Funannotate fails, maybe trying to create a file

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1

Hi everyone,

I am getting an error in Funannotate but the same options work in a different galaxy server.

This is the error message I get:

[Jun 18 12:07 PM]: Genome loaded: 24,079 scaffolds; 50,288,274 bp; 1.57% repeats masked
[Jun 18 12:07 PM]: Mapping 557,291 proteins to genome using diamond and exonerate
Traceback (most recent call last):
File “/usr/local/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-p2g.py”, line 252, in
os.makedirs(tmpdir)
File “/usr/local/lib/python3.8/os.py”, line 223, in makedirs
mkdir(name, mode)
OSError: [Errno 30] Read-only file system: ‘/tmp/p2g_610c8399-3f9b-4c08-983a-1b5b2bfa8477’
Traceback (most recent call last):
File “/usr/local/bin/funannotate”, line 10, in
sys.exit(main())
File “/usr/local/lib/python3.8/site-packages/funannotate/funannotate.py”, line 716, in main
mod.main(arguments)
File “/usr/local/lib/python3.8/site-packages/funannotate/predict.py”, line 1558, in main
lib.exonerate2hints(Exonerate, hintsP)
File “/usr/local/lib/python3.8/site-packages/funannotate/library.py”, line 4600, in exonerate2hints
with open(file, “r”) as input:
FileNotFoundError: [Errno 2] No such file or directory: ‘/data/jwd05e/main/070/950/70950016/working/output/predict_misc/protein_alignments.gff3’

2

This seems to be same issue: Can't identify the error in Funannotate

The same genomic data and options work perfectly in a different server, although the funannotate databases seem different. The one that works in the other server is labelled ‘2023-05-10-062530’, and the available ones here are different.

3

Hi @BShelb

This was using the rerun button, correct?

Instead, try selecting the available annotation datasets that the server hosts. Each might host slightly different versions. For most uses, which you use will probably not make a huge difference.

But if you are trying to reproduce an earlier analysis, sticking with the same server might be a good idea so that you are using the same exact index and not introducing another change outside of the actual input data or parameters.

Hope this helps, but you can explain more if I am misunderstanding. The two server URLs would be one place to start…

Thanks!

4

Thanks for your reply. This bug has been fixed now.

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