STAR FATAL ERROR in reads input

[zhangjy859]

Hi,

I recently encountered some errors, which seem to suggest that my fastq file is incorrect.

My command is:

STAR  \
    --soloType SmartSeq\
     --readFilesManifest ${configure.txt} \
      --genomeDir ${genome} \
      --runThreadN ${threads}  \
      --soloUMIdedup Exact \ 
      --soloStrand Unstranded \ 
      --outSAMtype BAM SortedByCoordinate \
      --outSAMunmapped Within  \
      --outSAMattributes All \
       --outFileNamePrefix ${output} 2> ${log}

However, based on the following two reasons, I believe this is not a problem with the fastq file.

1. Although each error that occurs when running STAR is related to the fastq file, its location is random.

2. Based on the error message, we checked the file and we believe there is no problem here. eg:

Regarding the error mentioned here, we checked the fastq file.

cat $fastq1 | grep SRR6039238.261247 | wc -l
1 ## only one reads with id SRR6039238.261247 in fastq1

We manually checked this read and confirmed that

We checked paired fastq2 using the same steps and found no problem. As an additional check, we used other tools, such as bwa (even though it makes no sense) to map the files to the reference genome, and we did not notice any error reported.