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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb1 in position 2: invalid start byte #697

Open Upasana1991 opened 2 years ago

Upasana1991 commented 2 years ago

Hi when I run the the command "./orthofinder.py -f Proteomes/primary_transcripts/" on the two proteomes It gives me this error below OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms

2022-05-06 11:57:35 : Starting OrthoFinder 2.5.4 32 thread(s) for highly parallel tasks (BLAST searches etc.) 4 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "mcl -h" - ok Test can run "fastme -i /net/scratch2/n81047us/orthoF/OrthoFinder-2.5.4/Proteomes/primary_transcripts/OrthoFinder/Results_May06_1/WorkingDirectory/SimpleTest.phy -o /net/scratch2/n81047us/orthoF/OrthoFinder-2.5.4/Proteomes/primary_transcripts/OrthoFinder/Results_May06_1/WorkingDirectory/SimpleTest.tre" - ok Traceback (most recent call last): File "./orthofinder.py", line 7, in main(args) File "/net/scratch2/n81047us/orthoF/OrthoFinder-2.5.4/scripts_of/main.py", line 1761, in main speciesInfoObj = ProcessesNewFasta(fastaDir, options.dna) File "/net/scratch2/n81047us/orthoF/OrthoFinder-2.5.4/scripts_of/main.py", line 1624, in ProcessesNewFasta for iLine, line in enumerate(fastaFile): File "/opt/gridware/depots/8e896c5a/el7/pkg/apps/python3/3.6.4/gcc-4.8.5/lib/python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb1 in position 2: invalid start byte

could suggest me wheat should I do to make this work.

tayyrov commented 2 years ago

Hi,

It seems you have a problem with the input fasta files. Make sure that the all input fasta files are unzipped. I can replicate your error when at least one of the input fasta files is zipped. best

Upasana1991 commented 2 years ago

Hi David Thanks for your reply, I figured out before I received your email and it worked. Best regards

Upasana

From: tayyrov @.> Date: Monday, 30 May 2022 at 10:15 To: davidemms/OrthoFinder @.> Cc: Upasana Singh @.>, Author @.> Subject: Re: [davidemms/OrthoFinder] UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb1 in position 2: invalid start byte (Issue #697)

Hi,

It seems you have a problem with the input fasta files. Make sure that the all input fasta files are unzipped. I can replicate your error when at least one of the input fasta files is zipped. best

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Bon-jour commented 10 months ago

diamond 0.9.14 can solve this problem try yi try