search

katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
Other
123 stars 65 forks source link

Could not determine forward/reverse read status for input file #71

Closed FelipeMelis closed 7 years ago

FelipeMelis commented 7 years ago

Hello

The reads subjected to trimming are not detected as forward or reverse by srst2 and i obtain the following error:

09/08/2016 13:18:04 Could not determine forward/reverse read status for input file SaB1_1_trimmed.fastq 09/08/2016 13:18:04 Could not determine forward/reverse read status for input file SaB1_2_trimmed.fastq

katholt commented 7 years ago

This is because your read files are not named in a format that SRST2 understands. Please see the readme https://github.com/katholt/srst2#input-read-formats-and-options

Basically if you name the files as SaB1_trimmed_1.fastq and SaB1_trimmed_2.fastq it should work fine.