trim_galore error: Cutadapt terminated with exit signal: '256'

Question

[szp770]

Hi, I am using trim-galore to trim double-end fastq files, however, it reports this error: """ Cutadapt terminated with exit signal: '256'. """

Answer 1

[GenoMax]

While you did not provide the full error message a past thread indicates that you may have corrupt data files: Trim galore terminates with exit signal: '256'

If this is not the case please add additional details in original post.

[szp770]

cutadapt: error: In read named 'A00783:648:HWMWJDSXY:1:2309:16658:34663 2:N:0:GGACTCCT+GTAAGGAG': length of quality sequence (150) and length of read (189) do not match

[GenoMax]

That confirms that your fastq file is corrupt. You can either download a new copy or find and delete the offending reads from both R1/R2 files.

[szp770]

great, I will first try to download a new copy of files.