multiple_join_paired_ends.py failing despite providing right read indicators

[Angela Zou]

Hello, this is the command I am currently using:

multiple_join_paired_ends.py -i paired -o joined_fastq_files -p $location/multi_join_params.txt --read1_indicator '_1' --read2_indicator '_2'

These are example file names 

SRR2668681_1.fastq.gz  

SRR2668681_2.fastq.gz  

SRR2668682_1.fastq.gz  

SRR2668682_2.fastq.gz  

SRR2668683_1.fastq.gz  

SRR2668683_2.fastq.gz  

I keep getting the error message:

ValueError: Invalid filename found for splitting on input for file SRR2668811_2.fastq.gz, check input read1_indicator and read2_indicator parameters as well.

If I take out the pair of SRR2668811 files, then I will get an error message for a different pair of files. I am not sure what I am doing wrong as the read indicator parameters are correct. 

Thanks! 

[Jamie Morton]

Hi Angela,

I just forwarded this question -- so expect a response in a bit.

Best,

Jamie

[Angela Zou]

Hi Jamie,

I actually solved the problem, turns out renaming the files to _R1 and _R2 works, but _1 and _2 do not work. Thanks anyway. 

Angela 

[Jamie Morton]

Awesome!  Glad that you were able to find a solution!