Error in STAR when mapping

Question

[luzglongoria]

Hi there,

I am working with fastq files (paired reads) and with a reference genome. I need to do the mapping with STAR. I have done the index part and it's ok:

STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /home/path/to/folder/ --genomeFastaFiles /home/path/to/genome_reference --readFilesCommand zcat samples.txt --sjdbGTFfile /home/path/to/genome_reference/annotation_file

However, when I try to run STAR for mapping

STAR --runThreadN 20 --genomeDir /home/path/to/folder/ --readFilesManifest /home/path/to/all_fastq_files/samples.txt

I used to have an error like this one:

Dec 03 12:55:45 ..... started STAR run
Dec 03 12:55:45 ..... loading genome
Dec 03 12:55:53 ..... started mapping

EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length
@ST-E00494:118:HF3J7ALXX:7:2220:19593:58637
@ST-E00494:119:HF3GNALXX:6:1101:5457:11013 2:N:0:ACAAGCTA
+
SOLUTION: fix your fastq file

Dec 03 14:03:44 ...... FATAL ERROR, exiting

Not sure what is happening. I have check the files (mainly the one that STAR indicates has an error) with FastQC but it look ok for me (size, umber of bases...).

Any idea how to fix this problem?

Thank you in advance

[lieven.sterck]

sounds like you fastq files are corrupt.

Did you do pre-processing of those fastq files?

I'm not sure if FastQC will pick this up, so I suggest to start having a look at the IDs STAR reports. And check if sequence and quality string are of equal length

[luzglongoria]

Thanks for the comment!

I have checked the log.out file from STAR and it seems to be a problem with the .txt where the sample names where written. I put twice the same name. I am running again STAR. Hopefully this time it will run.

Answer 1

[Pierre Lindenbaum]

if the following cmd outputs anything, then your fastq is corrupted...

gunzip -c *.fq.gz  | paste - - - - | awk -F '\t' '(length($2)!=length($4))'

[GenoMax]

Not sure if validateFiles from Jim Kent utilities will be faster than this but worth mentioning as an alternative (link to download in this comment, C: Viewing and editing FASTQ files )

[luzglongoria]

Thank you! However, my files are in .fq format. They are not compress. How can I do?

[GenoMax]

Replace gunzip -c *.fq.gz with cat your_file.fq. Rest of command remains the same.

cat your_file.fq | paste - - - - | awk -F '\t' '(length($2)!=length($4))'