RemoveAll .: invalid argument

[Bin-cc]

Hi Philosopher group,

Maybe we need a new discussion to discuss the error I haven't solved for several weeks. Here, I would like to describe the detials when I use Philosopher pipeline. And then, it will be useful for you to help me to resolve those problems.

• Firstly, I used Philosopher pipeline for simple data analysis. I could run it successfully. But I found that if I used the Uniprot database contained reviewed+unreviewed proteins, it reported the error Cannot read file. open .meta\db.bin: The system cannot find the file specified. However, when I only changed the database and used reviewed Uniprot, I could complete it smoothly.

1. So, the first question is whether I can use the reviewed and unreviewed protein database in Philosopher, and how? (I can use this database successfully in FragPipe)

• Secondly, I used Philosopher pipeline for PPI analysis with the search engine MSFragger. I once ran it successfully with the Philosopher of version 3.4.13 with the search engine Comet. However, when I use the latest version of Philosopher and MSFragger, I always encounter the same problem RemoveAll .: invalid argument. I attached my philosopher.yml and fragger.params, and also the Processing&error.txt I had used in philosopher.yml to find the reason but obviously I failed.

  I want to point out that I used the reviewed Uniprot database with decoys and contam which could run successfuly in
  simple data analysis, and that while the error happened, the combined.pep.xml and combined.prot.xml had been producted.

2. So, the second question is what should I need to do next? Are there any details I ignored?

Thank you for your patience to read my questions. If you have any confusions about my description, please let me know. I really grateful that if you could help me to resolve those problems. Thanks!

All the best,
Bin

[prvst]

@Bin-cc you have to open new issues to report your problems. The forum is more for open discussions regarding the program. I'm going to create an issue for based on your post.