sam file error

Question

[Chironex]

Hi, I was converting my sam file (after alignment with bowtie2) in bam format. I encountered the error:

[E::sam_parse1] invalid QUAL character
[W::sam_read1_sam] Parse error at line 11129453

command:

samtools view -S -b -o input.bam ../alignment/input.sam 

Alignment works fine. This is the output:

22504890 reads; of these:
  18951369 (84.21%) were paired; of these:
    574151 (3.03%) aligned concordantly 0 times
    13965369 (73.69%) aligned concordantly exactly 1 time
    4411849 (23.28%) aligned concordantly >1 times
  3553521 (15.79%) were unpaired; of these:
    98535 (2.77%) aligned 0 times
    2418010 (68.05%) aligned exactly 1 time
    1036976 (29.18%) aligned >1 times
96.99% overall alignment rate

Answer 1

[ATpoint]

The sam file seems corrupt. Repeat the alignment. The suggested command to get bam right away is:

bowtie2 (...) | samtools view -o out.bam

[Chironex]

thank you.. I had to repeat 12 hours of aligment.. again!!

[ATpoint]

sam files do not randomly get corrupted. find out the cause.

[Chironex]

I have no clue, with other fastq files is working fine

[Chironex]

I found the problem. After trimmomatic's trimming, I get paired and unpaired fastq files. I feed bowtie2 with both, paired files and unpaired with the option -U. The point Is that unpaired fastq file (file.R2.U.fastq) was very low quality. Removing unpaired files, the sam file was not corrupted and I was able to convert It into bam.