harvardinformatics / degenotate

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empty bed and .tsv file #41

Closed rezenman closed 1 year ago

rezenman commented 1 year ago

Hey, Trying to run degenotate on a folder contacting a fasta file, Everything seems to work fine but I get an error at the end and my .bed and .tsv files are empty. Any help will be appreciated! Thanks

adding the output:

./degenotate/degenotate.py -s fasta_files/ -o annotated

Welcome to degenotate -- Degeneracy annotation for coding transcripts. Version 1.2.2 released on June 2023 degenotate was developed by Timothy Sackton, Gregg Thomas Website: https://github.com/harvardinformatics/degenotate

The date and time at the start is: 08.26.2023 | 13:16:33 Using Python executable located at: /home/labs/bfreich/shaharr/project/conda_envs/degenotate/bin/python3.10 Using Python version: 3.10.12 The program was called as: ./degenotate/degenotate.py -s fasta_files/ -o annotated


INPUT/OUTPUT INFO: Sequence directory: /home/labs/bfreich/shaharr/WGS2_NovaSeq_290323/degenotate/fasta_files Output directory: annotated Per-site degeneracy output: annotated/degeneracy-all-sites.bed Transcript count output: annotated/transcript-counts.tsv Log file: annotated.log

OPTIONS INFO: Option Current setting Current action -m 3 Transcripts shorter than this length will be ignored by degnotate. --quiet False Time, memory, and status info will be printed to the screen while degenotate is running. ------------------------------------------------------------------------------------------------------------------------------------------------------ Date Time Current step Status Elapsed time (s) Step time (s) ------------------------------------------------------------------------------------------------------------------------------------------------------ 08.26.2023 13:16:33 Reading CDS FASTA file(s) In progress... 08.26.2023 13:16:33 Reading CDS FASTA file(s) Success: 1 CDS read 0.01327 0.00415 08.26.2023 13:16:33 Caclulating degeneracy per transcript Processed 0 / 1 transcripts... Traceback (most recent call last): File "/home/labs/bfreich/shaharr/WGS2_NovaSeq_290323/degenotate/./degenotate/degenotate.py", line 94, in globs = degen.processCodons(globs) File "/home/labs/bfreich/shaharr/WGS2_NovaSeq_290323/degenotate/degenotate/degenotate_lib/degen.py", line 418, in processCodons OUT.writeBed(transcript_output['bed'], bedfile, globs['annotation'][transcript]['strand']); KeyError: 's288c'

tsackton commented 1 year ago

Hi @rezenman,

I can replicate this error on our test data, so it appears to be a bug in our code for processing a directory of transcript CDS files. Working on a fix now - stay tuned. Thanks for reporting.

Tim

tsackton commented 1 year ago

Hi @rezenman,

I've pushed an update to the 'develop' branch that fixes this issue in our test data. Can you please checkout this branch and see if it fixes the issue for you before I close this issue?

If you have installed degenotate via conda, you will need to clone a new version of degenotate for testing. Since your use does not require any dependencies, you can just do this via git clone -b develop https://github.com/harvardinformatics/degenotate and then you can cd to the degenotate directory and run with python degenotate.py.

Let us know if this works, or if you are still having issues.

Tim

rezenman commented 1 year ago

Hey, Thanks for the update. It works perfectly! Shahar