search

marcelm / dnaio

Efficiently read and write sequencing data from Python
https://dnaio.readthedocs.io/
MIT License
62 stars 9 forks source link

dnaio.exceptions.UnknownFileFormat #136

Open wook2014 opened 3 months ago

wook2014 commented 3 months ago

I am tring to use cutadapt to process my reads file, but I meet up with a problem 

dnaio.exceptions.UnknownFileFormat: Could not determine whether file '<_io.BytesIO object at 0x73ef2b228270>' is FASTA or FASTQ. The file extension is not available or not recognized, and the first character in the file is unexpected.

It is confused for me because I have checked my fastq file manually and I could not find errors. how could I locate the error data with the code 0x73ef2b228270 ? Is there another way to print the error line?

rhpvorderman commented 3 months ago

This bug needs a little more context.

Could you give:

wook2014 commented 3 months ago

I have checked and it seemed that this is caused by a previous step which using cutadapt to cut the adapter and produced several sequences that cut to 0 length.

rhpvorderman commented 2 months ago

Without a complete stacktrace, it is impossible to pinpoint the problem.