OrthoFinder
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davidemms
Gene_tree、orthologues 、Species_Tree and MultipleSequenceAlignments files are empty
When I use orthofinder to analyze 18 species, I always can't get the contents of Gene_tree、orthologues 、Species_Tree and MultipleSequenceAlignments four files. The command I use is as follows: orthofinder -f pep -M msa -S diamond -T raxml-ng -t 24 -a 24. So I would like to ask you, do you know what caused it? The running program will stop every time it reaches the following step
Inferring remaining multiple sequence alignments and gene trees
2022-01-30 03:23:52 : Done 0 of 32315
Is raxml still running? RAxML will take a very long time to infer the first 1000 trees. Have you tried running the line top command to see what process are running?
Best wishes David
hi david Thanks for your answer, I have tested with 2 species and got all the results, but when using 18 species it stops at the same step every time. I used the top command to check that raxml-ng is no longer running, so I don't know if this software has species restrictions? Or is there a limit to the sequence name? Most of my sequence names start with English letters and only contain underscores and numbers. Best wishes Hu ShaSha
when I try to replace raxml-ng with fasttree, I can get all result file, but the following error message will appear:
Inferring remaining multiple sequence alignments and gene trees
2022-02-04 02:50:36 : Done 0 of 29545 Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/ortho/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/ubuntu/anaconda3/envs/ortho/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/ubuntu/anaconda3/envs/ortho/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/ubuntu/anaconda3/envs/ortho/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")]) IndexError: list index out of range
So I would like to ask you, do you know what is the reason for this? Thank you very much for your reply. Best wishes Hu ShaSha
Hi Hu ShaSha
Would you be able to send me a link that I can download your input files from and I will try and debug the issue. The address is at the top of the "/home/ubuntu/anaconda3/envs/ortho/bin/scripts_of/main.py" file.
Best wishes David
Hi Thank you for your reply, the attachment is my protein sequence file and do you need any other files? Best wishes Shasha Hu
------------------ 原始邮件 ------------------ 发件人: "davidemms/OrthoFinder" @.>; 发送时间: 2022年2月23日(星期三) 下午4:06 @.>; @.@.>; 主题: Re: [davidemms/OrthoFinder] Gene_tree、orthologues 、Species_Tree and MultipleSequenceAlignments files are empty (Issue #665)
Hi Hu ShaSha
Would you be able to send me a link that I can download your input files from and I will try and debug the issue. The address is at the top of the "/home/ubuntu/anaconda3/envs/ortho/bin/scripts_of/main.py" file.
Best wishes David
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从QQ邮箱发来的超大附件
pep.zip (104.29M, 2022年03月27日 08:48 到期)进入下载页面：https://mail.qq.com/cgi-bin/ftnExs_download?t=exs_ftn_download&k=5f3930630207499ac1c74d151563004c5a0f0002520700524e080000504e060257581d5a03050a4e5b5c055506570a07550a05013364321306491e195a13325e&code=c90c3c2c
Just the protein sequence files. You'll need to send a link, replying to github with an email attachment doesn't work.
Hi, Below is a link of my protein sequence file, but I don't know if you can open it Link: https://pan.baidu.com/s/1912duhGQnUUc2R4Ixr1wIQ Extraction code: 5gfb