Error while mapping reads to assembly using bowtie

Question

[Biocode_user]

I am trying to map assembly back to the reads using bowtie. But with one of the libraries, i get an error

Error:

Warning: skipping mate #2 of read 'DHKW5DQ1:246:C1D7AACXX:4:1101:7855DDDDDDDDDD@BCEEDDDDDDD5AGAAGAAGTCDACADECCDTGGGCGCC' because length (0) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'DHKW5DQ1:246:C1D7AACXX:4:1101:7855DDDDDDDDDD@BCEEDDDDDDD5AGAAGAAGTCDACADECCDTGGGCGCC' because it was < 2 characters long
Error: Read ;GTT has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

Could anyone please help me to know .. What exactly is the problem with this?

[nterhoeven]

you seem to have a problem with your fastq file. You should take a look at it. Especially at the read named in the error message. Try:

grep -C 4 'DHKW5DQ1:246:C1D7AACXX:4:1101'

Answer 1

[Antonio R. Franco]

Error: Read ;GTT has more read characters than quality values

Take a look to this Wiki on fastq files to learn what is happening. The number of bases within a same read and its ascii values indicating the quality of these bases must be identical

Another problem can raise. If using paired data, sometimes after a trimming you erase the mate read. Some programs expect to find both, the main read and its mate

In addition.If you compare this read shown below with that shown in the wiki, you will notice that after the positional indication of the read (4:1101:7855), you have letter corresponding to the quality (D and E and @ are not bases), and then it comes the base sequence itself. I don't know where you got this, but this is not a regular fastq read

DHKW5DQ1:246:C1D7AACXX:4:1101:7855DDDDDDDDDD@BCEEDDDDDDD5AGAAGAAGTCDACADECCDTGGGCGCC'