I using the bcl2fastq tool and nextseq bcl files.
The bcl files look good but after I use the bcl2fastq tool to produce fastq files (paired end with adapter trimming) the first Read is corrupted and contains no sequences:
size: 545 - NAME_2_S1_R1_001.fastq.gz
size: 5323354262 - NAME_2_S1_R2_001.fastq.gz
Maybe I have to define, that I use paired end in the Sample Sheet?
If I check the archive then I get
NAME_2_S1_R1_001.fastq.gz: ASCII text
NAME_2_S1_R2_001.fastq.gz: gzip compressed data, extra field
But in the logfile (bcl2fastq start with nohup) I can´t see that any error occurs.
And as a result if I try to map it to the reference (using bwa) then I get the following error:
the 1st file has fewer sequences
Hope, that somebody can help me :)