Error: Error reading input stream at line 51600321: Invalid character (ASCII 0) in sequence

[Betula0422]

Hi, when I used run_dbcan.py to analyze my unigene sets, I revieced this error: Error: Error reading input stream at line 51600321: Invalid character (ASCII 0) in sequence

Here is my command: python run_dbcan.py --db_dir {mypath}/db \ --hmm_cov 0.35 --hmm_eval 1e-15 --hmm_cpu 20 \ --dia_eval 1e-102 --dia_cpu 20 \ --out_dir {mypath}/dbcan2 --out_pre genemark {mypath}/unigene.fasta meta

I think that this error may be caused by spaces in the unigene.fasta, so I used this command to search the spaces in unigene.fasta: grep " " unigene.fasta. But there wasn't any space in the file.

Could you tell me what caused the error?

Best wishes!

[linnabrown]

The ASCII code for space is 32 not 0. It shows that you have ASCII 0 in line 51600321. You need to double check it by yourself to remove the invalid character.

[Betula0422]

The ASCII code for space is 32 not 0. It shows that you have ASCII 0 in line 51600321. You need to double check it by yourself to remove the invalid character.

Thank you for your suggestions. I check the line 51600321 and it shows ">w2.gene_1367553". I don't think there is ASCII 0 in line 51600321. I search the ASCII 0 in unigene.fasta and it shows there isn't any ASCII 0 in the file.

In the out_dir, there are four files which are shown below. The file "genemarkdiamond.out" is empty. 0 Jan 10 07:33 genemarkdiamond.out 115M Jan 13 2022 genemarkh.out 12G Jan 10 07:33 genemarkprodigal.gff 8.1G Jan 10 07:33 genemarkuniInput

I can't figure out what's wrong with my file. I'm looking forward to your reply.

[linnabrown]

https://github.com/bbuchfink/diamond/issues/333#issuecomment-597292589

a trailing whitespace?

[Betula0422]

bbuchfink/diamond#333 (comment)

a trailing whitespace?

No, I have deleted the trailing whitespace in the file but this error still exists. T^T

[linnabrown]

I really have no idea what's going on. If you don't mind, you can send me your input file to me and let me check that.

[Betula0422]

Thank you so much! I will try to run this code again. If the error still exists, I will send my input file to you. Thank you again for your patient answers!