A Linux server reports an error when processing RNA-seq data comparison

STAR --runThreadN 5 --genomeDir 03index_dir \
--readFilesCommand zcat \
--readFilesIn 02claen_data/*_trimmed.fq.gz \
--outFileNamePrefix 04aligen_out/sample1

There is no problem with the code, but the fq.gz data cannot be read for comparison.I'm really at a loss, I hope someone can help me out, thank you!

linux

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updated 2.1 years ago by GenoMax

• written 2.1 years ago by 211122070082 •

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

code_formatting

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written 2.1 years ago by Pierre Lindenbaum

From STAR manual:

Multiple samples can be mapped in one job. For single-end reads use a comma separated
list (no spaces around commas), e.g. --readFilesIn sample1.fq,sample2.fq,sample3.fq.
For paired-end reads, use comma separated list for read1 /space/ comma separated
list for read2, e.g.: --readFilesIn sample1read1.fq,sample2read1.fq,sample3read1.fq
sample1read2.fq,sample2read2.fq,sample3read2.fq.

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written 2.1 years ago by GenoMax

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