-packages/epic2/main.py", line 35, in _main effective_genome_length, chromsizes = egl_and_chromsizes(args) File "epic2/src/genome_info.pyx", line 352, in epic2.src.genome_info.egl_and_chromsizes File "epic2/src/genome_info.pyx", line 240, in epic2.src.genome_info.create_genome_size_dict

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Turckie commented 1 year ago

Thank you for the response! I solved the problem of providing a custom chromosome file. I had an empty line at the end of the file which lead to the error. After correcting that, the analysis run through.

That being said, I would prefer to add my genome to the database and provide the calculated effective genome size for different read length with epic-effective that worked with epic but seems not part of epic2. Could you please write a little instruction where exactely the files go and possibly include epic2-effective? I work with plant genomes which are often missing in the genome databases. Thanks, Franziska

Sent from Nine

Von: "endrebak.ada" @.***> Gesendet: Sonntag, 30. April 2023 11:22 An: biocore-ntnu/epic2 Cc: Franziska; Author Betreff: Re: [biocore-ntnu/epic2] epic2 does not work for custom genome (Issue #69)

Are you able to share the data with me?

On Wed, 26 Apr 2023 at 13:39, Franziska @.***> wrote:

Although in absence of genome data in the epic2 repository the program should work with only chromosizes and effective genome fraction, in our case is does not. We have tried to add our genome data within epic, but did not manage to make it run. This is the error message: Traceback (most recent call last): File "/scratch/ngscourse/lib/miniconda/bin/epic2", line 257, in _main(args) File "/scratch/ngscourse/lib/miniconda/lib/python3.10/site-packages/epic2/main.py", line 35, in _main effective_genome_length, chromsizes = egl_and_chromsizes(args) File "epic2/src/genome_info.pyx", line 352, in epic2.src.genome_info.egl_and_chromsizes File "epic2/src/genome_info.pyx", line 240, in epic2.src.genome_info.create_genome_size_dict

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