Skip to content

Alignment error #2674

@seandris1

Description

@seandris1

Hello,

I am trying to map fastq files to transcript coordinates. I run this on a cluster using slurm, and the job is always directly cancelled with the following error: STAR: bgzf.c:158: bgzf_open: Assertion `compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE' failed.

Indexing the genome seemingly worked, and I have tried to align the files to a previously indexed mouse genome that I used to align Fastq files in the past. I have tried to change around some of the options, but I have received the same error each time. if it helps, my code is: STAR --runThreadN 1 --genomeDir path_to_genome --readFilesIn path_to_files --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --quantMode GeneCounts

any help would be great. Thank you!
-Sean

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions