STAR aligner fatal error

Question

[m.wlodarczyk214]

Hi,

I tried running STAR on my fastq files with trimmed adapters (I have nanopore reads, thus I used Porechop to do this), but unfortunately I got an error:

EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length

SOLUTION: fix your fastq file

My STAR command looks like this:

srun STAR --genomeDir STAR_index --readFilesIn CLL-0857.trimmed.fastq \
    --runThreadN 2 --quantMode GeneCounts --outFileNamePrefix CLL-0857_

Then I ran the following command:

grep "^@acab0714-29a2-4dd3-b464-dfd8deaed03e" CLL-0857.trimmed.fastq

and I got the output:

@acab0714-29a2-4dd3-b464-dfd8deaed03e runid=60fd6b513b1c9ce3b82055fa93c35f71101f4e3e read=12 ch=496 start_time=2021-05-11T12:55:16Z flow_cell_id=FAP05984 protocol_group_id=MIKROBIOM_NPM1_CLL-0857 sample_id=CLL-0857

How can I fix my fastq files? What may gone wrong? I've also tried to map my fastq file before adapter trimming and I got the same error (but it concerned different fastq file).

Thanks for any help :)

[h.mon]

I don't think STAR is the proper tool for Nanopore reads, as it is developed towards short, (relatively) high quality Illumina reads. You should try minimap2 , or another aligner developed to deal with long, noisy reads.

[MohammadAlkadi]

Would you try: grep -4 "@acab0714-29a2-4dd3-b464-dfd8deaed03e" CLL-0857.trimmed.fastq

adding -4 will show you the lines after the read name line thus the sequence and quality lines. Error message suggested an error in the oringinal basecalling or in the file transfer. Sometimes when the transfer(cut/copy and paste) is not complete, writing the file got stopped in the middle and thus trimming the last read. To exclude this possibility would you write:

tail -4 CLL-0857.trimmed.fastq